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1. Linking genetic markers and crop model parameters using neural networks to enhance genomic prediction of integrative traits

Author: Florian Larue, Lauriane Rouan, David Pot, Jean-François Rami, Delphine Luquet, and Grégory Beurier
Subjects: convolutional neural networks, crop growth model, genomic prediction, sorghum, CGM-WGP, Plant culture, SB1-1110
Abstract: IntroductionPredicting the performance (yield or other integrative traits) of cultivated plants is complex because it involves not only estimating the genetic value of the candidates to selection, the interactions between the genotype and the environment (GxE) but also the epistatic interactions between genomic regions for a given trait, and the interactions between the traits contributing to the integrative trait. Classical Genomic Prediction (GP) models mostly account for additive effects and are not suitable to estimate non-additive effects such as epistasis. Therefore, the use of machine learning and deep learning methods has been previously proposed to model those non-linear effects.MethodsIn this study, we propose a type of Artificial Neural Network (ANN) called Convolutional Neural Network (CNN) and compare it to two classical GP regression methods for their ability to predict an integrative trait of sorghum: aboveground fresh weight accumulation. We also suggest that the use of a crop growth model (CGM) can enhance predictions of integrative traits by decomposing them into more heritable intermediate traits.ResultsThe results show that CNN outperformed both LASSO and Bayes C methods in accuracy, suggesting that CNN are better suited to predict integrative traits. Furthermore, the predictive ability of the combined CGM-GP approach surpassed that of GP without the CGM integration, irrespective of the regression method used.DiscussionThese results are consistent with recent works aiming to develop Genome-to-Phenotype models and advocate for the use of non-linear prediction methods, and the use of combined CGM-GP to enhance the prediction of crop performances.
Published: 2024
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2. Mobilizing sorghum genetic diversity: Biochemical and histological‐assisted design of a stem ideotype for biomethane production

Author: Hélène Laurence Thomas, David Pot, Sylvie Jaffuel, Jean‐Luc Verdeil, Christelle Baptiste, Laurent Bonnal, Gilles Trouche, Denis Bastianelli, Eric Latrille, Angélique Berger, Caroline Calatayud, Céline Chauvergne, Virginie Rossard, Patrice Jeanson, Joël Alcouffe, and Hélène Carrère
Subjects: anaerobic digestion, animal feed, combustion, genetic diversity, heritability, ideotype, Renewable energy sources, TJ807-830, Energy industries. Energy policy. Fuel trade, HD9502-9502.5
Abstract: Abstract Sorghum currently contributes to the species portfolio that is supporting bioenergy production including anaerobic digestion. Although agro‐morphological ideotypes maximizing biogas production have been recently proposed, there is a crucial need to refine our understanding of the impacts of the stem composition and structure on this processing trait in order to ensure genetic gains in the mid to long terms. This study aims to assess the potential of Sorghum bicolor ssp bicolor stem genetic diversity to maximize genetic gains for biogas production and define a biogas stem ideotype. In this context, a panel of 57 genotypes, encompassing most of the stem composition variability available in cultivated sorghum, was characterized over five sites. Simultaneous histological and biochemical characterizations were performed. A high broad sense heritability associated with a moderate genetic variability was detected for stem biogas potential ensuring significant genetic gains in the future. In addition, the development of a stem histological phenotyping pipeline made it possible to describe the genetic diversity available for the internode anatomy and the repartition of key cell wall components. Consistently with previous studies, moderate to high heritability was observed for stem biochemical components. Genetic correlation, hierarchical clustering, and multiple stepwise regression analyses identified soluble sugar content as the first main driver of biogas potential genetic variability. Nevertheless, breeding programs should anticipate that biogas yield improvement will also rely on the monitoring of the cell wall components and their distribution in the stem jointly with the soluble sugar content. According to the assets of sorghum in terms of adaptation to environmental stresses and the present results regarding the identification of stem ideotypes suitable for different value chains, this species will surely play a key role to optimize the economic and environmental sustainability of the agrosystems that are currently facing the effects of climate change.
Published: 2021
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3. SL-Cloud: A Cloud-based resource to support synthetic lethal interaction discovery [version 2; peer review: 2 approved]

Author: William Longabaugh, John Phan, Christopher J. Kemp, David Pot, Guangrong Qin, Bahar Tercan, Boris Aguilar, Taek-Kyun Kim, Ilya Shmulevich, and Nyasha Chambwe
Subjects: synthetic lethality, cloud computing, cancer genomics, cancer dependency, systems biology, functional genomics, eng, Medicine, Science
Abstract: Synthetic lethal interactions (SLIs), genetic interactions in which the simultaneous inactivation of two genes leads to a lethal phenotype, are promising targets for therapeutic intervention in cancer, as exemplified by the recent success of PARP inhibitors in treating BRCA1/2-deficient tumors. We present SL-Cloud, a new component of the Institute for Systems Biology Cancer Gateway in the Cloud (ISB-CGC), that provides an integrated framework of cloud-hosted data resources and curated workflows to enable facile prediction of SLIs. This resource addresses two main challenges related to SLI inference: the need to wrangle and preprocess large multi-omic datasets and the availability of multiple comparable prediction approaches. SL-Cloud enables customizable computational inference of SLIs and testing of prediction approaches across multiple datasets. We anticipate that cancer researchers will find utility in this tool for discovery of SLIs to support further investigation into potential drug targets for anticancer therapies.
Published: 2022
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4. Flavor precursors and sensory attributes of coffee submitted to different post-harvest processing

Author: Cíntia Sorane Good Kitzberger, David Pot, Pierre Marraccini, Luiz Filipe Protasio Pereira, and Maria Brígida dos Santos Scholz
Subjects: coffea arabica, chemical composition, post-harvest process, green coffee beans, roasted coffee beans, Agriculture (General), S1-972, Food processing and manufacture, TP368-456
Abstract: Post-harvest processing (PHP) modifies the quality of the coffee and increases the value of coffee production. The choice of PHP to apply depends primarily on the available infrastructure, local climatic conditions and the desired end-value. The objective of this study was to evaluate the influence of PHP on the physico-chemical characteristics of green and roasted coffee beans and their sensory attributes. Coffee cherries from IAPAR 59 cultivar were processed as natural coffee (CN), semi-dry coffee (CD), de-pulped coffee (CP) and floating coffee (CF). Total and reducing sugars, phenolic compounds, chlorogenic acids, lipids, proteins, caffeine and water content were determined in coffee beans collected during (10thday) and at the end of each processing. The roasted beans and their sensory attributes were also analyzed. The greatest changes at the ending point of the processes were found in total and reducing sugars, phenolic compounds, chlorogenic acids and lipids contents. The PHP presented different weight loss to achieve the same visual brown color and luminosity. Beverage sensory attributes were influenced by the PHP: CN and CP coffees presented similar intensities of coffee aroma, but higher intensity of green grassy aroma, and taste were found in CF and CN coffees. Aroma and taste precursors were modified during the PHP and these were associated to husk removal of the coffee beans, suggesting an activation of the germination metabolism during the PHP. This study allowed the characterization of the effects of the different post-harvest processing on the roasted coffee beans and provides the foundations to monitor their efficiencies in the future.
Published: 2020
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5. The Road to Sorghum Domestication: Evidence From Nucleotide Diversity and Gene Expression Patterns

Author: Concetta Burgarella, Angélique Berger, Sylvain Glémin, Jacques David, Nancy Terrier, Monique Deu, and David Pot
Subjects: domestication, bottleneck, selection, nucleotide diversity, gene expression, sorghum, Plant culture, SB1-1110
Abstract: Native African cereals (sorghum, millets) ensure food security to millions of low-income people from low fertility and drought-prone regions of Africa and Asia. In spite of their agronomic importance, the genetic bases of their phenotype and adaptations are still not well-understood. Here we focus on Sorghum bicolor, which is the fifth cereal worldwide for grain production and constitutes the staple food for around 500 million people. We leverage transcriptomic resources to address the adaptive consequences of the domestication process. Gene expression and nucleotide variability were analyzed in 11 domesticated and nine wild accessions. We documented a downregulation of expression and a reduction of diversity both in nucleotide polymorphism (30%) and gene expression levels (18%) in domesticated sorghum. These findings at the genome-wide level support the occurrence of a global reduction of diversity during the domestication process, although several genes also showed patterns consistent with the action of selection. Nine hundred and forty-nine genes were significantly differentially expressed between wild and domesticated gene pools. Their functional annotation points to metabolic pathways most likely contributing to the sorghum domestication syndrome, such as photosynthesis and auxin metabolism. Coexpression network analyzes revealed 21 clusters of genes sharing similar expression patterns. Four clusters (totaling 2,449 genes) were significantly enriched in differentially expressed genes between the wild and domesticated pools and two were also enriched in domestication and improvement genes previously identified in sorghum. These findings reinforce the evidence that the combined and intricated effects of the domestication and improvement processes do not only affect the behaviors of a few genes but led to a large rewiring of the transcriptome. Overall, these analyzes pave the way toward the identification of key domestication genes valuable for genetic resources characterization and breeding purposes.
Published: 2021
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6. Genotypic covariations of traits underlying sorghum stem biomass production and quality and their regulations by water availability: Insight from studies at organ and tissue levels

Author: Delphine Luquet, Lisa Perrier, Anne Clément‐Vidal, Sylvie Jaffuel, Jean‐Luc Verdeil, Sandrine Roques, Armelle Soutiras, Christelle Baptiste, Denis Fabre, Denis Bastianelli, Laurent Bonnal, Pascal Sartre, Lauriane Rouan, and David Pot
Subjects: biomass sorghum, cell wall components, histology, soluble sugar, stem internode, water deficit, Renewable energy sources, TJ807-830, Energy industries. Energy policy. Fuel trade, HD9502-9502.5
Abstract: Abstract Sweet and biomass sorghum are expected to contribute increasingly to bioenergy production. Better understanding the impacts of the genotypic and environmental variabilities on biomass component traits and their properties is essential to optimize energy yields. This study aimed to evaluate whether traits contributing to stem biomass growth and biochemical composition at different biological scales (co)vary with the genotype and the water status in sorghum. Height genotypes were studied over two years in field conditions in southern France under two water treatments (well watered vs. 25 days’ dry down during stem elongation). Main stem internode number, size, (non)structural carbohydrate, and lignin contents were measured at the end of the stress period and/or at final harvest, together with biochemical and histological analyses of the youngest expanded internode. The tallest genotypes showed the highest stem dry weights and lignin contents. Stem (structural) biomass density was positively correlated with lignin content, particularly in internode parenchyma. Stem soluble sugar and lignin contents were inversely proportional across genotypes and water conditions. Genotypes contrasted for drought sensitivity and recovery capacity of stem growth and biochemical composition. The length and cell wall deposition of internodes expanding under water deficit were reduced and did not recover, these responses being weakly correlated. Genotypic variability was pointed out in the growth recovery of internodes expanding under re‐watered conditions. According to the observed genotypic variability and the absence of antagonistic correlations between the responses of the different traits to water availability, it is suggested that biomass sorghum varieties optimizing their responses to water availability in terms of growth and cell wall deposition can be developed for different bioenergy targets.
Published: 2019
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7. Transcriptional Regulation of Sorghum Stem Composition: Key Players Identified Through Co-expression Gene Network and Comparative Genomics Analyses

Author: Lauriane Hennet, Angélique Berger, Noemi Trabanco, Emeline Ricciuti, Jean-François Dufayard, Stéphanie Bocs, Denis Bastianelli, Laurent Bonnal, Sandrine Roques, Laura Rossini, Delphine Luquet, Nancy Terrier, and David Pot
Subjects: cell wall, gene co-expression network analysis, internode, phylogeny, transcription factor, NAC, Plant culture, SB1-1110
Abstract: Most sorghum biomass accumulates in stem secondary cell walls (SCW). As sorghum stems are used as raw materials for various purposes such as feed, energy and fiber reinforced polymers, identifying the genes responsible for SCW establishment is highly important. Taking advantage of studies performed in model species, most of the structural genes contributing at the molecular level to the SCW biosynthesis in sorghum have been proposed while their regulatory factors have mostly not been determined. Validation of the role of several MYB and NAC transcription factors in SCW regulation in Arabidopsis and a few other species has been provided. In this study, we contributed to the recent efforts made in grasses to uncover the mechanisms underlying SCW establishment. We reported updated phylogenies of NAC and MYB in 9 different species and exploited findings from other species to highlight candidate regulators of SCW in sorghum. We acquired expression data during sorghum internode development and used co-expression analyses to determine groups of co-expressed genes that are likely to be involved in SCW establishment. We were able to identify two groups of co-expressed genes presenting multiple evidences of involvement in SCW building. Gene enrichment analysis of MYB and NAC genes provided evidence that while NAC SECONDARY WALL THICKENING PROMOTING FACTOR NST genes and SECONDARY WALL-ASSOCIATED NAC DOMAIN PROTEIN gene functions appear to be conserved in sorghum, NAC master regulators of SCW in sorghum may not be as tissue compartmentalized as in Arabidopsis. We showed that for every homolog of the key SCW MYB in Arabidopsis, a similar role is expected for sorghum. In addition, we unveiled sorghum MYB and NAC that have not been identified to date as being involved in cell wall regulation. Although specific validation of the MYB and NAC genes uncovered in this study is needed, we provide a network of sorghum genes involved in SCW both at the structural and regulatory levels.
Published: 2020
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8. Autoencoding Genetic Markers to Predict the Value of Ecophysiological Model Parameters - Proof of Concept Using a Sorghum Diversity Panel

Author: Florian Larue, Grégory Beurier, Lauriane Rouan, David Pot, Jean-François Rami, and Delphine Luquet
Subjects: autoencoder, snp, gene-based modeling, ecophysiological model, parameter estimation, General Works
Abstract: Crop growth modelling formalizes the biological processes at which genotype X environment interactions (GxE) are expressed. It has the potential to evaluate, in silico, the effect of elementary traits and related genetic factors on phenotype and yield elaborations. Recent studies showed that, by driving the value of crop model parameters using a genomic selection model, yield was predicted more accurately than by a classical genetic model. However these studies dealt with few, integrative parameters and a narrow genetic diversity, i.e., a reduced number of molecular markers. This contrasts with the necessity to make crop models more responsive to climate change variables and thus increase the number of physiological parameters, while studying wider genetic diversity to seek for adaptive markers. With this respect, methods that reduce the dimensionality of the problem are needed. The autoencoder, a semi-supervised machine learning method, can reduce the number of predictors (markers) without prior information, by compressing input data into an encoded neural network layer. Applied to genetic diversity, it should ease modelling and predicting the genetic value of crop model parameters underlying GxE and yield variability, compared to classical regression methods. This study aimed at testing the autoencoding of the genetic data (ca. 1.5M markers) within a West-African sorghum diversity panel of 200 individuals. It evaluated then the relevance of autoencoded data to predict the genetic value of the dozen of crop/plant parameters controlling growth and plasticity in Ecomeristem model, estimated using data from an experiment in the Phenoarch platform.
Published: 2020
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9. Plasticity of Sorghum Stem Biomass Accumulation in Response to Water Deficit: A Multiscale Analysis from Internode Tissue to Plant Level

Author: Lisa Perrier, Lauriane Rouan, Sylvie Jaffuel, Anne Clément-Vidal, Sandrine Roques, Armelle Soutiras, Christelle Baptiste, Denis Bastianelli, Denis Fabre, Cécile Dubois, David Pot, and Delphine Luquet
Subjects: sorghum, stem biomass, water deficit, internode growth, (non)-structural carbohydrates, lignocellulose, Plant culture, SB1-1110
Abstract: Sorghum is increasingly used as a biomass crop worldwide. Its genetic diversity provides a large range of stem biochemical composition suitable for various end-uses as bioenergy or forage. Its drought tolerance enables it to reasonably sustain biomass production under water limited conditions. However, drought effect on the accumulation of sorghum stem biomass remains poorly understood which limits progress in crop improvement and management. This study aimed at identifying the morphological, biochemical and histological traits underlying biomass accumulation in the sorghum stem and its plasticity in response to water deficit. Two hybrids (G1, G4) different in stem biochemical composition (G4, more lignified, less sweet) were evaluated during 2 years in the field in Southern France, under two water treatments differentiated during stem elongation (irrigated; 1 month dry-down until an average soil water deficit of -8.85 bars). Plant phenology was observed weekly. At the end of the water treatment and at final harvest, plant height, stem and leaf dry-weight and the size, biochemical composition and tissue histology of internodes at 2–4 positions along the stem were measured. Stem biomass accumulation was significantly reduced by drought (in average 42% at the end of the dry-down). This was due to the reduction of the length, but not diameter, of the internodes expanded during water deficit. These internodes had more soluble sugar but lower lignin and cellulose contents. This was associated with a decrease of the areal proportion of lignified cell wall in internode outer zone whereas the areal proportion of this zone was not affected. All internodes for a given genotype and environment followed a common histochemical dynamics. Hemicellulose content and the areal proportion of inner vs. outer internode tissues were set up early during internode growth and were not drought responsive. G4 exhibited a higher drought sensitivity than G1 for plant height only. At final harvest, the stem dry weight was only 18% lower in water deficit (re-watered) compared to well-watered treatment and internodes growing during re-watering were similar to those on the well-watered plants. These results are being valorized to refine the phenotyping of sorghum diversity panels and breeding populations.
Published: 2017
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10. Evolutionary forces affecting synonymous variations in plant genomes.

Author: Yves Clément, Gautier Sarah, Yan Holtz, Felix Homa, Stéphanie Pointet, Sandy Contreras, Benoit Nabholz, François Sabot, Laure Sauné, Morgane Ardisson, Roberto Bacilieri, Guillaume Besnard, Angélique Berger, Céline Cardi, Fabien De Bellis, Olivier Fouet, Cyril Jourda, Bouchaib Khadari, Claire Lanaud, Thierry Leroy, David Pot, Christopher Sauvage, Nora Scarcelli, James Tregear, Yves Vigouroux, Nabila Yahiaoui, Manuel Ruiz, Sylvain Santoni, Jean-Pierre Labouisse, Jean-Louis Pham, Jacques David, and Sylvain Glémin
Subjects: Genetics, QH426-470
Abstract: Base composition is highly variable among and within plant genomes, especially at third codon positions, ranging from GC-poor and homogeneous species to GC-rich and highly heterogeneous ones (particularly Monocots). Consequently, synonymous codon usage is biased in most species, even when base composition is relatively homogeneous. The causes of these variations are still under debate, with three main forces being possibly involved: mutational bias, selection and GC-biased gene conversion (gBGC). So far, both selection and gBGC have been detected in some species but how their relative strength varies among and within species remains unclear. Population genetics approaches allow to jointly estimating the intensity of selection, gBGC and mutational bias. We extended a recently developed method and applied it to a large population genomic dataset based on transcriptome sequencing of 11 angiosperm species spread across the phylogeny. We found that at synonymous positions, base composition is far from mutation-drift equilibrium in most genomes and that gBGC is a widespread and stronger process than selection. gBGC could strongly contribute to base composition variation among plant species, implying that it should be taken into account in plant genome analyses, especially for GC-rich ones.
Published: 2017
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11. Domestication reduces alternative splicing expression variations in sorghum.

Author: Vincent Ranwez, Audrey Serra, David Pot, and Nathalie Chantret
Subjects: Medicine, Science
Abstract: Domestication is known to strongly reduce genomic diversity through population bottlenecks. The resulting loss of polymorphism has been thoroughly documented in numerous cultivated species. Here we investigate the impact of domestication on the diversity of alternative transcript expressions using RNAseq data obtained on cultivated and wild sorghum accessions (ten accessions for each pool). In that aim, we focus on genes expressing two isoforms in sorghum and estimate the ratio between expression levels of those isoforms in each accession. Noticeably, for a given gene, one isoform can either be overexpressed or underexpressed in some wild accessions, whereas in the cultivated accessions, the balance between the two isoforms of the same gene appears to be much more homogenous. Indeed, we observe in sorghum significantly more variation in isoform expression balance among wild accessions than among domesticated accessions. The possibility exists that the loss of nucleotide diversity due to domestication could affect regulatory elements, controlling transcription or degradation of these isoforms. Impact on the isoform expression balance is discussed. As far as we know, this is the first time that the impact of domestication on transcript isoform balance has been studied at the genomic scale. This could pave the way towards the identification of key domestication genes with finely tuned isoform expressions in domesticated accessions while being highly variable in their wild relatives.
Published: 2017
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12. Transcriptome Analysis of Leaves, Flowers and Fruits Perisperm of Coffea arabica L. Reveals the Differential Expression of Genes Involved in Raffinose Biosynthesis.

Author: Suzana Tiemi Ivamoto, Osvaldo Reis, Douglas Silva Domingues, Tiago Benedito Dos Santos, Fernanda Freitas de Oliveira, David Pot, Thierry Leroy, Luiz Gonzaga Esteves Vieira, Marcelo Falsarella Carazzolle, Gonçalo Amarante Guimarães Pereira, and Luiz Filipe Protasio Pereira
Subjects: Medicine, Science
Abstract: Coffea arabica L. is an important crop in several developing countries. Despite its economic importance, minimal transcriptome data are available for fruit tissues, especially during fruit development where several compounds related to coffee quality are produced. To understand the molecular aspects related to coffee fruit and grain development, we report a large-scale transcriptome analysis of leaf, flower and perisperm fruit tissue development. Illumina sequencing yielded 41,881,572 high-quality filtered reads. De novo assembly generated 65,364 unigenes with an average length of 1,264 bp. A total of 24,548 unigenes were annotated as protein coding genes, including 12,560 full-length sequences. In the annotation process, we identified nine candidate genes related to the biosynthesis of raffinose family oligossacarides (RFOs). These sugars confer osmoprotection and are accumulated during initial fruit development. Four genes from this pathway had their transcriptional pattern validated by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Furthermore, we identified ~24,000 putative target sites for microRNAs (miRNAs) and 134 putative transcriptionally active transposable elements (TE) sequences in our dataset. This C. arabica transcriptomic atlas provides an important step for identifying candidate genes related to several coffee metabolic pathways, especially those related to fruit chemical composition and therefore beverage quality. Our results are the starting point for enhancing our knowledge about the coffee genes that are transcribed during the flowering and initial fruit development stages.
Published: 2017
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13. Genetic structure, linkage disequilibrium and signature of selection in Sorghum: lessons from physically anchored DArT markers.

Author: Sophie Bouchet, David Pot, Monique Deu, Jean-François Rami, Claire Billot, Xavier Perrier, Ronan Rivallan, Laëtitia Gardes, Ling Xia, Peter Wenzl, Andrzej Kilian, and Jean-Christophe Glaszmann
Subjects: Medicine, Science
Abstract: Population structure, extent of linkage disequilibrium (LD) as well as signatures of selection were investigated in sorghum using a core sample representative of worldwide diversity. A total of 177 accessions were genotyped with 1122 informative physically anchored DArT markers. The properties of DArTs to describe sorghum genetic structure were compared to those of SSRs and of previously published RFLP markers. Model-based (STRUCTURE software) and Neighbor-Joining diversity analyses led to the identification of 6 groups and confirmed previous evolutionary hypotheses. Results were globally consistent between the different marker systems. However, DArTs appeared more robust in terms of data resolution and bayesian group assignment. Whole genome linkage disequilibrium as measured by mean r(2) decreased from 0.18 (between 0 to 10 kb) to 0.03 (between 100 kb to 1 Mb), stabilizing at 0.03 after 1 Mb. Effects on LD estimations of sample size and genetic structure were tested using i. random sampling, ii. the Maximum Length SubTree algorithm (MLST), and iii. structure groups. Optimizing population composition by the MLST reduced the biases in small samples and seemed to be an efficient way of selecting samples to make the best use of LD as a genome mapping approach in structured populations. These results also suggested that more than 100,000 markers may be required to perform genome-wide association studies in collections covering worldwide sorghum diversity. Analysis of DArT markers differentiation between the identified genetic groups pointed out outlier loci potentially linked to genes controlling traits of interest, including disease resistance genes for which evidence of selection had already been reported. In addition, evidence of selection near a homologous locus of FAR1 concurred with sorghum phenotypic diversity for sensitivity to photoperiod.
Published: 2012
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14. SL-Cloud: A Cloud-based resource to support synthetic lethal interaction discovery [version 2; peer review: 2 approved]

Author: Bahar Tercan, Guangrong Qin, Taek-Kyun Kim, Boris Aguilar, John Phan, William Longabaugh, David Pot, Christopher J. Kemp, Nyasha Chambwe, and Ilya Shmulevich
Subjects: Software Tool Article, Articles, synthetic lethality, cloud computing, cancer genomics, cancer dependency, systems biology, functional genomics
Abstract: Synthetic lethal interactions (SLIs), genetic interactions in which the simultaneous inactivation of two genes leads to a lethal phenotype, are promising targets for therapeutic intervention in cancer, as exemplified by the recent success of PARP inhibitors in treating BRCA1/2-deficient tumors. We present SL-Cloud, a new component of the Institute for Systems Biology Cancer Gateway in the Cloud (ISB-CGC), that provides an integrated framework of cloud-hosted data resources and curated workflows to enable facile prediction of SLIs. This resource addresses two main challenges related to SLI inference: the need to wrangle and preprocess large multi-omic datasets and the availability of multiple comparable prediction approaches. SL-Cloud enables customizable computational inference of SLIs and testing of prediction approaches across multiple datasets. We anticipate that cancer researchers will find utility in this tool for discovery of SLIs to support further investigation into potential drug targets for anticancer therapies.
Published: 2022
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15. SL-Cloud: A Cloud-based resource to support synthetic lethal interaction discovery [version 1; peer review: 1 approved, 1 approved with reservations]

Author: Bahar Tercan, Guangrong Qin, Taek-Kyun Kim, Boris Aguilar, John Phan, William Longabaugh, David Pot, Christopher J. Kemp, Nyasha Chambwe, and Ilya Shmulevich
Subjects: Software Tool Article, Articles, synthetic lethality, cloud computing, cancer genomics, cancer dependency, systems biology, functional genomics
Abstract: Synthetic lethal interactions (SLIs), genetic interactions in which the simultaneous inactivation of two genes leads to a lethal phenotype, are promising targets for therapeutic intervention in cancer, as exemplified by the recent success of PARP inhibitors in treating BRCA1/2-deficient tumors. We present SL-Cloud, a new component of the Institute for Systems Biology Cancer Gateway in the Cloud (ISB-CGC), that provides an integrated framework of cloud-hosted data resources and curated workflows to enable facile prediction of SLIs. This resource addresses two main challenges related to SLI inference: the need to wrangle and preprocess large multi-omic datasets and the availability of multiple comparable prediction approaches. SL-Cloud enables customizable computational inference of SLIs and testing of prediction approaches across multiple datasets. We anticipate that cancer researchers will find utility in this tool for discovery of SLIs to support further investigation into potential drug targets for anticancer therapies.
Published: 2022
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16. Whole Genome Variant Dataset for Enriching Studies across 18 Different Cancers

Author: John Torcivia, Kawther Abdilleh, Fabian Seidl, Owais Shahzada, Rebecca Rodriguez, David Pot, and Raja Mazumder
Subjects: General Medicine, TCGA, WGS, cancer variations, WGS analysis
Abstract: Whole genome sequencing (WGS) has helped to revolutionize biology, but the computational challenge remains for extracting valuable inferences from this information. Here, we present the cancer-associated variants from the Cancer Genome Atlas (TCGA) WGS dataset. This set of data will allow cancer researchers to further expand their analysis beyond the exomic regions of the genome to the entire genome. A total of 1342 WGS alignments available from the consortium were processed with VarScan2 and deposited to the NCI Cancer Cloud. The sample set covers 18 different cancers and reveals 157,313,519 pooled (non-unique) cancer-associated single-nucleotide variations (SNVs) across all samples. There was an average of 117,223 SNVs per sample, with a range from 1111 to 775,470 and a standard deviation of 163,273. The dataset was incorporated into BigQuery, which allows for fast access and cross-mapping, which will allow researchers to enrich their current studies with a plethora of newly available genomic data.
Published: 2022

17. Supplemental video 4 from NCI Imaging Data Commons

Author: Ron Kikinis, Keyvan Farahani, Ulrike Wagner, Todd Pihl, Ilya Shmulevich, Erik Ziegler, George White, Mi Tian, Daniela P. Schacherer, Madelyn Reyes, Davide Punzo, James Petts, Suzanne Paquette, Chad Osborne, Igor Octaviano, Henning Höfener, Markus D. Herrmann, William Clifford, Dennis Bontempi, Afshin Akbarzadeh, Rob Lewis, André Homeyer, Hugo J.W.L. Aerts, Steve Pieper, David A. Clunie, David Pot, William J.R. Longabaugh, and Andrey Fedorov
Abstract: Supplemental video 4 from NCI Imaging Data Commons
Published: 2023

18. Data from NCI Imaging Data Commons

Author: Ron Kikinis, Keyvan Farahani, Ulrike Wagner, Todd Pihl, Ilya Shmulevich, Erik Ziegler, George White, Mi Tian, Daniela P. Schacherer, Madelyn Reyes, Davide Punzo, James Petts, Suzanne Paquette, Chad Osborne, Igor Octaviano, Henning Höfener, Markus D. Herrmann, William Clifford, Dennis Bontempi, Afshin Akbarzadeh, Rob Lewis, André Homeyer, Hugo J.W.L. Aerts, Steve Pieper, David A. Clunie, David Pot, William J.R. Longabaugh, and Andrey Fedorov
Abstract: The National Cancer Institute (NCI) Cancer Research Data Commons (CRDC) aims to establish a national cloud-based data science infrastructure. Imaging Data Commons (IDC) is a new component of CRDC supported by the Cancer Moonshot. The goal of IDC is to enable a broad spectrum of cancer researchers, with and without imaging expertise, to easily access and explore the value of deidentified imaging data and to support integrated analyses with nonimaging data. We achieve this goal by colocating versatile imaging collections with cloud-based computing resources and data exploration, visualization, and analysis tools. The IDC pilot was released in October 2020 and is being continuously populated with radiology and histopathology collections. IDC provides access to curated imaging collections, accompanied by documentation, a user forum, and a growing number of analysis use cases that aim to demonstrate the value of a data commons framework applied to cancer imaging research.Significance:This study introduces NCI Imaging Data Commons, a new repository of the NCI Cancer Research Data Commons, which will support cancer imaging research on the cloud.
Published: 2023

19. Supplemental video 2 from NCI Imaging Data Commons

Author: Ron Kikinis, Keyvan Farahani, Ulrike Wagner, Todd Pihl, Ilya Shmulevich, Erik Ziegler, George White, Mi Tian, Daniela P. Schacherer, Madelyn Reyes, Davide Punzo, James Petts, Suzanne Paquette, Chad Osborne, Igor Octaviano, Henning Höfener, Markus D. Herrmann, William Clifford, Dennis Bontempi, Afshin Akbarzadeh, Rob Lewis, André Homeyer, Hugo J.W.L. Aerts, Steve Pieper, David A. Clunie, David Pot, William J.R. Longabaugh, and Andrey Fedorov
Abstract: Supplemental video 2 from NCI Imaging Data Commons
Published: 2023

20. Supplemental video 3 from NCI Imaging Data Commons

Author: Ron Kikinis, Keyvan Farahani, Ulrike Wagner, Todd Pihl, Ilya Shmulevich, Erik Ziegler, George White, Mi Tian, Daniela P. Schacherer, Madelyn Reyes, Davide Punzo, James Petts, Suzanne Paquette, Chad Osborne, Igor Octaviano, Henning Höfener, Markus D. Herrmann, William Clifford, Dennis Bontempi, Afshin Akbarzadeh, Rob Lewis, André Homeyer, Hugo J.W.L. Aerts, Steve Pieper, David A. Clunie, David Pot, William J.R. Longabaugh, and Andrey Fedorov
Abstract: Supplemental video 3 from NCI Imaging Data Commons
Published: 2023

21. Supplemental video 1 from NCI Imaging Data Commons

Author: Ron Kikinis, Keyvan Farahani, Ulrike Wagner, Todd Pihl, Ilya Shmulevich, Erik Ziegler, George White, Mi Tian, Daniela P. Schacherer, Madelyn Reyes, Davide Punzo, James Petts, Suzanne Paquette, Chad Osborne, Igor Octaviano, Henning Höfener, Markus D. Herrmann, William Clifford, Dennis Bontempi, Afshin Akbarzadeh, Rob Lewis, André Homeyer, Hugo J.W.L. Aerts, Steve Pieper, David A. Clunie, David Pot, William J.R. Longabaugh, and Andrey Fedorov
Abstract: Supplemental video 1 from NCI Imaging Data Commons
Published: 2023

22. Characterization of adaptation mechanisms in sorghum using a multi-reference back-cross nested association mapping design and envirotyping

Author: Vincent Garin, Chiaka Diallo, Mohamed Lamine Tekete, Korotimi Thera, Baptiste Guitton, Karim Dagno, Abdoulaye G. Diallo, Mamoutou Kouressy, Willmar Leiser, Fred Rattunde, Ibrahima Sissoko, Aboubacar Toure, Baloua Nebie, Moussa Samake, Jana Kholova, Julien Frouin, David Pot, Michel Vaksmann, Eva Weltzien, Niaba Teme, and Jean-Francois Rami
Abstract: The identification of haplotypes influencing traits of agronomic interest, with well-defined effects across environments, is of key importance to develop varieties adapted to their context of use. It requires advanced crossing schemes, multi-environment characterization and relevant statistical tools. Here we present a sorghum multi-reference back-cross nested association mapping (BCNAM) population composed of 3901 lines produced by crossing 24 diverse parents to three elite parents from West and Central Africa (WCA-BCNAM). The population was characterized in environments contrasting for photoperiod, rainfall, temperature, and soil fertility. To analyse this multi-parental and multi-environment design, we developed a new methodology for QTL detection and parental effect estimation. In addition, envirotyping data were mobilized to determine the influence of specific environmental covariables on the genetic effects, which allowed spatial projections of the QTL effects. We mobilized this strategy to analyse the genetic architecture of flowering time and plant height, which represent key adaptation mechanisms in environments like West Africa. Our results allowed a better characterisation of well-known genomic regions influencing flowering time concerning their response to photoperiod with Ma6 and Ma1 being photoperiod sensitive and candidate gene Elf3 being insensitive. We also accessed a better understanding of plant height genetic determinism with the combined effects of phenology dependent (Ma6) and independent (qHT7.1 and Dw3) genomic regions. Therefore, we argue that the WCA-BCNAM constitutes a key genetic resource to feed breeding programs in relevant elite parental lines and develop climate-smart varieties.
Published: 2023

23. A cloud‐based resource for genome coordinate‐based exploration and large‐scale analysis of chromosome aberrations and gene fusions in cancer

Author: Janet Wang, Jeanne Zheng, Elaine E. Lee, Boris Aguilar, John Phan, Kawther Abdilleh, Ronald C. Taylor, William Longabaugh, Bertil Johansson, Fredrik Mertens, Felix Mitelman, David Pot, and Thomas LaFramboise
Subjects: Cancer Research, Genetics
Published: 2023

24. A hybrid DDA/DIA-PASEF based assay library for a deep proteotyping of triple-negative breast cancer

Author: Petr Lapcik, Klara Synkova, Lucia Janacova, Pavla Bouchalova, David Potesil, Rudolf Nenutil, and Pavel Bouchal
Subjects: Science
Abstract: Abstract Triple-negative breast cancer (TNBC) is the most aggressive subtype of breast cancer, and deeper proteome coverage is needed for its molecular characterization. We present comprehensive library of targeted mass spectrometry assays specific for TNBC and demonstrate its applicability. Proteins were extracted from 105 TNBC tissues and digested. Aliquots were pooled, fractionated using hydrophilic chromatography and analyzed by LC-MS/MS in data-dependent acquisition (DDA) parallel accumulation-serial fragmentation (PASEF) mode on timsTOF Pro LC-MS system. 16 individual lysates were analyzed in data-independent acquisition (DIA)-PASEF mode. Hybrid library was generated in Spectronaut software and covers 244,464 precursors, 168,006 peptides and 11,564 protein groups (FDR = 1%). Application of our library for pilot quantitative analysis of 16 tissues increased identification numbers in Spectronaut 18.5 and DIA-NN 1.8.1 software compared to library-free setting, with Spectronaut achieving the best results represented by 190,310 precursors, 140,566 peptides, and 10,463 protein groups. In conclusion, we introduce assay library that offers the deepest coverage of TNBC proteome to date. The TNBC library is available via PRIDE repository (PXD047793).
Published: 2024
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25. DYNAMIC CHANGES IN POLYPHENOLIC COMPOUNDS AND ANTIOXIDANT ACTIVITY IN SORGHUM GRAINS AFTER GERMINATION

Author: Carolina Thomaz dos Santos D'Almeida, Nancy Terrier, David Pot, Marie-Hélène Morel, Luiz Claudio Cameron, Hamza Mameri, and Mariana Simões Larraz Ferreira
Published: 2022

26. NCI Imaging Data Commons

Author: Suzanne M. Paquette, Robert F. Lewis, George White, Steve Pieper, Madelyn Reyes, William J.R. Longabaugh, Dennis Bontempi, Igor Octaviano, Ilya Shmulevich, Afshin Akbarzadeh, Ulrike Wagner, Chad Osborne, David A. Clunie, Erik Ziegler, Andrey Fedorov, Mi Tian, Ron Kikinis, Henning Höfener, James Petts, William Clifford, Keyvan Farahani, Todd Pihl, Daniela P. Schacherer, David Pot, Davide Punzo, Markus D. Herrmann, Hugo J.W.L. Aerts, André Homeyer, Beeldvorming, MUMC+: DA BV Research (9), RS: Carim - B06 Imaging, and Publica
Subjects: Diagnostic Imaging, Cancer Research, Biomedical Research, Databases, Factual, Computer science, Cloud computing, Pilot Projects, Cancer imaging, Imaging data, Article, User-Computer Interface, Documentation, Neoplasms, Computer Graphics, Image Processing, Computer-Assisted, Humans, Use case, Computer Security, business.industry, CANCER GENOMICS CLOUD, Computational Biology, Reproducibility of Results, Cloud Computing, Data science, National Cancer Institute (U.S.), United States, Visualization, Oncology, Data Interpretation, Statistical, Programming Languages, Analysis tools, business, Commons, Radiology, Software
Abstract: The National Cancer Institute (NCI) Cancer Research Data Commons (CRDC) aims to establish a national cloud-based data science infrastructure. Imaging Data Commons (IDC) is a new component of CRDC supported by the Cancer Moonshot. The goal of IDC is to enable a broad spectrum of cancer researchers, with and without imaging expertise, to easily access and explore the value of deidentified imaging data and to support integrated analyses with nonimaging data. We achieve this goal by colocating versatile imaging collections with cloud-based computing resources and data exploration, visualization, and analysis tools. The IDC pilot was released in October 2020 and is being continuously populated with radiology and histopathology collections. IDC provides access to curated imaging collections, accompanied by documentation, a user forum, and a growing number of analysis use cases that aim to demonstrate the value of a data commons framework applied to cancer imaging research. Significance: This study introduces NCI Imaging Data Commons, a new repository of the NCI Cancer Research Data Commons, which will support cancer imaging research on the cloud.
Published: 2021

27. Population structure and genetic relationships between Ethiopian and Brazilian Coffea arabica genotypes revealed by SSR markers

Author: David Pot, Luiz Filipe Protasio Pereira, Bruna Silvestre Rodrigues da Silva, Leonardo Godoy Androcioli, Gustavo Cesar Sant'ana, Pierre Charmetant, Gustavo Hiroshi Sera, Douglas Silva Domingues, Camila Lucas Chaves, Thierry Leroy, Rafaelle Vecchia Ferreira, Instituto Agronômico do Paraná (IAPAR), Universidade Estadual de Londrina (UEL), UMR AGAP, Montpellier SupAgro, Mestrado em Agricultura Conservacionista, Universidade Estadual Paulista (Unesp), Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA), Instituto Agronômico do Parana, Empresa Brasileira de Pesquisa Agropecuária (Embrapa), Ministério da Agricultura, Pecuária e Abastecimento [Brasil] (MAPA), Governo do Brasil-Governo do Brasil, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), State University of Londrina = Universidade Estadual de Londrina, Universidade Estadual Paulista Júlio de Mesquita Filho = São Paulo State University (UNESP), Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior - Brazil (CAPES) : 001, CAPES - Agropolis Foundation : 1203-001 ANR-10-LABX-0001-01, INCT Cafe, CNPq, CAPES, Brazilian Coffee Research Consortium, and ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010)
Subjects: [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, 0106 biological sciences, 0301 basic medicine, Genotyping Techniques, Cultivated and wild gene pools, Coffea, Plant Science, 01 natural sciences, Genetic diversity, F30 - Génétique et amélioration des plantes, Coffea spp, Population structure and relationships, Genotype, Marqueur génétique, Phylogeny, 2. Zero hunger, SSR markers, biology, Coffea arabica, General Medicine, Horticulture, Microsatellite, Populationstructure and relationships, Génotype, Canephora, 010603 evolutionary biology, 03 medical and health sciences, Variation génétique, Genetics, Allele, Structure de la population, Ressource génétique, Polymorphism, Genetic, biology.organism_classification, Plant Breeding, 030104 developmental biology, Genetic distance, Insect Science, Animal Science and Zoology, Microsatellite Repeats
Abstract: Made available in DSpace on 2019-10-06T15:42:46Z (GMT). No. of bitstreams: 0 Previous issue date: 2019-04-15 Agropolis Fondation Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Information about population structure and genetic relationships within and among wild and brazilian Coffea arabica L. genotypes is highly relevant to optimize the use of genetic resources for breeding purposes. In this study, we evaluated genetic diversity, clustering analysis based on Jaccard’s coefficient and population structure in 33 genotypes of C. arabica and of three diploid Coffea species (C. canephora, C. eugenioides and C. racemosa) using 30 SSR markers. A total of 206 alleles were identified, with a mean of 6.9 over all loci. The set of SSR markers was able to discriminate all genotypes and revealed that Ethiopian accessions presented higher genetic diversity than commercial varieties. Population structure analysis indicated two genetic groups, one corresponding to Ethiopian accessions and another corresponding predominantly to commercial cultivars. Thirty-four private alleles were detected in the group of accessions collected from West side of Great Rift Valley. We observed a lower average genetic distance of the C. arabica genotypes in relation to C. eugenioides than C. canephora. Interestingly, commercial cultivars were genetically closer to C. eugenioides than C. canephora and C. racemosa. The great allelic richness observed in Ethiopian Arabica coffee, especially in Western group showed that these accessions can be potential source of new alleles to be explored by coffee breeding programs. Instituto Agronômico do Paraná (IAPAR), Rodovia Celso Garcia Cid, 375 Km Centro de Ciências Biológicas Área de Genética e Biologia Molecular Universidade Estadual de Londrina (UEL), CP 10.011 CIRAD UMR AGAP AGAP Univ. Montpellier CIRAD INRA INRIA Montpellier SupAgro Departamento de Agronomia Universidade Estadual de Londrina (UEL), CP 6001 Instituto Agronômico do Paraná (IAPAR) Mestrado em Agricultura Conservacionista, CP 481 Instituto de Biociências de Rio Claro Universidade Estadual Paulista (UNESP) Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA Café) Laboratório de Biotecnologia de Plantas – IAPAR Embrapa Café, Rodovia Celso Garcia Cid, 375 km Instituto de Biociências de Rio Claro Universidade Estadual Paulista (UNESP)
Published: 2019

28. The road to sorghum domestication: evidence from nucleotide diversity and gene expression patterns

Author: David Pot, Monique Deu, Sylvain Glémin, Angélique Berger, Nancy Terrier, Jacques David, and Concetta Burgarella
Subjects: 2. Zero hunger, 0106 biological sciences, Genetics, 0303 health sciences, biology, food and beverages, Single-nucleotide polymorphism, Sorghum, biology.organism_classification, 01 natural sciences, Phenotype, Nucleotide diversity, Transcriptome, 03 medical and health sciences, Population bottleneck, Domestication, Gene, 030304 developmental biology, 010606 plant biology & botany
Abstract: Native African cereals (sorghum, millets) ensure food security to millions of low-income people from low fertility and drought-prone regions of Africa and Asia. In spite of their agronomic importance, the genetic bases of their phenotype and adaptations are still not well understood. Here we focus on Sorghum bicolor, which is the fifth cereal worldwide for grain production and constitutes the staple food for around 500 million people. We leverage transcriptomic resources to address the adaptive consequences of the domestication process. Gene expression and nucleotide variability were analyzed in 11 domesticated and 9 wild accessions. We documented a downregulation of expression and a reduction of diversity both in nucleotide polymorphism (30%) and gene expression levels (18%) in domesticated sorghum. These findings at the genome-wide level support the occurrence of a genetic bottleneck in the domestication history of sorghum, although several genes showed also patterns consistent with the action of selection. Nine hundred and forty-nine genes were significantly differentially expressed between wild and domesticated gene pools. Their functional annotation points to metabolic pathways most likely contributing to the sorghum domestication syndrome, such as photosynthesis and auxin metabolism. Coexpression network analyses revealed 21 clusters of genes sharing similar expression patterns. Four clusters (totalizing 2449 genes) were significantly enriched in differentially expressed genes between the wild and domesticated pools and two were also enriched in domestication and improvement genes previously identified in sorghum. These findings reinforce the evidence that domestication and improvement do not only affect the behaviors of a few genes but led to a large rewiring of the transcriptome during the domestication event and the improvement process. Overall, these analyses pave the way towards the identification of key domestication genes valuable for genetic resources characterization and breeding purposes.
Published: 2020

29. Autoencoding Genetic Markers to Predict the Value of Ecophysiological Model Parameters - Proof of Concept Using a Sorghum Diversity Panel

Author: Jean-François Rami, David Pot, Grégory Beurier, Florian Larue, Lauriane Rouan, and Delphine Luquet
Subjects: autoencoder, Genetic diversity, Artificial neural network, Estimation theory, In silico, food and beverages, snp, lcsh:A, Biology, Autoencoder, Regression, ecophysiological model, Genetic marker, Genetic model, Statistics, gene-based modeling, lcsh:General Works, parameter estimation
Abstract: Crop growth modelling formalizes the biological processes at which genotype X environment interactions (GxE) are expressed. It has the potential to evaluate, in silico, the effect of elementary traits and related genetic factors on phenotype and yield elaborations. Recent studies showed that, by driving the value of crop model parameters using a genomic selection model, yield was predicted more accurately than by a classical genetic model. However these studies dealt with few, integrative parameters and a narrow genetic diversity, i.e., a reduced number of molecular markers. This contrasts with the necessity to make crop models more responsive to climate change variables and thus increase the number of physiological parameters, while studying wider genetic diversity to seek for adaptive markers. With this respect, methods that reduce the dimensionality of the problem are needed. The autoencoder, a semi-supervised machine learning method, can reduce the number of predictors (markers) without prior information, by compressing input data into an encoded neural network layer. Applied to genetic diversity, it should ease modelling and predicting the genetic value of crop model parameters underlying GxE and yield variability, compared to classical regression methods. This study aimed at testing the autoencoding of the genetic data (ca. 1.5M markers) within a West-African sorghum diversity panel of 200 individuals. It evaluated then the relevance of autoencoded data to predict the genetic value of the dozen of crop/plant parameters controlling growth and plasticity in Ecomeristem model, estimated using data from an experiment in the Phenoarch platform.
Published: 2020

30. Integrating genetic analysis and crop modeling: A major QTL can finely adjust photoperiod-sensitive sorghum flowering

Author: David Pot, Niaba Teme, Korotimi Théra, Mohamed L. Tekete, Jean-François Rami, Mamoutou Kouressy, Michel Vaksmann, Baptiste Guitton, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), IER, USTTB FST, Bamako, Mali, Partenaires INRAE, IER CRRA Sotuba, BP262, Bamako, Mali, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Generation Challenge Programme : G4008.48, Agropolis fondation : AF 1301-010/FC 2013-1890, and Cariplo fondation : AF 1301-010/FC 2013-1890
Subjects: 0106 biological sciences, 0301 basic medicine, QTL, Sélection, adaptation aux changements climatiques, Facteur climatique, 01 natural sciences, F30 - Génétique et amélioration des plantes, Flowering, Génétique des populations, Floraison, Photopériodicité, 2. Zero hunger, photoperiodism, education.field_of_study, biology, Phenology, F63 - Physiologie végétale : reproduction, Physiologie végétale, Rendement des cultures, Trait, Phénologie, Génotype, Locus des caractères quantitatifs, P40 - Météorologie et climatologie, Population, Soil Science, Quantitative trait locus, Crop, 03 medical and health sciences, Grain quality, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, education, Sorghum, U10 - Méthodes mathématiques et statistiques, Modélisation des cultures, 15. Life on land, biology.organism_classification, ELF3, 030104 developmental biology, Agronomy, Crop modeling, Agronomy and Crop Science, Photoperiod-sensitivity, 010606 plant biology & botany
Abstract: AGAP; International audience; In West Africa Sudano-Sahelian zone, sorghum sensitivity to photoperiod is a major trait for flowering adjustment toward the end of the rainy season. This trait ensures that conditions for crop development are optimal. Improving the understanding of the genetic control of flowering time in sorghum is thus an important step toward breeding climate resilient varieties for meeting the challenge of climate smart agriculture. In the wake of green revolution, most sorghum breeders eliminated photoperiod sensitivity to develop early maturing varieties. The evidence is now that simultaneous improvement of production, yield stability and grain quality requires the development of photoperiod-sensitive varieties. A segregating sorghum population derived from a cross between two photoperiod sensitive elite parents was evaluated in three different locations and five environments. CERES crop model was applied to decompose the flowering time of each genotype into basic vegetative phase, critical photoperiod and photoperiod sensitivity. Phenology and model derived variables were used for genetic analysis. The three model parameters were controlled by specific genomic regions. A major QTL affecting critical photoperiod was identified, whereas only independent minor QTLs were found for basic vegetative phase and photoperiod sensitivity. Candidate gene analysis in the major QTL region allowed us to propose a candidate gene (ELF3) involved in the circadian clock as a key regulator of flowering time in photoperiod-sensitive sorghum. Our findings provide critical information supporting the development of photoperiod-sensitive genotypes specifically adapted to climate variability encountered in Sudano-Sahelian zone.
Published: 2018

31. Nucleotide Diversity of the Coding and Promoter Regions of DREB1D, a Candidate Gene for Drought Tolerance in Coffea Species

Author: Luana Ferreira Torres, Tharyn Reichel, Dominique This, David Pot, Gabriel Sergio Costa Alves, Luciana Perreira Freire, Felipe Vinecky, Natalia Gomes Vieira, Sinara Oliveira de Aquino, Luciano Vilela Paiva, Alan Carvalho Andrade, Pierre Marraccini, Hervé Etienne, Embrapa Recursos Genéticos e Biotecnologia [Brasília], Federal University of Lavras, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), UMR - Interactions Plantes Microorganismes Environnement (UMR IPME), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud]), Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Consorcio Pesquisa Cafe, Instituto Nacional de Ciencia e Tecnologia - Cafe (Conselho Nacional de Desenvolvimento Cientifico e Tecnologico/Fundacao de Amparo a Pesquisa do Estado de Minas Gerais), and Coordenacao de Aperfeicoamento de Pessoal de Nivel Superior/Comite Francais d'Evaluation de la Cooperation Universitaire et Scientifique avec le Bresil : 407-2012
Subjects: 0106 biological sciences, 0301 basic medicine, Résistance génétique, Candidate gene, Tolérance à la sécheresse, adaptation aux changements climatiques, Coffea, Plant Science, Coffee, 01 natural sciences, Genetic diversity, F30 - Génétique et amélioration des plantes, Nucleotide diversity, Haplotype, 2. Zero hunger, Genetics, food and beverages, Coffea arabica, Drought stress, Canephora, Drought tolerance, Biology, Coffea canephora, 03 medical and health sciences, Variation génétique, Genetic variation, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, Gene, DREB1D, fungi, Promoter, Coffea eugenioides, 15. Life on land, biology.organism_classification, 030104 developmental biology, Gène, 13. Climate action, H50 - Troubles divers des plantes, 010606 plant biology & botany
Abstract: International audience; Climate change is posing a major challenge to coffee production worldwide leading to a need for the development of coffee cultivars with increased drought tolerance. In several plant species, the use of DREB genes in crop improvement has achieved promising results to desiccation tolerance engineering. Recent studies reported CcDREB1D specific patterns of expression in Coffea canephora and functional evidence of this gene involvement in drought stress responses. However, knowledge on natural diversity of this gene is largely unknown. In this context, this study aimed at evaluating the sequence variability of the DREB1D gene in several Coffea genotypes. Nucleotide variation in promoters and coding regions of this gene were evaluated in a population consisting of 38 genotypes of C. canephora, C. arabica and C. eugenioides, most of them characterized by different phenotypes (tolerance vs. susceptibility) in relation to drought. The genetic diversity of the loci revealed different haplotypes for the promoter and coding regions. In particular, our findings suggest association between drought tolerance and the genetic variations on DREB1D promoter regions, but not with those from its corresponding coding regions. Gene expression studies revealed up-regulated expression of DREB1D gene upon drought mainly in leaves of drought-tolerant clones of C. canephora, and in response to drought, high, and low temperatures in leaves of C. arabica, suggesting a key role of this gene in coffee responses to abiotic stress.
Published: 2018

32. NCI Imaging Data Commons

Author: Andriy Fedorov, Todd Pihl, Markus D. Herrmann, Robert F. Lewis, David A. Clunie, Keyvan Farahani, Hugo J.W.L. Aerts, Steve Pieper, André Homeyer, Ulrike Wagner, William J.R. Longabaugh, David Pot, and Ron Kikinis
Subjects: Cancer Research, Radiation, Information retrieval, business.industry, Interface (computing), Cloud computing, Visualization, Metadata, DICOM, Annotation, Documentation, Oncology, DICOMweb, Medicine, Radiology, Nuclear Medicine and imaging, skin and connective tissue diseases, business
Abstract: Purpose/Objective(s) National Cancer Institute (NCI) Cancer Research Data Commons (CRDC) aims to establish a cloud-based data science infrastructure. Imaging Data Commons (IDC) is a component of CRDC supported by the Cancer Moonshot™, which aims to enable access and exploration of de-identified imaging data, and to support integrated analyses with non-imaging data. IDC will interoperate with other components of CRDC, which include repositories of other types of data, such as genomics and proteomics repositories, and computational resources to perform analysis of the data. IDC builds on the strengths of the established efforts such as The Cancer Imaging Archive (TCIA) to collect and share FAIR (Findable Accessible Interoperable Reusable) imaging data. Materials/Methods IDC uses a combination of commercially available tools and capabilities provided by Google Cloud Platform (GCP) together with a range of open-source components. While the initial focus is to support clinical radiology and radiotherapy data, IDC aims to provide similar capabilities for brightfield microscopy, multi-channel immunofluorescence and other imaging modalities. Equally important is the ability to support the results of imaging data analysis, such as annotations of regions of interest in the images or various descriptors of image findings. The IDC search portal provides an interface for exploring the data, defining cohorts, and summarizing attributes of the cohort. Images can be viewed in the integrated browser-based viewer, which uses DICOMweb to access the IDC data. IDC data is public and contains no Protected Health Information (PHI). As CDRC grows, imaging datasets will be increasingly cross-linked to genomic, proteomic, and clinical data about the subjects. Results The pilot of IDC was released in October 2020, including 28 collections of the TCIA: radiology images related to The Cancer Genome Atlas (TCGA) project, and several collections prioritized to establish the capabilities of IDC in handling image-derived data. DICOM and collection-level metadata is available from the BigQuery tables, and does not require a project configured with billing. The IDC portal is available at https://portal.imagingdatacommons.cancer.gov, and integrates a customized web viewer that supports visualization of both the images and image annotations (specifically, visualization of DICOM Segmentation and Radiotherapy Structure Set is supported, including multiplanar reformatting). IDC also provides documentation and a user forum. Conclusion The IDC pilot available to the cancer research community explores the promise of cloud-hosted public imaging collections co-located with the compute resources and a growing number of tools to support data analysis. Production release of IDC is planned for Fall 2021, and will include all of the public TCIA collections, including those that contain imaging and annotation data from radiotherapy studies and clinical trials.
Published: 2021

33. Proteomic analysis of ascitic extracellular vesicles describes tumour microenvironment and predicts patient survival in ovarian cancer

Author: Anna Vyhlídalová Kotrbová, Kristína Gömöryová, Antónia Mikulová, Hana Plešingerová, Stanislava Sladeček, Marek Kravec, Šárka Hrachovinová, David Potěšil, Garett Dunsmore, Camille Blériot, Mathilde Bied, Jan Kotouček, Markéta Bednaříková, Jitka Hausnerová, Luboš Minář, Igor Crha, Michal Felsinger, Zbyněk Zdráhal, Florent Ginhoux, Vít Weinberger, Vitězslav Bryja, and Vendula Pospíchalová
Subjects: ascites, extracellular vesicles (EV), fallopian tube and peritoneum (HGSC), high‐grade serous carcinoma of the ovary, macrophage, ovarian cancer (OC), Cytology, QH573-671
Abstract: Abstract High‐grade serous carcinoma of the ovary, fallopian tube and peritoneum (HGSC), the most common type of ovarian cancer, ranks among the deadliest malignancies. Many HGSC patients have excess fluid in the peritoneum called ascites. Ascites is a tumour microenvironment (TME) containing various cells, proteins and extracellular vesicles (EVs). We isolated EVs from patients’ ascites by orthogonal methods and analyzed them by mass spectrometry. We identified not only a set of ‘core ascitic EV‐associated proteins’ but also defined their subset unique to HGSC ascites. Using single‐cell RNA sequencing data, we mapped the origin of HGSC‐specific EVs to different types of cells present in ascites. Surprisingly, EVs did not come predominantly from tumour cells but from non‐malignant cell types such as macrophages and fibroblasts. Flow cytometry of ascitic cells in combination with analysis of EV protein composition in matched samples showed that analysis of cell type‐specific EV markers in HGSC has more substantial prognostic potential than analysis of ascitic cells. To conclude, we provide evidence that proteomic analysis of EVs can define the cellular composition of HGSC TME. This finding opens numerous avenues both for a better understanding of EV's role in tumour promotion/prevention and for improved HGSC diagnostics.
Published: 2024
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34. The ISB Cancer Genomics Cloud: A Flexible Cloud-Based Platform for Cancer Genomics Research

Author: Matthew Bookman, Suzanne M. Paquette, Varsha Dhankani, Michael Miller, Kalle Leinonen, Nicole A. Deflaux, Mark Backus, Todd Pihl, Madelyn Reyes, Sheila Reynolds, Joseph Slagel, Jonathan Bingham, David L Gibbs, David Pot, William J.R. Longabaugh, Abigail Hahn, Zack Rodebaugh, Ilya Shmulevich, and Phyliss Lee
Subjects: 0301 basic medicine, Cancer Research, SQL, Computer science, Datasets as Topic, Cloud computing, Bioinformatics, Article, 03 medical and health sciences, 0302 clinical medicine, Documentation, Neoplasms, Humans, Web application, computer.programming_language, Internet, Genome, Human, business.industry, GENCODE, Research, Computational Biology, Genomics, Cloud Computing, Data science, National Cancer Institute (U.S.), United States, ComputingMethodologies_PATTERNRECOGNITION, 030104 developmental biology, Workflow, Oncology, 030220 oncology & carcinogenesis, Data as a service, business, computer, Software
Abstract: The ISB Cancer Genomics Cloud (ISB-CGC) is one of three pilot projects funded by the National Cancer Institute to explore new approaches to computing on large cancer datasets in a cloud environment. With a focus on Data as a Service, the ISB-CGC offers multiple avenues for accessing and analyzing The Cancer Genome Atlas, TARGET, and other important references such as GENCODE and COSMIC using the Google Cloud Platform. The open approach allows researchers to choose approaches best suited to the task at hand: from analyzing terabytes of data using complex workflows to developing new analysis methods in common languages such as Python, R, and SQL; to using an interactive web application to create synthetic patient cohorts and to explore the wealth of available genomic data. Links to resources and documentation can be found at www.isb-cgc.org. Cancer Res; 77(21); e7–10. ©2017 AACR.
Published: 2017

35. Sorghum biomethane potential varies with the genotype and the cultivation site

Author: Denis Bastianelli, Laurent Bonnal, Gilles Trouche, David Pot, Hélène Carrère, Hélène Laurence Thomas, Eric Latrille, Laboratoire de Biotechnologie de l'Environnement [Narbonne] (LBE), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Systèmes d'élevage méditerranéens et tropicaux (UMR SELMET), Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), ANR-11-BTBR-0006-BFF, Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), and ANR-11-BTBR-0006,BFF,Biomasse pour le futur(2011)
Subjects: 0106 biological sciences, anaerobic digestion, genotype, [SDV]Life Sciences [q-bio], sorgho, Biomass, 02 engineering and technology, Multiple cropping, 01 natural sciences, 0202 electrical engineering, electronic engineering, information engineering, Gene–environment interaction, Waste Management and Disposal, variabilité genotypique, 2. Zero hunger, food and beverages, biogaz, potentiel méthane, Digestion, Génotype, Méthane, Environmental Engineering, multi-site trials, essai multisite, F60 - Physiologie et biochimie végétale, Biochimie, 020209 energy, digestion anaérobie, Context (language use), Biology, Crop, 010608 biotechnology, Genetic variation, Traitement anaérobique, biogas, Expérimentation au champ, Renewable Energy, Sustainability and the Environment, Crop yield, P34 - Biologie du sol, 15. Life on land, Sorghum, biology.organism_classification, Agronomy, sorghum
Abstract: With its high biomass yield potential and its adaptability to a large spectrum of crop management schemes (dedicated, double cropping), sorghum is a relevant candidate crop for anaerobic digestion. Moreover, the large genotypic variability of its biochemical composition offers opportunities to cultivate specific varieties that fit the expectations of different end-users. Within this context, the need to evaluate the variability of biomethane potential (BMP) among different genotypes cultivated at various geographical sites has become crucial. In this study, four sorghum genotypes were grown at three different sites and harvested at the same maturity stage (dough grain stage). Consistent BMP obtained from different assays enabled genotype comparisons. The methane potentials observed between genotypes and production sites ranged between 200 ± 5 NmLCH4/gTS and 259 ± 12 NmLCH4/gTS. Evaluation of the genotypic and cultivation site effects produced highly significant results, thus accounting for 36 and 34%, respectively, of the phenotypic variability.
Published: 2019

36. Desmocollin-1 is associated with pro-metastatic phenotype of luminal A breast cancer cells and is modulated by parthenolide

Author: Petr Lapcik, Petr Sulc, Lucia Janacova, Katerina Jilkova, David Potesil, Pavla Bouchalova, Petr Müller, and Pavel Bouchal
Subjects: DIA, Proteomics, Pull-down, DSC1, Breast cancer, Metastasis, Cytology, QH573-671
Abstract: Abstract Background Desmocollin-1 (DSC1) is a desmosomal transmembrane glycoprotein that maintains cell-to-cell adhesion. DSC1 was previously associated with lymph node metastasis of luminal A breast tumors and was found to increase migration and invasion of MCF7 cells in vitro. Therefore, we focused on DSC1 role in cellular and molecular mechanisms in luminal A breast cancer and its possible therapeutic modulation. Methods Western blotting was used to select potential inhibitor decreasing DSC1 protein level in MCF7 cell line. Using atomic force microscopy we evaluated effect of DSC1 overexpression and modulation on cell morphology. The LC–MS/MS analysis of total proteome on Orbitrap Lumos and RNA-Seq analysis of total transcriptome on Illumina NextSeq 500 were performed to study the molecular mechanisms associated with DSC1. Pull-down analysis with LC–MS/MS detection was carried out to uncover DSC1 protein interactome in MCF7 cells. Results Analysis of DSC1 protein levels in response to selected inhibitors displays significant DSC1 downregulation (p-value ≤ 0.01) in MCF7 cells treated with NF-κB inhibitor parthenolide. Analysis of mechanic cell properties in response to DSC1 overexpression and parthenolide treatment using atomic force microscopy reveals that DSC1 overexpression reduces height of MCF7 cells and conversely, parthenolide decreases cell stiffness of MCF7 cells overexpressing DSC1. The LC–MS/MS total proteome analysis in data-independent acquisition mode shows a strong connection between DSC1 overexpression and increased levels of proteins LACRT and IGFBP5, increased expression of IGFBP5 is confirmed by RNA-Seq. Pathway analysis of proteomics data uncovers enrichment of proliferative MCM_BIOCARTA pathway including CDK2 and MCM2-7 after DSC1 overexpression. Parthenolide decreases expression of LACRT, IGFBP5 and MCM_BIOCARTA pathway specifically in DSC1 overexpressing cells. Pull-down assay identifies DSC1 interactions with cadherin family proteins including DSG2, CDH1, CDH3 and tyrosine kinase receptors HER2 and HER3; parthenolide modulates DSC1-HER3 interaction. Conclusions Our systems biology data indicate that DSC1 is connected to mechanisms of cell cycle regulation in luminal A breast cancer cells, and can be effectively modulated by parthenolide. Graphical Abstract
Published: 2023
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37. The phenotypic and genetic effects of drought-induced stress on wood specific conductivity and anatomical properties in white spruce seedlings, and relationships with growth and wood density

Author: André Soro, Patrick Lenz, Jean-Romain Roussel, Simon Nadeau, David Pothier, Jean Bousquet, and Alexis Achim
Subjects: xylem specific hydraulic conductivity, conifer, drought-induced stress, heritability, phenotypic and genetic correlations, tracheids, Plant culture, SB1-1110
Abstract: Drought frequency and intensity are projected to increase with climate change, thus amplifying stress on forest trees. Resilience to drought implicates physiological traits such as xylem conductivity and wood anatomical traits, which are related to growth and wood density. Integrating drought-stress response traits at the juvenile stage into breeding criteria could help promote the survival of planted seedlings under current and future climate and thus, improve plantation success. We assessed in greenhouse the influence of drought-induced stress on 600 two-year-old white spruce (Picea glauca) seedlings from 25 clonal lines after two consecutive growing seasons. Three levels of drought-induced stress were applied: control, moderate and severe. Seedlings were also planted at a 45° angle to clearly separate compression from normal wood. We looked at the phenotypic and genetic effects of drought stress on xylem specific hydraulic conductivity, lumen diameter, tracheid diameter and length, and the number of pits per tracheid in the normal wood. We detected no significant effects of drought stress except for tracheid length, which decreased with increasing drought stress. We found low to high estimates of trait heritability, which generally decreased with increasing drought stress. Genetic correlations were higher than phenotypic correlations for all treatments. Specific conductivity was genetically highly correlated positively with lumen diameter and tracheid length under all treatments. Tracheid length and diameter were always negatively correlated genetically, indicating a trade-off in resource allocation. Moderate to high genetic correlations sometimes in opposite direction were observed between physico-anatomical and productivity traits, also indicating trade-offs. A large variation was observed among clones for all physico-anatomical traits, but clonal ranks were generally stable between control and drought-induced treatments. Our results indicate the possibility of early screening of genetic material for desirable wood anatomical attributes under normal growing conditions, thus allowing to improve the drought resilience of young trees.
Published: 2023
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38. Developing New Sorghum Based Value Chains for Biomaterials and Energy: Process Optimization and Ideotype Definition

Author: David Pot, Nicolas Le Moigne, Hélène Carrère, Denis Bastianelli, Laurent Gazull, Anne Clément-Vidal, Armelle Soutiras, Sylvie Jaffuel, Jean-Luc Verdeil, Lata Soccalingame, Stéphane Corn, Hélène Thomas, Laurent Bonnal, Loan Vo, Lucie Chupin, Patrick Navard, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Centre des Matériaux des Mines d'Alès (C2MA), IMT - MINES ALES (IMT - MINES ALES), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT), Laboratoire de Biotechnologie de l'Environnement [Narbonne] (LBE), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Systèmes d'élevage méditerranéens et tropicaux (UMR SELMET), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Centre de Mise en Forme des Matériaux (CEMEF), Centre National de la Recherche Scientifique (CNRS)-PSL Research University (PSL)-MINES ParisTech - École nationale supérieure des mines de Paris, Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Département Systèmes Biologiques (Cirad-BIOS), Pôle Matériaux Polymères Avancés (Pôle MPA), Institut Mines-Télécom [Paris] (IMT)-Institut Mines-Télécom [Paris] (IMT)-IMT - MINES ALES (IMT - MINES ALES), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Département Environnements et Sociétés (Cirad-ES), Forêts et Sociétés (UPR Forêts et Sociétés), MINES ParisTech - École nationale supérieure des mines de Paris, and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)
Subjects: [SPI]Engineering Sciences [physics], ComputingMilieux_MISCELLANEOUS, [SPI.MAT]Engineering Sciences [physics]/Materials
Abstract: International audience; Sorghum is expected to contribute significantly to the growing needs of ligno cellulosic biomass that will support the productions of renewable energy, biomaterials and innovative biorefinery approaches. The agronomic and genetic assets of sorghum will facilitate these contributions. Nevertheless, in order to fine tune the varieties to the expectations of the growers (agronomic behavior) and of the different value chains (quality parameters) there is a crucial need to i) optimize the production process of sorghum based derived products and ii) to accurately define the target ideotypes to consider in breeding programs depending on the end-products and contexts considered. As a first step, we considered three end products: methane, biocomposite and feed. For the first two targets, we optimized the process of production by adjusting the pre-treatments and fine tuning-the different steps of the processes. As a second step we aimed at identifying the sorghum traits that contributed to the final properties of the end products. To reach this objective, we characterized at the biochemical, histological and physical levels a panel of diversity that encompassed most of the chemical variability of sorghum biomass. This panel was also characterized for its feed and biocomposite properties and for its biomethane production potential. This allowed the identification of the sets of biomass properties to target for the different end-products. As a last step, specifically for the energy targets (methane and second generation ethanol), we performed a spatially based multicriteria analysis at the regional level (anchoring the analysis on the French Midi Pyrenées region) to assess the relevance of different types of crop management and end product value chains in accordance with the local constraints (i.e. water availability, technical context). These three steps provided us with a decision tool to orientate breeding efforts depending on the targeted end-product, the environmental and technical contexts.
Published: 2018

39. Genome-wide association study reveals candidate genes influencing lipids and diterpenes contents in Coffea arabica L

Author: Gustavo C, Sant'Ana, Luiz F P, Pereira, David, Pot, Suzana T, Ivamoto, Douglas S, Domingues, Rafaelle V, Ferreira, Natalia F, Pagiatto, Bruna S R, da Silva, Lívia M, Nogueira, Cintia S G, Kitzberger, Maria B S, Scholz, Fernanda F, de Oliveira, Gustavo H, Sera, Lilian, Padilha, Jean-Pierre, Labouisse, Romain, Guyot, Pierre, Charmetant, Thierry, Leroy, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Empresa Brasileira de Pesquisa Agropecuária (Embrapa), Ministério da Agricultura, Pecuária e Abastecimento [Brasil] (MAPA), Governo do Brasil-Governo do Brasil, State University of Londrina = Universidade Estadual de Londrina, Universidade Estadual Paulista Júlio de Mesquita Filho = São Paulo State University (UNESP), Département Systèmes Biologiques (Cirad-BIOS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), UMR - Interactions Plantes Microorganismes Environnement (UMR IPME), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud]), Brazilian Coffee Research Consortium, CAPES-Agropolis Foundation through the 'Investissements d'avenir' program (Labex Agro) : 1203-001 ANR-10-LABX-0001-01, CAPES :015/13 FAPESP, Ciencia sem Fronteiras, CAPES PVE 084/13, Brazilian Coffee Research Consortium, INCT Cafe, CNPq, ANR-10-LABX-0001,AGRO,Agricultural Sciences for sustainable Development(2010), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Inst Agron Parana, CIRAD, Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA), Universidade Estadual Paulista (Unesp), and Univ Montpellier
Subjects: F60 - Physiologie et biochimie végétale, Quantitative Trait Loci, lcsh:Medicine, Coffea, Polymorphism, Single Nucleotide, Article, F30 - Génétique et amélioration des plantes, Plante sauvage, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, Teneur en lipides, Diterpénoïde, lcsh:Science, Plant Proteins, Génome, Lipide, lcsh:R, Sequence Analysis, DNA, Coffea arabica, Lipids, Amélioration des plantes, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Biosynthetic Pathways, Agricultural sciences, lcsh:Q, Diterpenes, Fève de café, Sciences agricoles, Genome-Wide Association Study
Abstract: Made available in DSpace on 2018-11-26T15:46:08Z (GMT). No. of bitstreams: 0 Previous issue date: 2018-01-11 Brazilian Coffee Research Consortium Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP) Ciencia sem Fronteiras Brazilian Coffee Research Consortium, INCT Cafe Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Lipids, including the diterpenes cafestol and kahweol, are key compounds that contribute to the quality of coffee beverages. We determined total lipid content and cafestol and kahweol concentrations in green beans and genotyped 107 Coffea arabica accessions, including wild genotypes from the historical FAO collection from Ethiopia. A genome-wide association study was performed to identify genomic regions associated with lipid, cafestol and kahweol contents and cafestol/kahweol ratio. Using the diploid Coffea canephora genome as a reference, we identified 6,696 SNPs. Population structure analyses suggested the presence of two to three groups (K = 2 and K = 3) corresponding to the east and west sides of the Great Rift Valley and an additional group formed by wild accessions collected in western forests. We identified 5 SNPs associated with lipid content, 4 with cafestol, 3 with kahweol and 9 with cafestol/kahweol ratio. Most of these SNPs are located inside or near candidate genes related to metabolic pathways of these chemical compounds in coffee beans. In addition, three trait-associated SNPs showed evidence of directional selection among cultivated and wild coffee accessions. Our results also confirm a great allelic richness in wild accessions from Ethiopia, especially in accessions originating from forests in the west side of the Great Rift Valley. Inst Agron Parana, Lab Biotecnol Vegetal, BR-86047902 Londrina, PR, Brazil CIRAD, UMR AGAP, F-34398 Montpellier, France Empresa Brasileira Pesquisa Agr, BR-0770901 Brasilia, DF, Brazil Univ Estadual Paulista, Inst Biociencias, BR-13506900 Rio Claro, SP, Brazil Univ Montpellier, IRD, CIRAD, IPME, BP 64501, F-34394 Montpellier, France Univ Montpellier, AGAP, CIRAD, INRA,Montpellier SupAgro, Montpellier, France Univ Estadual Paulista, Inst Biociencias, BR-13506900 Rio Claro, SP, Brazil CAPES: 1203-001 CAPES: ANR-10-LABX-0001-01 CAPES: 015/13 Ciencia sem Fronteiras: CAPES PVE 084/13
Published: 2018

40. A previously uncharacterized Factor Associated with Metabolism and Energy (FAME/C14orf105/CCDC198/1700011H14Rik) is related to evolutionary adaptation, energy balance, and kidney physiology

Author: Julian Petersen, Lukas Englmaier, Artem V. Artemov, Irina Poverennaya, Ruba Mahmoud, Thibault Bouderlique, Marketa Tesarova, Ruslan Deviatiiarov, Anett Szilvásy-Szabó, Evgeny E. Akkuratov, David Pajuelo Reguera, Hugo Zeberg, Marketa Kaucka, Maria Eleni Kastriti, Jan Krivanek, Tomasz Radaszkiewicz, Kristína Gömöryová, Sarah Knauth, David Potesil, Zbynek Zdrahal, Ranjani Sri Ganji, Anna Grabowski, Miriam E. Buhl, Tomas Zikmund, Michaela Kavkova, Håkan Axelson, David Lindgren, Rafael Kramann, Christoph Kuppe, Ferenc Erdélyi, Zoltán Máté, Gábor Szabó, Till Koehne, Tibor Harkany, Kaj Fried, Jozef Kaiser, Peter Boor, Csaba Fekete, Jan Rozman, Petr Kasparek, Jan Prochazka, Radislav Sedlacek, Vitezslav Bryja, Oleg Gusev, and Igor Adameyko
Subjects: Science
Abstract: Abstract In this study we use comparative genomics to uncover a gene with uncharacterized function (1700011H14Rik/C14orf105/CCDC198), which we hereby name FAME (Factor Associated with Metabolism and Energy). We observe that FAME shows an unusually high evolutionary divergence in birds and mammals. Through the comparison of single nucleotide polymorphisms, we identify gene flow of FAME from Neandertals into modern humans. We conduct knockout experiments on animals and observe altered body weight and decreased energy expenditure in Fame knockout animals, corresponding to genome-wide association studies linking FAME with higher body mass index in humans. Gene expression and subcellular localization analyses reveal that FAME is a membrane-bound protein enriched in the kidneys. Although the gene knockout results in structurally normal kidneys, we detect higher albumin in urine and lowered ferritin in the blood. Through experimental validation, we confirm interactions between FAME and ferritin and show co-localization in vesicular and plasma membranes.
Published: 2023
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41. Comprehensive genomic characterization of head and neck squamous cell carcinomas

Author: Ni Zhao, Carter Van Waes, Lori Boice, Ashley H. Salazar, Petar Stojanov, Michael B. Prystowsky, Akinyemi I. Ojesina, Tara M. Lichtenberg, Nikolaus Schultz, Joshua M. Stuart, Mitchell J. Frederick, Julie M. Gastier-Foster, Jeffrey N. Myers, Bradley A. Ozenberger, Margaret L. Gulley, Jean C. Zenklusen, Inanc Birol, Christina Yau, Mark E. Sherman, Saianand Balu, Angela Hadjipanayis, Barry S. Taylor, Piotr A. Mieczkowski, Anthony Saleh, Carol G. Shores, Ezra E.W. Cohen, Joonil Jung, Ari B. Kahn, Lisa Wise, Peter S. Hammerman, Pei Lin, Marc Ladanyi, Mark C. Weissler, Scott L. Carter, Michele C. Hayward, Rehan Akbani, Todd Pihl, J. Jack Lee, Sophie C. Egea, Harshad S. Mahadeshwar, Leigh B. Thorne, Matthew G. Soloway, Troy Shelton, Andrea Haddad, William N. William, Wiktoria Maria Suchorska, Johanna Gardner, Marco A. Marra, Julie Ahn, Travis I. Zack, Lihua Zou, Bayardo Perez-Ordonez, David A. Wheeler, Daniel Crain, Adrian Ally, Deepak Srinivasan, Jay Bowen, Aaron D. Black, Jing Wang, Ludmila Danilova, Roy Tarnuzzer, Brenda Diergaarde, Tod D. Casasent, Dean Cheng, Giovanni Ciriello, Ken Burnett, Jeff Bruce, Wojciech Golusiński, Jonathan G. Seidman, Corbin D. Jones, Daniel J. Weisenberger, Lisa A. Peterson, Thomas M. Harris, Angeliki Pantazi, Nina Thiessen, Curtis R. Pickering, Chandra Sekhar Pedamallu, Yingchun Liu, William Lee, Andrzej Mackiewicz, Hailei Zhang, Ronglai Shen, B. Arman Aksoy, Lixing Yang, Jeffrey Roach, Simion I. Chiosea, John Waldron, David Van Den Berg, James Stephen Marron, Tanja Davidsen, Liming Yang, Maciej Wiznerowicz, Benjamin Gross, Paul M. Weinberger, Yufeng Liu, Reanne Bowlby, Zhixiang Zuo, Bartosz Szybiak, Roni J. Bollag, Samuel S. Freeman, Heather M. Walline, Gad Getz, Scott Morris, Michael S. Noble, Charles Saller, Sahil Seth, Richard A. Gibbs, Jonathan C. Irish, Hollie A. Harper, George E. Sandusky, S. Onur Sumer, Trevor Hackman, Gordon B. Mills, Carol R. Bradford, Payal Sipahimalani, Nipun Kakkar, Robert Penny, Jennifer Drummond, Adam M. Zanation, Rebecca Carlsen, Andrew J. Mungall, Harshavardhan Doddapaneni, James G. Herman, Sylvia Wrenn, Andy Chu, Nilsa C. Ramirez, Patrick Kwok Shing Ng, Patrick K. Kimes, Tina Wong, Mark E. Prince, Han Si, Kristian Cibulskis, Katherine Tarvin, Peter W. Laird, Jiabin Tang, Raja R. Seethala, Michael Parfenov, Jan F. Prins, Erin Curley, Hui Cheng, Donna M. Muzny, Lynda Chin, D. Neil Hayes, Margi Sheth, Carmen Gomez-Fernandez, Jessica Walton, Paul C. Boutros, Ariane Nguyen, Kristen M. Leraas, Robert L. Ferris, Greg Eley, Christopher C. Benz, Jaegil Kim, Thomas E. Carey, Douglas B. Chepeha, Janae V. Simons, Jiexin Zhang, Laura S. Rozek, Maureen A. Sartor, Christopher A. Bristow, Justin A. Bishop, Adel K. El-Naggar, Nishant Agrawal, Yiling Lu, Carrie Sougnez, Evan G. Taylor, Raju Kucherlapati, Scott M. Lippman, Colleen Mitchell, Wendell G. Yarbrough, Chu Chen, Donghui Tan, Bhishamjit S. Chera, Michael Mayo, Wenbin Liu, Ranabir Guin, W. Kimryn Rathmell, Mayya Malakh, Jessica Frick, John N. Weinstein, Kevin Lau, Michelle Q. Pham, Gideon Dresdner, Luc G. T. Morris, David Mallery, Zhining Wang, Yichao Sun, Lynn M. Herbert, Christine M. Komarck, Lauren Averett Byers, Angela Tam, Thomas Bodenheimer, Doug Voet, Christie Kovar, Junyuan Wu, Walker Hale, Charles M. Perou, Angela B.Y. Hui, Kenna R. Mills Shaw, Timothy J. Triche, Dong Zeng, Steven J.M. Jones, Matthew D. Wilkerson, Jinze Liu, Yan Guo, Hsu Chao, Tamara R. Jones, Katherine A. Hoadley, Stuart R. Jefferys, Thomas C. Motter, Matthew Meyerson, Konstanty Korski, Timothy A. Chan, Mark A. Jensen, Julien Baboud, Alexei Protopopov, David I. Heiman, Nils Gehlenborg, Heidi J. Sofia, Aaron D. Tward, Eric S. Lander, Yunhu Wan, Scot Waring, Peggy Yena, Robert I. Haddad, Daniel DiCara, Gordon Saksena, Juok Cho, Richard A. Moore, Darshan Singh, Peter J. Park, Matthew Ibbs, Robert A. Holt, Andrew D. Cherniack, Tanguy Y. Seiwert, Lee Lichtenstein, Anders Jacobsen, Rameen Beroukhim, Brandee T. Brown, Stephen C. Benz, Paweł Golusiński, Vonn Walter, Lixia Diao, Erik Zmuda, Scott Frazer, Michael S. Lawrence, Nils Weinhold, Jacqueline E. Schein, Xiaojia Ren, Denise Brooks, Elizabeth Buda, Jianjiong Gao, Jianhua Zhang, William W. Shockley, J. Todd Auman, Xingzhi Song, Jennifer R. Grandis, Jonathan B. McHugh, Stacey Gabriel, Martin L. Ferguson, Jeffrey S. Reid, Joseph Paulauskis, Umadevi Veluvolu, John A. Demchok, Moiz S. Bootwalla, Fei-Fei Liu, Alan P. Hoyle, Shaowu Meng, Mei Huang, Ann Marie Egloff, Christina Beard, Liu Xi, Ricardo Ramirez, Donna Morton, Lisle E. Mose, Leslie Cope, Marjorie Romkes, Zubair Khan, Noreen Dhalla, Candace Shelton, Boris Reva, Stephen B. Baylin, Miruna Balasundaram, Psalm Haseley, Andrew Wei Xu, Yan Shi, A. Gordon Robertson, Gregory T. Wolf, Darlene Lee, Steven E. Schumacher, Semin Lee, Rileen Sinha, Dennis T. Maglinte, Haiyan I. Li, William K. Funkhouser, Yi Han, Sam Ng, Joel S. Parker, Kai Wang, Zhong Chen, You Hong Fan, Yaron S.N. Butterfield, Jeffrey S. Moyer, Robert A. Burton, David Pot, Chris Sander, Daryl Waggott, Joseph A. Califano, Netty Santoso, and Kyle Chang
Subjects: Male, DNA Copy Number Variations, Somatic cell, Biology, Article, 03 medical and health sciences, 0302 clinical medicine, CDKN2A, Humans, HRAS, Molecular Targeted Therapy, RNA, Neoplasm, Gene, neoplasms, 030304 developmental biology, Genetics, 0303 health sciences, Multidisciplinary, Oncogene, Genome, Human, Squamous Cell Carcinoma of Head and Neck, Wnt signaling pathway, DNA, Neoplasm, Genomics, Oncogenes, Cell cycle, 3. Good health, Gene Expression Regulation, Neoplastic, Head and Neck Neoplasms, 030220 oncology & carcinogenesis, Mutation, Cancer research, Carcinoma, Squamous Cell, Female, FAT1, Signal Transduction, Transcription Factors
Abstract: The Cancer Genome Atlas profiled 279 head and neck squamous cell carcinomas (HNSCCs) to provide a comprehensive landscape of somatic genomic alterations. Here we show that human-papillomavirus-associated tumours are dominated by helical domain mutations of the oncogene PIK3CA, novel alterations involving loss of TRAF3, and amplification of the cell cycle gene E2F1. Smoking-related HNSCCs demonstrate near universal loss-of-function TP53 mutations and CDKN2A inactivation with frequent copy number alterations including amplification of 3q26/28 and 11q13/22. A subgroup of oral cavity tumours with favourable clinical outcomes displayed infrequent copy number alterations in conjunction with activating mutations of HRAS or PIK3CA, coupled with inactivating mutations of CASP8, NOTCH1 and TP53. Other distinct subgroups contained loss-of-function alterations of the chromatin modifier NSD1, WNT pathway genes AJUBA and FAT1, and activation of oxidative stress factor NFE2L2, mainly in laryngeal tumours. Therapeutic candidate alterations were identified in most HNSCCs.
Published: 2015

42. Correction: Kolesar et al. Role of Nse1 Subunit of SMC5/6 Complex as a Ubiquitin Ligase. Cells 2022, 11, 165

Author: Peter Kolesar, Karel Stejskal, David Potesil, Johanne M. Murray, and Jan J. Palecek
Subjects: n/a, Cytology, QH573-671
Abstract: In the original publication [...]
Published: 2024
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43. Processing and properties of sorghum stem fragment-polyethylene composites

Author: Thi To Loan Vo, Calypso Beloli, Erika Di Giuseppe, Lucie Chupin, Armelle Soutiras, David Pot, Laurent Bonnal, Anne Clément-Vidal, Denis Bastianelli, Patrick Navard, Jordi Girones, Centre de Mise en Forme des Matériaux (CEMEF), MINES ParisTech - École nationale supérieure des mines de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Systèmes d'élevage méditerranéens et tropicaux (UMR SELMET), Centre National de la Recherche Scientifique (CNRS)-PSL Research University (PSL)-MINES ParisTech - École nationale supérieure des mines de Paris, and Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)
Subjects: Tige, Modulus, Mechanical properties, Polyéthylène, 02 engineering and technology, 01 natural sciences, F30 - Génétique et amélioration des plantes, [SPI.MAT]Engineering Sciences [physics]/Materials, Viscosity, chemistry.chemical_compound, Composite material, Traitement, Injection molding, Biocomposites, biology, Sorghum bicolor, Polyethylene, 021001 nanoscience & nanotechnology, Composition (visual arts), 0210 nano-technology, Génotype, biocomposite, Materials science, F60 - Physiologie et biochimie végétale, Sorgho, 010402 general chemistry, Ultimate tensile strength, Q60 - Traitement des produits agricoles non alimentaires, Sorghum, Propriété physicochimique, Izod impact strength test, biology.organism_classification, 0104 chemical sciences, Moulage par injection, chemistry, Propriété mécanique, Biocomposite, Agronomy and Crop Science
Abstract: International audience; Composites prepared with whole sorghum stem fragments reinforcing a polyethylene matrix were studied using ten different sorghum genotypes. Using a robust processing protocol, it is shown that for a given sorghum genotype, the composition of the stem fragments varies depending on the size of the sieved fragments but with the genotype effect being larger than the sieving effect. There is a variation of mechanical properties between the genotypes (from 0.6 to 1 GPa for modulus, from 7.2 to 11.5 MPa for tensile strength and from 4.4 to 6.2 kJ/m2 for impact strength). The genotypes giving the best tensile mechanical properties are the ones which have the highest viscosity, which show during blending the largest energy dissipation and which have the less decrease of size after processing. There is a weak correlation between tensile mechanical properties and resistance to impact suggesting that it is not the same tissues or physical properties which contribute to these two tests.
Published: 2017

44. Influence of the radial stem composition on the thermal behaviour of miscanthus and sorghum genotypes

Author: Grégory Mouille, Catherine Lapierre, Maryse Brancourt-Hulmel, Anne Clément-Vidal, David Pot, Dieter de Ridder, Luc Vincent, Armelle Soutiras, Stéphanie Arnoult, Emilie Gineau, Lucie Chupin, Alice Mija, Patrick Navard, Centre de Mise en Forme des Matériaux (CEMEF), Centre National de la Recherche Scientifique (CNRS)-PSL Research University (PSL)-MINES ParisTech - École nationale supérieure des mines de Paris, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Institut Jean-Pierre Bourgin (IJPB), Institut National de la Recherche Agronomique (INRA)-AgroParisTech, Unité Expérimentale Grandes Cultures Innovation Environnement (UE GCIE), Institut National de la Recherche Agronomique (INRA), Agrosystèmes et impacts environnementaux carbone-azote (Agro-Impact), Laboratoire de physique de la matière condensée (LPMC), Centre National de la Recherche Scientifique (CNRS)-Université Nice Sophia Antipolis (... - 2019) (UNS), Université Côte d'Azur (UCA)-Université Côte d'Azur (UCA), MINES ParisTech - École nationale supérieure des mines de Paris, Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Unité Expérimentale Grandes Cultures Innovation Environnement - Picardie (GCIE), Agroressources et Impacts environnementaux (AgroImpact), COMUE Université Côte d'Azur (2015-2019) (COMUE UCA)-COMUE Université Côte d'Azur (2015-2019) (COMUE UCA), program Investments for the Future [ANR-11-BTBR-0006-BFF], and ANR-11-BTBR-0006,BFF,Biomasse pour le futur(2011)
Subjects: 0106 biological sciences, Polymers and Plastics, Tige, 02 engineering and technology, 01 natural sciences, Lignin, [SPI.MAT]Engineering Sciences [physics]/Materials, chemistry.chemical_compound, Biomasse, 0202 electrical engineering, electronic engineering, information engineering, Materials Chemistry, Thermal analysis, Plant Stems, Temperature, Biochemical composition, food and beverages, Miscanthus, Composition chimique, Sorghum bicolor, Thermal behavior, Composition (visual arts), Propriété thermochimique, Lignocellulose, Génotype, Genotype, 020209 energy, Thermal resistance, F60 - Physiologie et biochimie végétale, Biology, Poaceae, Sugar, Sorghum, Propriété physicochimique, Organic Chemistry, biology.organism_classification, Température, chemistry, Agronomy, 010606 plant biology & botany
Abstract: International audience; The hypothesis made is that thermal resistance of sorghum and miscanthus stem pieces taken at well-defined positions of the stem is simply related to their biochemical composition. For miscanthus, two different genotypes and two internode levels were selected. For each region, the stem was divided into three radial layers. For sorghum, two different genotypes were selected and the stem was divided into the same three radial layers. The results show that the thermal analysis is only sensitive to very large variations of compositions. But aside of such large composition differences, it is impossible to correlate thermal effects to biochemical composition even on very small size, well-identified pieces of plant materials. The interplay between sugar-based components, lignin and minerals is totally blurring the thermal response. Extreme care must be exercised when willing to explain why a given plant material has a thermal behaviour different of another plant material.
Published: 2017

45. Evolutionary forces affecting synonymous variations in plant genomes

Author: Roberto Bacilieri, Jean Louis Pham, Stéphanie Pointet, Christopher Sauvage, Fabien De Bellis, Guillaume Besnard, Yves Vigouroux, Gautier Sarah, Bouchaib Khadari, Jean-Pierre Labouisse, Céline Cardi, Claire Lanaud, Olivier Fouet, Jacques David, Sandy Contreras, Sylvain Santoni, Morgane Ardisson, Thierry Leroy, Manuel Ruiz, Nabila Yahiaoui, Angélique Berger, Sylvain Glémin, Nora Scarcelli, Benoit Nabholz, Cyril Jourda, James Tregear, Felix Homa, Laure Sauné, Yves Clément, David Pot, François Sabot, Yan Holtz, Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), École pratique des hautes études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226, Institut de biologie de l'ENS Paris (UMR 8197/1024) (IBENS), Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut National de la Recherche Agronomique (INRA)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Department of Cell and Molecular Biology, Science for Life Laboratory, Uppsala University, Sys2Diag-Modélisation et Ingénierie des Systèmes Complexes Biologiques pour le Diagnostic (Sys2Diag), Centre National de la Recherche Scientifique (CNRS)-Alcediag, Genoscreen [Lille], Institut Pasteur de Lille, Réseau International des Instituts Pasteur (RIIP)-Réseau International des Instituts Pasteur (RIIP), Institut de Recherche pour le Développement (IRD [France-Ouest]), Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Evolution et Diversité Biologique (EDB), Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées, Peuplements végétaux et bioagresseurs en milieu tropical (UMR PVBMT), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut de Recherche pour le Développement (IRD)-Institut National de la Recherche Agronomique (INRA)-Université de La Réunion (UR), Génétique et Amélioration des Fruits et Légumes (GAFL), Institut National de la Recherche Agronomique (INRA), ISEM 2017–091, ARCAD project W 0900-001, Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Institut de biologie de l'ENS Paris (IBENS), Département de Biologie - ENS Paris, École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-École normale supérieure - Paris (ENS-PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Institut de Recherche pour le Développement (IRD)-Université Toulouse III - Paul Sabatier (UT3), Université de Toulouse (UT)-Université de Toulouse (UT)-Centre National de la Recherche Scientifique (CNRS), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE), Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Département de Biologie - ENS Paris, Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Université de Montpellier (UM), Centre National de la Recherche Scientifique (CNRS), École normale supérieure - Paris (ENS Paris)-École normale supérieure - Paris (ENS Paris)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), PSL Research University (PSL), Institut National de la Santé et de la Recherche Médicale (INSERM), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Sysdiag-Modélisation et Ingénierie des Systèmes Complexes Biologiques pour le Diagnostic (SysDiag ), BIO-RAD-Centre National de la Recherche Scientifique (CNRS), Cap delta, SouthGreen Platform, Montpellier, SouthGreen Platform, Genoscreen, Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Centre National de la Recherche Scientifique (CNRS), Unité de recherche Génétique et amélioration des fruits et légumes (GALF), Université Paris sciences et lettres (PSL), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-École normale supérieure - Paris (ENS Paris), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Centre National de la Recherche Scientifique (CNRS)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Institut National de la Santé et de la Recherche Médicale (INSERM)-Centre National de la Recherche Scientifique (CNRS), Université Toulouse III - Paul Sabatier (UT3), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut de Recherche pour le Développement (IRD)-Centre National de la Recherche Scientifique (CNRS), Institut de Recherche pour le Développement (IRD)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de La Réunion (UR)-Institut National de la Recherche Agronomique (INRA), and KARLI, Mélanie
Subjects: 0106 biological sciences, [SDV]Life Sciences [q-bio], Population genetics, Gene Expression, Plant Genomes, génome végétal, Plant Science, Plant Genetics, phylogeny, 01 natural sciences, Genome, F30 - Génétique et amélioration des plantes, [SDV.GEN.GPL] Life Sciences [q-bio]/Genetics/Plants genetics, Plant Genomics, ComputingMilieux_MISCELLANEOUS, Flowering Plants, Data Management, Genetics, 0303 health sciences, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Genomics, Plants, Plant genomes, Phylogenetics, Homogeneous, Codon usage bias, [SDE]Environmental Sciences, Transcriptome Analysis, Genome, Plant, Research Article, Biotechnology, Computer and Information Sciences, Substitution Mutation, lcsh:QH426-470, Gene Conversion, Biology, Monocotyledons, Evolution, Molecular, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, Magnoliopsida, séquençage, [SDV.BID.EVO] Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], phylogénie, Evolutionary Systematics, Gene conversion, Selection, Genetic, Genetik, analyse du transcriptome, Selection (genetic algorithm), 030304 developmental biology, Taxonomy, Evolutionary Biology, Polymorphism, Genetic, Organisms, Biology and Life Sciences, Computational Biology, Plant Taxonomy, 15. Life on land, Genome Analysis, GC Rich Sequence, lcsh:Genetics, Mutation, Plant Biotechnology, analyse fonctionnelle du génome, 010606 plant biology & botany
Abstract: Base composition is highly variable among and within plant genomes, especially at third codon positions, ranging from GC-poor and homogeneous species to GC-rich and highly heterogeneous ones (particularly Monocots). Consequently, synonymous codon usage is biased in most species, even when base composition is relatively homogeneous. The causes of these variations are still under debate, with three main forces being possibly involved: mutational bias, selection and GC-biased gene conversion (gBGC). So far, both selection and gBGC have been detected in some species but how their relative strength varies among and within species remains unclear. Population genetics approaches allow to jointly estimating the intensity of selection, gBGC and mutational bias. We extended a recently developed method and applied it to a large population genomic dataset based on transcriptome sequencing of 11 angiosperm species spread across the phylogeny. We found that at synonymous positions, base composition is far from mutation-drift equilibrium in most genomes and that gBGC is a widespread and stronger process than selection. gBGC could strongly contribute to base composition variation among plant species, implying that it should be taken into account in plant genome analyses, especially for GC-rich ones., Author summary In protein coding genes, base composition strongly varies within and among plant genomes, especially at positions where changes do not alter the coded protein (synonymous variations). Some species, such as the model plant Arabidopsis thaliana, are relatively GC-poor and homogeneous while others, such as grasses, are highly heterogeneous and GC-rich. The causes of these variations are still debated: are they mainly due to selective or neutral processes? Answering to this question is important to correctly infer whether variations in base composition may have functional roles or not. We extended a population genetics method to jointly estimate the different forces that may affect synonymous variations and applied it to genomic datasets in 11 flowering plant species. We found that GC-biased gene conversion, a neutral process associated with recombination that mimics selection by favouring G and C bases, is a widespread and stronger process than selection and that it could explain the large variation in base composition observed in plant genomes. Our results bear implications for analysing plant genomes and for correctly interpreting what could be functional or not.
Published: 2017

46. Transcriptome analysis of leaves, flowers and fruits perisperm of Coffea arabica L. Reveals the differential expression of genes involved in raffinose biosynthesis

Author: Thierry Leroy, Fernanda Freitas de Oliveira, David Pot, Luiz Filipe Protasio Pereira, Tiago Benedito dos Santos, Douglas Silva Domingues, Luiz Gonzaga Esteves Vieira, Suzana Tiemi Ivamoto, Marcelo Falsarella Carazzolle, Gonçalo A.G. Pereira, Osvaldo Reis, Universidade Estadual de Londrina (UEL), Instituto Agronómico do Paraná (IAPAR), Universidade Estadual de Campinas (UNICAMP), Universidade Estadual Paulista (Unesp), UMR AGAP, Universidade do Oeste Paulista (UNOESTE), and Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA)
Subjects: 0301 basic medicine, Candidate gene, Molecular biology, Métabolisme des glucides, Sequence assembly, Fleur, lcsh:Medicine, Coffea, Plant Science, Biochemistry, F30 - Génétique et amélioration des plantes, Transcriptome, Database and Informatics Methods, Sequencing techniques, Gene Expression Regulation, Plant, Expression des gènes, lcsh:Science, Multidisciplinary, Plant Anatomy, Feuille, food and beverages, Agriculture, RNA sequencing, Coffea arabica, Genomics, Plants, Genomic Databases, Nucleic acids, PCR, Organ Specificity, Fève de café, Qualité, Transcriptome Analysis, Research Article, F60 - Physiologie et biochimie végétale, Crops, Flowers, Biology, Research and Analysis Methods, Biosynthesis, Fruits, 03 medical and health sciences, Open Reading Frames, Raffinose, Botany, Genetics, Non-coding RNA, Gene, Illumina dye sequencing, Génie génétique, Transcription génique, Gene Expression Profiling, lcsh:R, Organisms, Computational Biology, Biology and Life Sciences, Molecular Sequence Annotation, Genome Analysis, Gene regulation, Gene expression profiling, Plant Leaves, Metabolic pathway, MicroRNAs, 030104 developmental biology, Biological Databases, Molecular biology techniques, Fruit, DNA Transposable Elements, RNA, lcsh:Q, Gene expression, Crop Science
Abstract: Made available in DSpace on 2018-12-11T17:08:57Z (GMT). No. of bitstreams: 0 Previous issue date: 2017-01-01 Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq) Coffea arabica L. is an important crop in several developing countries. Despite its economic importance, minimal transcriptome data are available for fruit tissues, especially during fruit development where several compounds related to coffee quality are produced. To understand the molecular aspects related to coffee fruit and grain development, we report a large-scale transcriptome analysis of leaf, flower and perisperm fruit tissue development. Illumina sequencing yielded 41,881,572 high-quality filtered reads. De novo assembly generated 65,364 unigenes with an average length of 1,264 bp. A total of 24,548 unigenes were annotated as protein coding genes, including 12,560 full-length sequences. In the annotation process, we identified nine candidate genes related to the biosynthesis of raffinose family oligossacarides (RFOs). These sugars confer osmoprotection and are accumulated during initial fruit development. Four genes from this pathway had their transcriptional pattern validated by quantitative reverse transcription polymerase chain reaction (qRT-PCR). Furthermore, we identified ∼24,000 putative target sites for microRNAs (miRNAs) and 134 putative transcriptionally active transposable elements (TE) sequences in our dataset. This C. arabica transcriptomic atlas provides an important step for identifying candidate genes related to several coffee metabolic pathways, especially those related to fruit chemical composition and therefore beverage quality. Our results are the starting point for enhancing our knowledge about the coffee genes that are transcribed during the flowering and initial fruit development stages. Programa de Pós-GraduacEao em Genética e Biologia Molecular Centro de Ciencias Biológicas Universidade Estadual de Londrina (UEL) Laboratório de Biotecnologia Vegetal Instituto Agronómico do Paraná (IAPAR) Laboratório de Genômica e Expressao Departamento de Genética Evolução e Bioagentes Instituto de Biologia Universidade Estadual de Campinas (UNICAMP) Departamento de Botânica Instituto de Biociências de Rio Claro Universidade Estadual Paulista (UNESP) Centre de Coopération Internationale en Recherche Agronomique Pour le Développement UMR AGAP Programa de Pós Graduação em Agronomia Universidade do Oeste Paulista (UNOESTE) Empresa Brasileira de Pesquisa Agropecuária (Embrapa Café) Departamento de Botânica Instituto de Biociências de Rio Claro Universidade Estadual Paulista (UNESP)
Published: 2017

47. Diterpenes biochemical profile and transcriptional analysis of cytochrome P450s genes in leaves, roots, flowers, and during Coffea arabica L. fruit development

Author: Thierry Leroy, David Pot, Luiz Filipe Protasio Pereira, Douglas Silva Domingues, Maria Brígida dos Santos Scholz, Leonardo M. Sakuray, Suzana Tiemi Ivamoto, Cíntia Sorane Good Kitzberger, Luiz Gonzaga Esteves Vieira, Lucia Pires Ferreira, Laboratório de Biotecnologia Vegetal, Universidade Estadual de Londrina (UEL), Laboratório de Ecofisiologia Vegetal, UMR AGAP, Universidade do Oeste Paulista (UNOESTE), Universidade Estadual Paulista (Unesp), and Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA)
Subjects: 0106 biological sciences, 0301 basic medicine, Transcription, Genetic, Physiology, Biosynthèse, Cafestol, Kahweol, Fleur, Coffea, Plant Science, Plant Roots, Coffee, 01 natural sciences, Tissu végétal, F30 - Génétique et amélioration des plantes, chemistry.chemical_compound, Cytochrome P-450 Enzyme System, Gene Expression Regulation, Plant, Gene expression, Plant defense against herbivory, Diterpénoïde, Expression des gènes, Chromatography, High Pressure Liquid, Plant Proteins, biology, food and beverages, Feuille, Coffea arabica, Composition chimique, PCR, Diterpenes, medicine.drug, Développement biologique, F60 - Physiologie et biochimie végétale, Flowers, Genes, Plant, 03 medical and health sciences, Botany, Genetics, medicine, Q04 - Composition des produits alimentaires, Genetic Association Studies, Aroma, RT-qPCR, Cytochrome P450, biology.organism_classification, Plant Leaves, 030104 developmental biology, chemistry, Fruit, biology.protein, Diterpene, U30 - Méthodes de recherche, HPLC, 010606 plant biology & botany, Racine
Abstract: Made available in DSpace on 2018-12-11T16:45:05Z (GMT). No. of bitstreams: 0 Previous issue date: 2017-02-01 Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) Lipids are among the major chemical compounds present in coffee beans, and they affect the flavor and aroma of the coffee beverage. Coffee oil is rich in kaurene diterpene compounds, mainly cafestol (CAF) and kahweol (KAH), which are related to plant defense mechanisms and to nutraceutical and sensorial beverage characteristics. Despite their importance, the final steps of coffee diterpenes biosynthesis remain unknown. To understand the molecular basis of coffee diterpenes biosynthesis, we report the content dynamics of CAF and KAH in several Coffea arabica tissues and the transcriptional analysis of cytochrome P450 genes (P450). We measured CAF and KAH concentrations in leaves, roots, flower buds, flowers and fruit tissues at seven developmental stages (30–240 days after flowering - DAF) using HPLC. Higher CAF levels were detected in flower buds and flowers when compared to fruits. In contrast, KAH concentration increased along fruit development, peaking at 120 DAF. We did not detect CAF or KAH in leaves, and higher amounts of KAH than CAF were detected in roots. Using P450 candidate genes from a coffee EST database, we performed RT-qPCR transcriptional analysis of leaves, flowers and fruits at three developmental stages (90, 120 and 150 DAF). Three P450 genes (CaCYP76C4, CaCYP82C2 and CaCYP74A1) had transcriptional patterns similar to CAF concentration and two P450 genes (CaCYP71A25 and CaCYP701A3) have transcript accumulation similar to KAH concentration. These data warrant further investigation of these P450s as potential candidate genes involved in the final stages of the CAF and KAH biosynthetic pathways. Instituto Agronômico do Paraná (IAPAR) Laboratório de Biotecnologia Vegetal, CP 481 Universidade Estadual de Londrina (UEL), CP 6001 Instituto Agronômico do Paraná (IAPAR) Laboratório de Ecofisiologia Vegetal, CP 481 Centre de Coopération Internationale en Recherche Agronomique Pour le Développement (CIRAD) UMR AGAP Universidade do Oeste Paulista (UNOESTE), Rodovia Raposo Tavares, Km 572 Universidade Estadual Paulista (UNESP) Instituto de Biociências de Rio Claro, Avenida 24-A, 1515 Empresa Brasileira de Pesquisa Agropecuária (EMBRAPA Café) Universidade Estadual Paulista (UNESP) Instituto de Biociências de Rio Claro, Avenida 24-A, 1515
Published: 2017

48. Evolution and challenges of varietal improvement strategies

Author: Jean-Pierre Horry, Sylvie Lewicki, Robert Domaingue, Patrice This, David Pot, Frédéric Bakry, Serge Braconnier, and Gilles Trouche
Subjects: 0301 basic medicine, Engineering, P06 - Sources d'énergie renouvelable, Musa (bananes), F30 - Génétique et amélioration des plantes, 0302 clinical medicine, E14 - Économie et politique du développement, Banane, Agriculture durable, Exportation, Méthode d'amélioration génétique, Environmental resource management, Sorghum bicolor, E71 - Commerce international, Agro-industrie, General partnership, Process (engineering), Supply chain, Sorgho, 03 medical and health sciences, Production (economics), Production énergétique, Variété, Agricultural productivity, Durabilité, business.industry, End user, Étude de cas, Environmental economics, Amélioration des plantes, Produit alimentaire, 030104 developmental biology, Agriculture, Développement durable, Sustainability, business, 030217 neurology & neurosurgery
Abstract: Agricultural production and supply chains are facing major challenges in the form of increasing demand for food products, a diversified use of agricultural products including for non-food purposes, ecologically intensive agriculture, and the necessity of taking climate change into account. The creation and adoption of new varieties that are productive, diversified, better adapted, and more environmentally friendly can help cropping systems that seek to address these issues become more efficient. Plant breeding efforts must anticipate the needs of the end users and adapt to very different agri-chains, illustrated in this chapter by two examples: first, an agri-chain that is highly structured around targeted export products, for example, the dessert banana, which requires ideotypes that meet the requirements of production and marketing systems; and second, an emerging agri-chain for multi-use sorghum, characterized by new production objectives of increased energy potential and production of biomaterials, sometimes without compromising with the requirement of high grain yields. To meet the objectives and the sustainability of agri-chains, research into genetic improvement must propose new approaches, new tools, and innovative breeding methods. The objectives, and sometimes the entire breeding process, are shared with all the actors, especially the end users, as part of an enhanced partnership within agri-chains. The breeding strategy also depends on ease of access, better use of available and useful genetic resources, in-depth knowledge of the structure and diversity of these resources, genetic determinism of desirable traits, and pre-breeding approaches. All these scientific and partnership innovations ensure the necessary responsiveness to support the execution of current breeding processes and the identification of new varieties that meet current and future uses and services.
Published: 2017

49. A large set of 26 new reference transcriptomes dedicated to comparative population genomics in crops and wild relatives

Author: Gautier Sarah, Felix Homa, Stéphanie Pointet, Sandy Contreras, François Sabot, Benoit Nabholz, Sylvain Santoni, Laure Sauné, Morgane Ardisson, Nathalie Chantret, Christopher Sauvage, James Tregear, Cyril Jourda, David Pot, Yves Vigouroux, Hana Chair, Nora Scarcelli, Claire Billot, Nabila Yahiaoui, Roberto Bacilieri, Bouchaib Khadari, Michel Boccara, Adéline Barnaud, Jean-Pierre Péros, Jean-Pierre Labouisse, Jean-Louis Pham, Jacques David, Sylvain Glémin, Manuel Ruiz, Amélioration génétique et adaptation des plantes méditerranéennes et tropicales (UMR AGAP), Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro)-Institut National de la Recherche Agronomique (INRA)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro), Diversité, adaptation, développement des plantes (UMR DIADE), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Université de Montpellier (UM)-Centre National de la Recherche Scientifique (CNRS)-Institut de Recherche pour le Développement (IRD [France-Sud]), Institut des Sciences de l'Evolution de Montpellier (UMR ISEM), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École pratique des hautes études (EPHE)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), INRA - Mathématiques et Informatique Appliquées (Unité MIAJ), Institut National de la Recherche Agronomique (INRA), Centre de Biologie pour la Gestion des Populations (UMR CBGP), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Université de Montpellier (UM)-Institut de Recherche pour le Développement (IRD [France-Sud])-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Unité de recherche Génétique et amélioration des fruits et légumes (GALF), Diversité et génomes des plantes cultivées (UMR DGPC), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Institut National de la Recherche Agronomique (INRA)-Centre international d'études supérieures en sciences agronomiques (Montpellier SupAgro)-Institut national d’études supérieures agronomiques de Montpellier (Montpellier SupAgro), Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-École Pratique des Hautes Études (EPHE), Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Institut de recherche pour le développement [IRD] : UR226-Centre National de la Recherche Scientifique (CNRS), Génétique et Amélioration des Fruits et Légumes (GAFL), International Center for Tropical Agriculture [Colombie] (CIAT), Consultative Group on International Agricultural Research [CGIAR] (CGIAR), This study was conducted in the framework of ARCAD (http://www.arcad-project.org), a project funded by Agropolis Fondation under the reference ID ARCAD 0900-001. GS, FH and SP salaries were supported by ARCAD budget. SC was supported by INRA (Division of Plant Biology and Breeding)., Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro)-Institut national d'enseignement supérieur pour l'agriculture, l'alimentation et l'environnement (Institut Agro), Institut de Recherche pour le Développement (IRD [France-Sud])-Centre National de la Recherche Scientifique (CNRS)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad), École pratique des hautes études (EPHE), and Université Paris sciences et lettres (PSL)-Université Paris sciences et lettres (PSL)-Université de Montpellier (UM)-Centre de Coopération Internationale en Recherche Agronomique pour le Développement (Cirad)-Centre National de la Recherche Scientifique (CNRS)-Institut de recherche pour le développement [IRD] : UR226
Subjects: 0301 basic medicine, [SDV.SA]Life Sciences [q-bio]/Agricultural sciences, Reference transcriptomes, Évolution, comparative genomics, Genome, F30 - Génétique et amélioration des plantes, Population genomics, Plante sauvage, Contig Mapping, Génétique des populations, RNA-Seq, Pennisetum glaucum, 2. Zero hunger, Dioscorea, [SDV.BID.EVO]Life Sciences [q-bio]/Biodiversity/Populations and Evolution [q-bio.PE], Domestication des plantes, food and beverages, F70 - Taxonomie végétale et phytogéographie, Biological Evolution, ARN, Comparative genomics, essai comparatif, Genome, Plant, Biotechnology, Crops, Agricultural, Séquence nucléotidique, Biology, génomique, Crop, [SDV.GEN.GPL]Life Sciences [q-bio]/Genetics/Plants genetics, 03 medical and health sciences, Botany, Genetics, reference transcriptomes, Domestication, Blast2GO, Ecology, Evolution, Behavior and Systematics, [SDV.GEN.GPO]Life Sciences [q-bio]/Genetics/Populations and Evolution [q-bio.PE], Transcription génique, fungi, Digitaria exilis, 030104 developmental biology, Evolutionary biology, évolution génétique des populations, Metagenomics, Plante de culture, Transcriptome, Reference genome
Abstract: We produced a unique large data set of reference transcriptomes to obtain new knowledge about the evolution of plant genomes and crop domestication. For this purpose, we validated a RNA-Seq data assembly protocol to perform comparative population genomics. For the validation, we assessed and compared the quality of de novo Illumina short-read assemblies using data from two crops for which an annotated reference genome was available, namely grapevine and sorghum. We used the same protocol for the release of 26 new transcriptomes of crop plants and wild relatives, including still understudied crops such as yam, pearl millet and fonio. The species list has a wide taxonomic representation with the inclusion of 15 monocots and 11 eudicots. All contigs were annotated using BLAST, prot4EST and Blast2GO. A strong originality of the data set is that each crop is associated with close relative species, which will permit whole-genome comparative evolutionary studies between crops and their wild-related species. This large resource will thus serve research communities working on both crops and model organisms. All the data are available at http://arcad-bioinformatics.southgreen.fr/.
Published: 2017

50. Catechol-O-methyl transferase suppresses cell invasion and interplays with MET signaling in estrogen dependent breast cancer

Author: Lucia Janacova, Michaela Stenckova, Petr Lapcik, Sarka Hrachovinova, Pavla Bouchalova, David Potesil, Roman Hrstka, Petr Müller, and Pavel Bouchal
Subjects: Medicine, Science
Abstract: Abstract Catechol-O-methyl transferase (COMT) is involved in detoxification of catechol estrogens, playing cancer-protective role in cells producing or utilizing estrogen. Moreover, COMT suppressed migration potential of breast cancer (BC) cells. To delineate COMT role in metastasis of estrogen receptor (ER) dependent BC, we investigated the effect of COMT overexpression on invasion, transcriptome, proteome and interactome of MCF7 cells, a luminal A BC model, stably transduced with lentiviral vector carrying COMT gene (MCF7-COMT). 2D and 3D assays revealed that COMT overexpression associates with decreased cell invasion (p 1, adj. p 0.58, q
Published: 2023
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