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1. Genome‐Wide Diversity in Lowland and Highland Maize Landraces From Southern South America: Population Genetics Insights to Assist Conservation

Author

Pia Guadalupe Dominguez, Angela Veronica Gutierrez, Monica Irina Fass, Carla Valeria Filippi, Pablo Vera, Andrea Puebla, Raquel Alicia Defacio, Norma Beatriz Paniego, and Veronica Viviana Lia

Subjects
conservation, essential biodiversity variables, maize landraces, Northern Argentina, Evolution, QH359-425
Abstract

ABSTRACT Maize (Zea mays ssp. mays L.) landraces are traditional American crops with high genetic variability that conform a source of original alleles for conventional maize breeding. Northern Argentina, one the southernmost regions of traditional maize cultivation in the Americas, harbours around 57 races traditionally grown in two regions with contrasting environmental conditions, namely, the Andean mountains in the Northwest and the tropical grasslands and Atlantic Forest in the Northeast. These races encounter diverse threats to their genetic diversity and persistence in their regions of origin, with climate change standing out as one of the major challenges. In this work, we use genome‐wide SNPs derived from ddRADseq to study the genetic diversity of individuals representing the five groups previously described for this area. This allowed us to distinguish two clearly differentiated gene pools, the highland northwestern maize (HNWA) and the floury northeastern maize (FNEA). Subsequently, we employed essential biodiversity variables at the genetic level, as proposed by the Group on Earth Observations Biodiversity Observation Network (GEO BON), to evaluate the conservation status of these two groups. This assessment encompassed genetic diversity (Pi), inbreeding coefficient (F) and effective population size (Ne). FNEA showed low Ne values and high F values, while HNWA showed low Ne values and low Pi values, indicating that further genetic erosion is imminent for these landraces. Outlier detection methods allowed identification of putative adaptive genomic regions, consistent with previously reported flowering‐time loci and chromosomal regions displaying introgression from the teosinte Zea mays ssp. mexicana. Finally, species distribution models were obtained for two future climate scenarios, showing a notable reduction in the potential planting area of HNWA and a shift in the cultivation areas of FNEA. These results suggest that maize landraces from Northern Argentina may be unable to cope with climate change. Therefore, active conservation policies are advisable.

Published
2024
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2. Comparison of ddRADseq and EUChip60K SNP genotyping systems for population genetics and genomic selection in Eucalyptus dunnii (Maiden)

Author

Natalia Cristina Aguirre, Pamela Victoria Villalba, Martín Nahuel García, Carla Valeria Filippi, Juan Gabriel Rivas, María Carolina Martínez, Cintia Vanesa Acuña, Augusto J. López, Juan Adolfo López, Pablo Pathauer, Dino Palazzini, Leonel Harrand, Javier Oberschelp, Martín Alberto Marcó, Esteban Felipe Cisneros, Rocío Carreras, Ana Maria Martins Alves, José Carlos Rodrigues, H. Esteban Hopp, Dario Grattapaglia, Eduardo Pablo Cappa, Norma Beatriz Paniego, and Susana Noemí Marcucci Poltri

Subjects
double digest restriction-site associated DNA sequencing, genotyping by sequencing, SNP array, genomic prediction, ABLUP, GBLUP, Genetics, QH426-470
Abstract

Eucalyptus dunnii is one of the most important Eucalyptus species for short-fiber pulp production in regions where other species of the genus are affected by poor soil and climatic conditions. In this context, E. dunnii holds promise as a resource to address and adapt to the challenges of climate change. Despite its rapid growth and favorable wood properties for solid wood products, the advancement of its improvement remains in its early stages. In this work, we evaluated the performance of two single nucleotide polymorphism, (SNP), genotyping methods for population genetics analysis and Genomic Selection in E. dunnii. Double digest restriction-site associated DNA sequencing (ddRADseq) was compared with the EUChip60K array in 308 individuals from a provenance-progeny trial. The compared SNP set included 8,011 and 19,008 informative SNPs distributed along the 11 chromosomes, respectively. Although the two datasets differed in the percentage of missing data, genome coverage, minor allele frequency and estimated genetic diversity parameters, they revealed a similar genetic structure, showing two subpopulations with little differentiation between them, and low linkage disequilibrium. GS analyses were performed for eleven traits using Genomic Best Linear Unbiased Prediction (GBLUP) and a conventional pedigree-based model (ABLUP). Regardless of the SNP dataset, the predictive ability (PA) of GBLUP was better than that of ABLUP for six traits (Cellulose content, Total and Ethanolic extractives, Total and Klason lignin content and Syringyl and Guaiacyl lignin monomer ratio). When contrasting the SNP datasets used to estimate PAs, the GBLUP-EUChip60K model gave higher and significant PA values for six traits, meanwhile, the values estimated using ddRADseq gave higher values for three other traits. The PAs correlated positively with narrow sense heritabilities, with the highest correlations shown by the ABLUP and GBLUP-EUChip60K. The two genotyping methods, ddRADseq and EUChip60K, are generally comparable for population genetics and genomic prediction, demonstrating the utility of the former when subjected to rigorous SNP filtering. The results of this study provide a basis for future whole-genome studies using ddRADseq in non-model forest species for which SNP arrays have not yet been developed.

Published
2024
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3. Morphological and genetic diversity of maize landraces along an altitudinal gradient in the Southern Andes.

Author

Juan Gabriel Rivas, Angela Veronica Gutierrez, Raquel Alicia Defacio, Jorge Schimpf, Ana Laura Vicario, Horacio Esteban Hopp, Norma Beatriz Paniego, and Veronica Viviana Lia

Subjects
Medicine, Science
Abstract

Maize (Zea mays ssp. mays) is a major cereal crop worldwide and is traditionally or commercially cultivated almost all over the Americas. The North-Western Argentina (NWA) region constitutes one of the main diversity hotspots of the Southern Andes, with contrasting landscapes and a large number of landraces. Despite the extensive collections performed by the "Banco Activo de Germoplasma INTA Pergamino, Argentina" (BAP), most of them have not been characterized yet. Here we report the morphological and molecular evaluation of 30 accessions collected from NWA, along an altitudinal gradient between 1120 and 2950 meters above sea level (masl). Assessment of morphological variation in a common garden allowed the discrimination of two groups, which differed mainly in endosperm type and overall plant size. Although the groups retrieved by the molecular analyses were not consistent with morphological clusters, they showed a clear pattern of altitudinal structuring. Affinities among accessions were not in accordance with racial assignments. Overall, our results revealed that there are two maize gene pools co-existing in NWA, probably resulting from various waves of maize introduction in pre-Columbian times as well as from the adoption of modern varieties by local farmers. In conclusion, the NWA maize landraces preserved at the BAP possess high morphological and molecular variability. Our results highlight their potential as a source of diversity for increasing the genetic basis of breeding programs and provide useful information to guide future sampling and conservation efforts.

Published
2022
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4. Optimizing ddRADseq in Non-Model Species: A Case Study in Eucalyptus dunnii Maiden

Author

Natalia Cristina Aguirre, Carla Valeria Filippi, Giusi Zaina, Juan Gabriel Rivas, Cintia Vanesa Acuña, Pamela Victoria Villalba, Martín Nahuel García, Sergio González, Máximo Rivarola, María Carolina Martínez, Andrea Fabiana Puebla, Michele Morgante, Horacio Esteban Hopp, Norma Beatriz Paniego, and Susana Noemí Marcucci Poltri

Subjects
SNP, SSR, next generation sequencing, genotyping by sequencing, Agriculture
Abstract

Restriction site-associated DNA sequencing (RADseq) and its derived protocols, such as double digest RADseq (ddRADseq), offer a flexible and highly cost-effective strategy for efficient plant genome sampling. This has become one of the most popular genotyping approaches for breeding, conservation, and evolution studies in model and non-model plant species. However, universal protocols do not always adapt well to non-model species. Herein, this study reports the development of an optimized and detailed ddRADseq protocol in Eucalyptus dunnii, a non-model species, which combines different aspects of published methodologies. The initial protocol was established using only two samples by selecting the best combination of enzymes and through optimal size selection and simplifying lab procedures. Both single nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) were determined with high accuracy after applying stringent bioinformatics settings and quality filters, with and without a reference genome. To scale it up to 24 samples, we added barcoded adapters. We also applied automatic size selection, and therefore obtained an optimal number of loci, the expected SNP locus density, and genome-wide distribution. Reliability and cross-sequencing platform compatibility were verified through dissimilarity coefficients of 0.05 between replicates. To our knowledge, this optimized ddRADseq protocol will allow users to go from the DNA sample to genotyping data in a highly accessible and reproducible way.

Published
2019
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5. Main and epistatic QTL analyses for Sclerotinia Head Rot resistance in sunflower.

Author

Jeremías Enrique Zubrzycki, Carla Andrea Maringolo, Carla Valeria Filippi, Facundo José Quiróz, Verónica Nishinakamasu, Andrea Fabiana Puebla, Julio A Di Rienzo, Alberto Escande, Verónica Viviana Lia, Ruth Amalia Heinz, Horacio Esteban Hopp, Gerardo D L Cervigni, and Norma Beatriz Paniego

Subjects
Medicine, Science
Abstract

Sclerotinia Head Rot (SHR), a disease caused by Sclerotinia sclerotiorum, is one of the most limiting factors in sunflower production. In this study, we identified genomic loci associated with resistance to SHR to support the development of assisted breeding strategies. We genotyped 114 Recombinant Inbred Lines (RILs) along with their parental lines (PAC2 -partially resistant-and RHA266 -susceptible-) by using a 384 single nucleotide polymorphism (SNP) Illumina Oligo Pool Assay to saturate a sunflower genetic map. Subsequently, we tested these lines for SHR resistance using assisted inoculations with S. sclerotiorum ascospores. We also conducted a randomized complete-block assays with three replicates to visually score disease incidence (DI), disease severity (DS), disease intensity (DInt) and incubation period (IP) through four field trials (2010-2014). We finally assessed main effect quantitative trait loci (M-QTLs) and epistatic QTLs (E-QTLs) by composite interval mapping (CIM) and mixed-model-based composite interval mapping (MCIM), respectively. As a result of this study, the improved map incorporates 61 new SNPs over candidate genes. We detected a broad range of narrow sense heritability (h2) values (1.86-59.9%) as well as 36 M-QTLs and 13 E-QTLs along 14 linkage groups (LGs). On LG1, LG10, and LG15, we repeatedly detected QTLs across field trials; which emphasizes their putative effectiveness against SHR. In all selected variables, most of the identified QTLs showed high determination coefficients, associated with moderate to high heritability values. Using markers shared with previous Sclerotinia resistance studies, we compared the QTL locations in LG1, LG2, LG8, LG10, LG11, LG15 and LG16. This study constitutes the largest report of QTLs for SHR resistance in sunflower. Further studies focusing on the regions in LG1, LG10, and LG15 harboring the detected QTLs are necessary to identify causal alleles and contribute to unraveling the complex genetic basis governing the resistance.

Published
2017
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7. On-field phenotypic evaluation of sunflower populations for broad-spectrum resistance to Verticillium leaf mottle and wilt

Author

Norma Beatriz Paniego, Salvador Nicosia, H. Esteban Hopp, Juan Francisco Montecchia, Julio A. Di Rienzo, Ignacio Cerrudo, Carolina Troglia, Daniel Alvarez, Monica Irina Fass, Carla Maringolo, Alberto Escande, Verónica Viviana Lia, Ruth Amelia Heinz, Julio Horacio Gonzalez, and Facundo José Quiroz

Subjects
Fitomejoramiento, 0106 biological sciences, 0301 basic medicine, Germplasm, Veterinary medicine, 01 natural sciences, Plant breeding, Disease Resistance, Semilla de Girasol, Multidisciplinary, Germoplasma, Chromosome Mapping, Helianthus annuus, Sunflower, Phenotypes, Phenotype, Helianthus, Medicine, Sunflower seed, Genome, Plant, Crop Improvement, Agricultural genetics, Science, Quantitative Trait Loci, Argentina, Biology, Article, 03 medical and health sciences, Mejora de Cultivos, Ascomycota, Enfermedades de las Plantas, Verticillium dahliae, Girasol, Fenotipos, Biotic, Plant Diseases, Heritability, biology.organism_classification, Verticillium, Plant Leaves, Plant Breeding, 030104 developmental biology, Natural variation in plants, Verticillium wilt, Sunflower Seed, 010606 plant biology & botany
Abstract

Sunflower Verticillium Wilt and Leaf Mottle (SVW), caused by Verticillium dahliae (Kleb.; Vd), is a soil-borne disease affecting sunflower worldwide. A single dominant locus, known as V1, was formerly effective in controlling North-American Vd races, whereas races from Argentina, Europe and an emerging race from USA overcome its resistance. This emphasizes the need for identifying broad-spectrum genetic resistance (BSR) sources. Here we characterize two sunflower mapping populations (MPs) for SVW resistance: a biparental MP and the association MP from the National Institute of Agricultural Technology (INTA), under field growing conditions. Nine field-trials (FTs) were conducted in highly infested fields in the most SVW-affected region of Argentina. Several disease descriptors (DDs), including incidence and severity, were scored across four phenological stages. Generalized linear models were fitted according to the nature of each variable, adjusting mean phenotypes for inbred lines across and within FTs. Comparison of these responses allowed the identification of novel BSR sources. Furthermore, we present the first report of SVW resistance heritability, with estimates ranging from 35 to 45% for DDs related to disease incidence and severity, respectively. This study constitutes the largest SVW resistance characterization reported to date in sunflower, identifying valuable genetic resources for BSR-breeding to cope with a pathogen of increasing importance worldwide. EEA Pergamino Fil: Montecchia, Juan Francisco. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Agrobiotecnología y Biología Molecular (IABIMO); Argentina Fil: Fass, Mónica I. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnología. Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET). Instituto de Agrobiotecnología y Biología Molecular (IABIMO); Argentina Fil: Cerrudo, Ignacio. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; Argentina Fil: Quiroz, Facundo José. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; Argentina Fil: Nicosia, Salvador Maria. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnologoía. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Agrobiotecnología y Biología Molecular (IABIMO); Argentina Fil: Maringolo, Carla Andrea. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; Argentina Fil: Di Rienzo, Julio. Universidad Nacional de Córdoba. Facultad de Ciencias Agropecuarias; Argentina Fil: Troglia, Carolina Beatriz. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; Argentina Fil: Hopp, Horacio Esteban. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnologoía. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Agrobiotecnología y Biología Molecular (IABIMO); Argentina Fil: Hopp, Horacio Esteban. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina Fil: Escande, Alberto. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; Argentina Fil: Gonzalez, Julio Horacio. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Pergamino. Sección Girasol; Argentina Fil: Alvarez, Daniel. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Manfredi; Argentina Fil: Heinz, Ruth Amelia. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnologoía. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Agrobiotecnología y Biología Molecular (IABIMO); Argentina Fil: Lia, Veronica Viviana. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnologoía. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Agrobiotecnología y Biología Molecular (IABIMO); Argentina Fil: Lia, Veronica Viviana. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina Fil: Paniego, Norma Beatriz. Instituto Nacional de Tecnología Agropecuaria (INTA). Instituto de Biotecnologoía. Consejo Nacional de Investigaciones Científicas y Técnicas. Instituto de Agrobiotecnología y Biología Molecular (IABIMO); Argentina

Published
2021

8. Unveiling the genetic basis of Sclerotinia head rot resistance in sunflower

Author

Ruth Amelia Heinz, J. A. Di Rienzo, Andrea F. Puebla, Carla Maringolo, Facundo José Quiroz, Norma Beatriz Paniego, Verónica Viviana Lia, Carla Valeria Filippi, Horacio Esteban Hopp, Alberto Escande, Daniel Alvarez, and J. E. Zubrzycki

Subjects
Germplasm, Candidate gene, ARGENTINIAN GERMPLASM, Genotype, Population, Plant Science, SUNFLOWER, Biology, Plant disease resistance, Polymorphism, Single Nucleotide, ASSOCIATION MAPPING, Ascomycota, lcsh:Botany, Enfermedades de las Plantas, Genetics, DISEASE RESISTANCE, Girasol, Association mapping, education, Rots, Alleles, Genetic Association Studies, Sclerotinia, Plant Diseases, education.field_of_study, Disease resistance, Sclerotinia sclerotiorum, Chromosome Mapping, purl.org/becyt/ford/4.4 [https], Helianthus annuus, biology.organism_classification, Sunflower, Genética, Podredumbres, lcsh:QK1-989, Plant Breeding, Phenotype, Resistencia a la Enfermedad, Argentinian germplasm, Helianthus, purl.org/becyt/ford/4 [https], Microsatellite Repeats, Research Article
Abstract

Background: Sclerotinia sclerotiorum is a necrotrophic fungus that causes Sclerotinia head rot (SHR) in sunflower, with epidemics leading to severe yield losses. In this work, we present an association mapping (AM) approach to investigate the genetic basis of natural resistance to SHR in cultivated sunflower, the fourth most widely grown oilseed crop in the world. Results: Our association mapping population (AMP), which comprises 135 inbred breeding lines (ILs), was genotyped using 27 candidate genes, a panel of 9 Simple Sequence Repeat (SSR) markers previously associated with SHR resistance via bi-parental mapping, and a set of 384 SNPs located in genes with molecular functions related to stress responses. Moreover, given the complexity of the trait, we evaluated four disease descriptors (i.e, disease incidence, disease severity, area under the disease progress curve for disease incidence, and incubation period). As a result, this work constitutes the most exhaustive AM study of disease resistance in sunflower performed to date. Mixed linear models accounting for population structure and kinship relatedness were used for the statistical analysis of phenotype-genotype associations, allowing the identification of 13 markers associated with disease reduction. The number of favourable alleles was negatively correlated to disease incidence, disease severity and area under the disease progress curve for disease incidence, whereas it was positevily correlated to the incubation period. Conclusions: Four of the markers identified here as associated with SHR resistance (HA1848, HaCOI_1, G33 and G34) validate previous research, while other four novel markers (SNP117, SNP136, SNP44, SNP128) were consistently associated with SHR resistance, emerging as promising candidates for marker-assisted breeding. From the germplasm point of view, the five ILs carrying the largest combination of resistance alleles provide a valuable resource for sunflower breeding programs worldwide. Fil: Filippi, Carla Valeria. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Agrobiotecnología y Biología Molecular. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Agrobiotecnología y Biología Molecular; Argentina Fil: Zubrzycki, Jeremías Enrique. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Agrobiotecnología y Biología Molecular. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Agrobiotecnología y Biología Molecular; Argentina Fil: Di Rienzo, Julio Alejandro. Universidad Nacional de Córdoba. Facultad de Ciencias Agropecuarias; Argentina Fil: Quiroz, Facundo José. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires Sur. Estación Experimental Agropecuaria Balcarce; Argentina Fil: Puebla, Andrea Fabiana. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Agrobiotecnología y Biología Molecular. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Agrobiotecnología y Biología Molecular; Argentina Fil: Alvarez, D.. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Córdoba. Estación Experimental Agropecuaria Manfredi; Argentina Fil: Maringolo, C. A.. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires Sur. Estación Experimental Agropecuaria Balcarce; Argentina Fil: Escande, Alberto Raul. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires Sur. Estación Experimental Agropecuaria Balcarce; Argentina Fil: Hopp, Horacio Esteban. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Agrobiotecnología y Biología Molecular. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Agrobiotecnología y Biología Molecular; Argentina Fil: Heinz, Ruth Amelia. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Agrobiotecnología y Biología Molecular. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Agrobiotecnología y Biología Molecular; Argentina Fil: Paniego, Norma Beatriz. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Agrobiotecnología y Biología Molecular. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Agrobiotecnología y Biología Molecular; Argentina Fil: Lia, Veronica Viviana. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Agrobiotecnología y Biología Molecular. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Agrobiotecnología y Biología Molecular; Argentina

Published
2020
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9. ddRADseq-mediated detection of genetic variants in sugarcane

Author

Catalina Molina, Natalia Cristina Aguirre, Pablo Alfredo Vera, Carla Valeria Filippi, Andrea Fabiana Puebla, Susana Noemí Marcucci Poltri, Norma Beatriz Paniego, and Alberto Acevedo

Subjects
Genetics, Plant Science, General Medicine, Agronomy and Crop Science
Abstract

The article presents an optimization of the key parameters for the identification of SNPs in sugarcane using a GBS protocol based on two Illumina NextSeq and NovaSeq platforms. Sugarcane (Saccharum sp.), a world-wide known feedstock for sugar production, bioethanol, and energy, has an extremely complex genome, being highly polyploid and aneuploid. A double-digestion restriction site-associated DNA sequencing protocol (ddRADseq) was tested in four commercial sugarcane hybrids and one high-fibre biotype for the detection of single nucleotide polymorphisms (SNPs). In this work we tested two Illumina sequencing platforms, read size (70 vs. 150 bp), different sequencing coverage per individual (medium and high coverage), and single-reads versus paired-end reads. We also explored different variant calling strategies (with and without reference genome) and filtering schemes [combining two minor allele frequencies (MAFs) with three depth of coverage thresholds]. For the discovery of a large number of novel SNPs in sugarcane, we recommend longer size and paired-end reads, medium sequencing coverage per individual and Illumina platform NovaSeq6000 for a cost-effective approach, and filter parameters of lower MAF and higher depth coverages thresholds. Although the de novo analysis retrieved more SNPs, the reference-based method allows downstream characterization of variants. For the two best performing matrices, the number of SNPs per chromosome correlated positively with chromosome length, demonstrating the presence of variants throughout the genome. Multivariate comparisons, with both matrices, showed closer relationships among commercial hybrids than with the high-fibre biotype. Functional analysis of the SNPs demonstrated that more than half of them landed within regulatory regions, whereas the other half affected coding, intergenic and intronic regions. Allelic distances values were lower than 0.07 when analysing two replicated genotypes, confirming the protocol robustness.

Published
2022

10. On-field Phenotypic Evaluation of Sunflower Germplasm: Breeding for Broad-spectrum Resistance to Verticillium Leaf Mottle and Wilt

Author

Julio Horacio Gonzalez, Juan Francisco Montecchia, Ignacio Cerrudo, Salvador Nicosia, Verónica Viviana Lia, Carolina Troglia, Norma Beatriz Paniego, Ruth Amelia Heinz, Horacio Esteban Hopp, Carla Maringolo, Monica Irina Fass, Alberto Escande, Facundo Jose Quiroz, Daniel Alvarez, and Julio A. Di Rienzo

Subjects
Germplasm, Horticulture, Broad spectrum, Field (physics), Resistance (ecology), medicine, Mottle, Biology, medicine.disease, Verticillium, biology.organism_classification, Sunflower
Abstract

Sunflower Verticillium Wilt and Leaf Mottle (SVW), caused by Verticillium dahliae (Kleb.; Vd), is a soil-borne disease affecting sunflower worldwide. A single dominant locus, known as V1, was formerly effective in controlling North-American Vd races, whereas races from Argentina, Europe and an emerging race from USA overcome its resistance. This emphasizes the need for identifying broad-spectrum genetic resistance (BSR) sources. Here we characterize two sunflower Mapping Populations (MPs) for SVW resistance: a biparental MP and the association MP from the National Institute of Agricultural Technology (INTA), under field growing conditions. Nine field-trials (FTs) were conducted in highly infested fields in the most SVW-affected region of Argentina. Several disease descriptors (DDs), including incidence and severity, were scored across four phenological stages. Generalized linear models were fitted according to the nature of each variable, adjusting mean phenotypes for inbred lines (IL) across and within FTs. Comparison of these responses allowed the identification of novel BSR sources. Furthermore, we present the first report of SVW resistance heritability, with estimates ranging from 35% to 45% for DDs related to disease incidence and severity, respectively. This study constitutes the largest SVW resistance characterization reported to date in sunflower, identifying valuable genetic resources for BSR-breeding to cope with a pathogen of increasing importance worldwide.

Published
2021
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11. Plastome genomics in South American maize landraces: chloroplast lineages parallel the geographical structuring of nuclear gene pools

Author

Raquel Defacio, Mariana G. López, Pablo Alfredo Vera, Monica Irina Fass, Joaquín Dopazo, Juan Gabriel Rivas, Verónica Viviana Lia, José Carbonell-Caballero, Horacio Esteban Hopp, Andrea F. Puebla, Norma Beatriz Paniego, Agencia Nacional de Promoción Científica y Tecnológica (Argentina), Consejo Nacional de Investigaciones Científicas y Técnicas (Argentina), and Instituto Nacional de Tecnología Agropecuaria (Argentina)

Subjects
0106 biological sciences, 0301 basic medicine, Nuclear gene, Chloroplasts, maize landraces, Plant genetics, Genomics, Plant Science, Biology, Intraspecific variation, 01 natural sciences, Zea mays, 03 medical and health sciences, Indel, Phylogeny, Phylogenetic tree, Maize dispersal, Genetic Variation, cpSSR, Bayes Theorem, Gene Pool, Original Articles, South America, Phylogeography, 030104 developmental biology, Chloroplast DNA, Evolutionary biology, whole-plastome sequencing, Microsatellite, Gene pool, 010606 plant biology & botany
Abstract

33 páginas, 2 tablas, 4 figuras, Background and aims: The number of plastome sequences has increased exponentially during the last decade. However, there is still little knowledge of the levels and distribution of intraspecific variation. The aims of this study were to estimate plastome diversity within Zea mays and analyse the distribution of haplotypes in connection with the landrace groups previously delimited for South American maize based on nuclear markers. Methods: We obtained the complete plastomes of 30 South American maize landraces and three teosintes by means of next-generation sequencing (NGS) and used them in combination with data from public repositories. After quality filtering, the curated data were employed to search for single-nucleotide polymorphisms, indels and chloroplast simple sequence repeats. Exact permutational contingency tests were performed to assess associations between plastome and nuclear variation. Network and Bayesian phylogenetic analyses were used to infer evolutionary relationships among haplotypes. Key results: Our analyses identified a total of 124 polymorphic plastome loci, with the intergenic regions psbE-rps18, petN-rpoB, trnL_UAG-ndhF and rpoC2-atpI exhibiting the highest marker densities. Although restricted in number, these markers allowed the discrimination of 27 haplotypes in a total of 51 Zea mays individuals. Andean and lowland South American landraces differed significantly in haplotype distribution. However, overall differentiation patterns were not informative with respect to subspecies diversification, as evidenced by the scattered distribution of maize and teosinte plastomes in both the network and Bayesian phylogenetic reconstructions. Conclusions: Knowledge of intraspecific plastome variation provides the framework for a more comprehensive understanding of evolutionary processes at low taxonomic levels and may become increasingly important for future plant barcoding efforts. Whole-plastome sequencing provided useful variability to contribute to maize phylogeographic studies. The structuring of haplotype diversity in the maize landraces examined here clearly reflects the distinction between the Andean and South American lowland gene pools previously inferred based on nuclear markers., This work was supported by the Agencia Nacional de Promoción Científica y Técnica (PICT 2012 0325, PICT 2016 1101), the Consejo Nacional de Investigaciones Científicas y Tecnológicas (PIP 11220120100416CO 2013–2015), the Instituto Nacional de Tecnología Agropecuaria (PNBIO 1131044) and the DEANN Project.

Published
2020

12. Exploring sunflower responses to Sclerotinia head rot at early stages of infection using RNA-seq analysis

Author

Francisco García-García, Carla Maringolo, Maximo Rivarola, Verónica Viviana Lia, Joaquín Dopazo Blázquez, Monica Irina Fass, Ruth Amelia Heinz, Facundo José Quiroz, H. Esteban Hopp, Juan Francisco Montecchia, Guillermo F. Ehrenbolger, and Norma Beatriz Paniego

Subjects
0301 basic medicine, RNA Sequence, Transcription, Genetic, Respuesta Inmunológica, Gene Expression, RNA-Seq, SUNFLOWER, Breeding, purl.org/becyt/ford/1 [https], Pathosystem, 0302 clinical medicine, Cell Wall, Gene expression, EARLY RESPONSE, Immune Response, Defense Mechanisms, Disease Resistance, Genetics, Multidisciplinary, Mecanismo de Defensa, biology, Sclerotinia sclerotiorum, purl.org/becyt/ford/4.4 [https], Helianthus annuus, Secuencia de ARN, Medicine, Helianthus, RNA, Long Noncoding, Sclerotinia, Oxidation-Reduction, Expresión Génica, Genotype, SCLEROTINIA, Science, Plant disease resistance, Article, 03 medical and health sciences, Ascomycota, purl.org/becyt/ford/1.6 [https], Gene, Plant Diseases, Sequence Analysis, RNA, biology.organism_classification, 030104 developmental biology, RNA SEQ, Plant sciences, 030217 neurology & neurosurgery, purl.org/becyt/ford/4 [https]
Abstract

Sclerotinia head rot (SHR), caused by the necrotrophic fungus Sclerotinia sclerotiorum, is one of the most devastating sunflower crop diseases. Despite its worldwide occurrence, the genetic determinants of plant resistance are still largely unknown. Here, we investigated the Sclerotinia-sunflower pathosystem by analysing temporal changes in gene expression in one susceptible and two tolerant inbred lines (IL) inoculated with the pathogen under field conditions. Differential expression analysis showed little overlapping among ILs, suggesting genotype-specific control of cell defense responses possibly related to differences in disease resistance strategies. Functional enrichment assessments yielded a similar pattern. However, all three ILs altered the expression of genes involved in the cellular redox state and cell wall remodeling, in agreement with current knowledge about the initiation of plant immune responses. Remarkably, the over-representation of long non-coding RNAs (lncRNA) was another common feature among ILs. Our findings highlight the diversity of transcriptional responses to SHR within sunflower breeding lines and provide evidence of lncRNAs playing a significant role at early stages of defense. Fil: Fass, Mónica Irina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Agrobiotecnología y Biología Molecular. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Agrobiotecnología y Biología Molecular; Argentina Fil: Rivarola, Maximo Lisandro. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Agrobiotecnología y Biología Molecular. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Agrobiotecnología y Biología Molecular; Argentina Fil: Ehrenbolger, Guillermo Federico. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Agrobiotecnología y Biología Molecular. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Agrobiotecnología y Biología Molecular; Argentina Fil: Maringolo, Carla A.. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires Sur. Estación Experimental Agropecuaria Balcarce; Argentina Fil: Montecchia, Juan Francisco. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Agrobiotecnología y Biología Molecular. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Agrobiotecnología y Biología Molecular; Argentina Fil: Quiroz, Facundo José. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Buenos Aires Sur. Estación Experimental Agropecuaria Balcarce; Argentina Fil: García García, Francisco. Centro de Investigaciones Príncipe Felipe; España Fil: Dopazo Blázquez, Joaquín. Hospital Virgen del Rocio; España Fil: Hopp, Horacio Esteban. Universidad de Buenos Aires; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Agrobiotecnología y Biología Molecular. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Agrobiotecnología y Biología Molecular; Argentina Fil: Heinz, Ruth Amelia. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Agrobiotecnología y Biología Molecular. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Agrobiotecnología y Biología Molecular; Argentina Fil: Paniego, Norma Beatriz. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Agrobiotecnología y Biología Molecular. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Agrobiotecnología y Biología Molecular; Argentina Fil: Lia, Verónica Viviana. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Agrobiotecnología y Biología Molecular. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Agrobiotecnología y Biología Molecular; Argentina

Published
2020

13. Genetic Diversity, Population Structure and Linkage Disequilibrium Assessment among International Sunflower Breeding Collections

Author

Daniel Alvarez, Julio A. Di Rienzo, Maximo Rivarola, Norma Beatriz Paniego, Bruno Contreras Moreira, Carla Valeria Filippi, Ruth Amelia Heinz, Guy Naamati, Monica Irina Fass, Gabriela Alejandra Merino, Verónica Viviana Lia, Natalia Cristina Aguirre, and Juan Francisco Montecchia

Subjects
0106 biological sciences, 0301 basic medicine, Germplasm, Linkage disequilibrium, POPULATION STRUCTURE, sunflower, lcsh:QH426-470, Biotecnología Agropecuaria, Single-nucleotide polymorphism, SUNFLOWER, Biology, 01 natural sciences, Analysis of molecular variance, Article, Chromosomes, Plant, Linkage Disequilibrium, 03 medical and health sciences, Genetics, Genotyping, Genetics (clinical), Hybrid, BREEDING, Genetic diversity, Polymorphism, Genetic, purl.org/becyt/ford/4.4 [https], population structure, genetic diversity, Sunflower, lcsh:Genetics, Plant Breeding, 030104 developmental biology, Evolutionary biology, CIENCIAS AGRÍCOLAS, Seed Bank, breeding, Biotecnología Agrícola y Biotecnología Alimentaria, GENETIC DIVERSITY, Helianthus, LINKAGE DESEQUILIBRIUM, purl.org/becyt/ford/4 [https], 010606 plant biology & botany
Abstract

Sunflower germplasm collections are valuable resources for broadening the genetic base of commercial hybrids and ameliorate the risk of climate events. Nowadays, the most studied worldwide sunflower pre-breeding collections belong to INTA (Argentina), INRA (France), and USDA-UBC (United States of America&ndash, Canada). In this work, we assess the amount and distribution of genetic diversity (GD) available within and between these collections to estimate the distribution pattern of global diversity. A mixed genotyping strategy was implemented, by combining proprietary genotyping-by-sequencing data with public whole-genome-sequencing data, to generate an integrative 11,834-common single nucleotide polymorphism matrix including the three breeding collections. In general, the GD estimates obtained were moderate. An analysis of molecular variance provided evidence of population structure between breeding collections. However, the optimal number of subpopulations, studied via discriminant analysis of principal components (K = 12), the bayesian STRUCTURE algorithm (K = 6) and distance-based methods (K = 9) remains unclear, since no single unifying characteristic is apparent for any of the inferred groups. Different overall patterns of linkage disequilibrium (LD) were observed across chromosomes, with Chr10, Chr17, Chr5, and Chr2 showing the highest LD. This work represents the largest and most comprehensive inter-breeding collection analysis of genomic diversity for cultivated sunflower conducted to date.

Published
2020

14. Phenotyping Sunflower Genetic Resources for Sclerotinia Head Rot Response: Assessing Variability for Disease Resistance Breeding

Author

Jeremías Enrique Zubrzycki, Norma Beatriz Paniego, Ruth A. Heinz, Verónica Viviana Lia, Carla Maringolo, J. A. Di Rienzo, Alberto Escande, Daniel Alvarez, Facundo José Quiroz, Corina M. Fusari, D Cordes, Carla Valeria Filippi, and Horacio Esteban Hopp

Subjects
Fitomejoramiento, 0106 biological sciences, 0301 basic medicine, Germplasm, Veterinary medicine, Otras Biotecnología Agropecuaria, Resistencia Genética, Biotecnología Agropecuaria, Plant Science, Recursos Genéticos, Genetic Resistance, Plant disease resistance, Biology, 01 natural sciences, Genetic Resources, SCLEROTINIA SCLEROTIORUM, 03 medical and health sciences, Ascomycota, Inbred strain, Helianthus annuus, Humans, Fenotipos, Sclerotinia, Plant Diseases, Disease Resistance, Molecular breeding, RESISTENCIA, Heritability, biology.organism_classification, Sunflower, Phenotypes, Plant Breeding, 030104 developmental biology, Resistencia a la Enfermedad, Agronomy, CIENCIAS AGRÍCOLAS, GIRASOL, MEJORAMIENTO CULTIVOS, Helianthus, Agronomy and Crop Science, 010606 plant biology & botany
Abstract

Sclerotinia head rot (SHR) is one of the most serious constraints to sunflower (Helianthus annuus L. var. macrocarpus) production worldwide. Here, we evaluated the response to SHR in a sunflower inbred panel from a large INTA germplasm collection, consisting of 137 inbred lines (ILs). Field trials were performed over five consecutive seasons using a twice-replicated randomized complete-block design. Disease incidence, disease severity, incubation period and area under disease progress curve for disease incidence and severity were determined after controlled inoculation with the pathogen. Statistical analysis using mixed-effect models detected significant differences among ILs for all variables (P

Published
2017
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15. Exploring gene networks in two sunflower lines with contrasting leaf senescence phenotype using a system biology approach

Author

Sofia Ailin Bengoa Luoni, Salvador Nicosia, Johanna Marino, Saleh Alseekh, Maximo Rivarola, Norma Beatriz Paniego, Nicolas Blanchet, Nicolas B. Langlade, Francisco Horacio Astigueta, Ruth Amelia Heinz, Alisdair R. Fernie, Janet Higgins, Paula Fernández, Sebastián Moschen, Instituto Nacional de Tecnología Agropecuaria (INTA), Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de San Martin (UNSAM), BBSRC Earlham Institute, Partenaires INRAE, Max Planck Institute for Plant Breeding Research (MPIPZ), Laboratoire des interactions plantes micro-organismes (LIPM), Institut National de la Recherche Agronomique (INRA)-Centre National de la Recherche Scientifique (CNRS), INTA PE : 1131022, 1131043, ANPCyT : PICT 2012-0390, PIP CONICET PIP, 11220120100262CO, European Union (EU) : PIRSES-GA-2013-612583, SUNRISE, Heliasen Project : PICT 2014-0175, and European Project: 612583,EC:FP7:PEOPLE,FP7-PEOPLE-2013-IRSES,DEANN(2014)

Subjects
0106 biological sciences, Biotecnología, Leaves, Candidate gene, System biology, Time Factors, SUNFLOWER, Plant Science, 01 natural sciences, CANDIDATE GENES, Transcriptome, Gene Expression Regulation, Plant, lcsh:Botany, Gene Regulatory Networks, 2. Zero hunger, Genetics, 0303 health sciences, Vegetal Biology, Systems Biology, purl.org/becyt/ford/4.4 [https], food and beverages, Functional genomics, Genomics, Phenotype, Sunflower, Leaf senescence, Candidate genes, Helianthus Annuus, SYSTEM BIOLOGY, lcsh:QK1-989, Phenotypes, Avejentamiento, Hojas, Helianthus, Biotechnology, Research Article, Senescence, Systems biology, Biology, 03 medical and health sciences, Species Specificity, Helianthus annuus, [SDV.BV]Life Sciences [q-bio]/Vegetal Biology, FUNCTIONAL GENOMICS, LEAF SENESCENCE, Girasol, Fenotipos, Gene, 030304 developmental biology, Genética, Plant Leaves, Biologie végétale, purl.org/becyt/ford/4 [https], 010606 plant biology & botany
Abstract

Background: Leaf senescence is a complex process, controlled by multiple genetic and environmental variables. In sunflower, leaf senescence is triggered abruptly following anthesis thereby limiting the capacity of plants to keep their green leaf area during grain filling, which subsequently has a strong impact on crop yield. Recently, we performed a selection of contrasting sunflower inbred lines for the progress of leaf senescence through a physiological, cytological and molecular approach. Here we present a large scale transcriptomic analysis using RNA-seq and its integration with metabolic profiles for two contrasting sunflower inbred lines, R453 and B481-6 (early and delayed senescence respectively), with the aim of identifying metabolic pathways associated to leaf senescence. Results: Gene expression profiles revealed a higher number of differentially expressed genes, as well as, higher expression levels in R453, providing evidence for early activation of the senescence program in this line. Metabolic pathways associated with sugars and nutrient recycling were differentially regulated between the lines. Additionally, we identified transcription factors acting as hubs in the co-expression networks; some previously reported as senescence-associated genes in model species but many are novel candidate genes. Conclusions: Understanding the onset and the progress of the senescence process in crops and the identification of these new candidate genes will likely prove highly useful for different management strategies to mitigate the impact of senescence on crop yield. Functional characterization of candidate genes will help to develop molecular tools for biotechnological applications in breeding crop yield. Fil: Moschen, Sebastián Nicolás. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Tucuman-Santiago del Estero. Estación Experimental Agropecuaria Famaillá; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Agrobiotecnología y Biología Molecular. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Agrobiotecnología y Biología Molecular; Argentina Fil: Marino, Johanna Magali. Universidad Nacional de San Martín; Argentina Fil: Nicosia, Salvador. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Agrobiotecnología y Biología Molecular. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Agrobiotecnología y Biología Molecular; Argentina Fil: Higgins, Janet. Earlham Institute; Reino Unido Fil: Alseekh, Saleh. No especifíca; Fil: Astigueta, Francisco Horacio. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Agrobiotecnología y Biología Molecular. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Agrobiotecnología y Biología Molecular; Argentina Fil: Bengoa Luoni, Sofia Ailin. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico Conicet - La Plata. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús). Universidad Nacional de San Martín. Instituto de Investigaciones Biotecnológicas. Instituto de Investigaciones Biotecnológicas "Dr. Raúl Alfonsín" (sede Chascomús); Argentina Fil: Rivarola, Maximo Lisandro. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Agrobiotecnología y Biología Molecular. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Agrobiotecnología y Biología Molecular; Argentina Fil: Fernie, Alisdair R.. No especifíca; Fil: Blanchet, Nicolas. Centre National de la Recherche Scientifique; Francia Fil: Langlade, Nicolas B.. Centre National de la Recherche Scientifique; Francia Fil: Paniego, Norma Beatriz. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Agrobiotecnología y Biología Molecular. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Agrobiotecnología y Biología Molecular; Argentina Fil: Fernández, Paula. No especifíca; Fil: Heinz, Ruth Amelia. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Agrobiotecnología y Biología Molecular. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Agrobiotecnología y Biología Molecular; Argentina

Published
2019
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16. Identification and characterization of contrasting sunflower genotypes to early leaf senescence process combining molecular and physiological studies ( Helianthus annuus L.)

Author

C.S. Villán, M.P. López Fernández, Sebastián Moschen, A.I. López Gialdi, Norma Beatriz Paniego, Ruth A. Heinz, Sara Maldonado, and Paula Fernández

Subjects
0106 biological sciences, 0301 basic medicine, Senescence, Otras Biotecnología Agropecuaria, Genotype, Biotecnología Agropecuaria, Plant Science, Biology, 01 natural sciences, 03 medical and health sciences, Inbred strain, Helianthus annuus, Gene expression, Botany, Genetics, LEAF SENESCENCE, Gel electrophoresis, purl.org/becyt/ford/4.4 [https], General Medicine, HELIANTHUS ANNUUS, Sunflower, Plant Leaves, genomic DNA, 030104 developmental biology, CIENCIAS AGRÍCOLAS, PHYSIOLOGICAL ANALYSYS, FLOW CYTOMETRY, Helianthus, Agronomy and Crop Science, purl.org/becyt/ford/4 [https], 010606 plant biology & botany
Abstract

Leaf senescence is a complex mechanism ruled by multiple genetic and environmental variables that affect crop yields. It is the last stage in leaf development, is characterized by an active decline in photosynthetic rate, nutrients recycling and cell death. The aim of this work was to identify contrasting sunflower inbred lines differing in leaf senescence and to deepen the study of this process in sunflower. Ten sunflower genotypes, previously selected by physiological analysis from 150 inbred genotypes, were evaluated under field conditions through physiological, cytological and molecular analysis. The physiological measurement allowed the identification of two contrasting senescence inbred lines, R453 and B481-6, with an increase in yield in the senescence delayed genotype. These findings were confirmed by cytological and molecular analysis using TUNEL, genomic DNA gel electrophoresis, flow sorting and gene expression analysis by qPCR. These results allowed the selection of the two most promising contrasting genotypes, which enables future studies and the identification of new biomarkers associated to early senescence in sunflower. In addition, they allowed the tuning of cytological techniques for a non-model species and its integration with molecular variables. Fil: López, Agustín Ignacio. Universidad Nacional de San Martín. Escuela de Ciencia y Tecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Moschen, Sebastián Nicolás. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Villan, Claudio Sebastian. Universidad Nacional de Misiones. Facultad de Ciencias Exactas, Químicas y Naturales; Argentina Fil: Lopez Fernandez, Maria Paula. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Maldonado, Sara Beatriz. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Paniego, Norma Beatriz. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Heinz, Ruth Amelia. Universidad de Buenos Aires. Facultad de Ciencias Exactas y Naturales; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Fernández, Paula del Carmen. Universidad Nacional de San Martín. Escuela de Ciencia y Tecnología; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina

Published
2016

17. De novo transcriptome sequencing and SSR markers development for Cedrela balansae C.DC., a native tree species of northwest Argentina

Author

Norma Beatriz Paniego, Noga Zelener, Maria Florencia Pomponio, María Virginia Inza, Maximo Rivarola, Paula Fernández, Sergio González, H. Esteban Hopp, Luis Fornes, Cintia V. Acuña, Susana Torales, and Susana N. Marcucci Poltri

Subjects
0301 basic medicine, Molecular biology, Cedrela species, Microsatellite Loci, Database and Informatics Methods, Árboles Maderables, Sequencing techniques, Computer software, DNA sequencing, Meliaceae, Data Management, Multidisciplinary, microsatellite marker, High-Throughput Nucleotide Sequencing, 454 sequencing, purl.org/becyt/ford/4.4 [https], Phylogenetic Analysis, Genomics, Secuencia Nucleotídica, Phylogenetics, Marcadores Genéticos, Biotecnología Agrícola y Biotecnología Alimentaria, Medicine, Primary Forests, Databases, Nucleic Acid, Sequence Analysis, Transcriptome Analysis, Tree species, Research Article, Next-Generation Sequencing, Genetic Markers, Computer and Information Sciences, Cedrela, Bioinformatics, Science, Biotecnología Agropecuaria, Argentina, Marcadores Moleculares, Región Noroeste, Argentina, Biology, Research and Analysis Methods, 03 medical and health sciences, Sequence Motif Analysis, Gene Types, Bosques Nativos, Botany, Genetics, Computer Simulation, Evolutionary Systematics, Timber Trees, Taxonomy, Evolutionary Biology, Sequence Assembly Tools, Gene Expression Profiling, Bosque Primario, Nucleotide Sequence, Biology and Life Sciences, Computational Biology, Genome Analysis, Genética, Transcriptome Sequencing, Molecular biology techniques, 030104 developmental biology, Genetic Loci, CIENCIAS AGRÍCOLAS, Cedrela balansae, Transcriptome, purl.org/becyt/ford/4 [https]
Abstract

The endangered Cedrela balansae C.DC. (Meliaceae) is a high-value timber species with great potential for forest plantations that inhabits the tropical forests in Northwestern Argentina. Research on this species is scarce because of the limited genetic and genomic information available. Here, we explored the transcriptome of C. balansae using 454 GS FLX Titanium next-generation sequencing (NGS) technology. Following de novo assembling, we identified 27,111 non-redundant unigenes longer than 200 bp, and considered these transcripts for further downstream analysis. The functional annotation was performed searching the 27,111 unigenes against the NR-Protein and the Interproscan databases. This analysis revealed 26,977 genes with homology in at least one of the Database analyzed. Furthermore, 7,774 unigenes in 142 different active biological pathways in C. balansae were identified with the KEGG database. Moreover, after in silico analyses, we detected 2,663 simple sequence repeats (SSRs) markers. A subset of 70 SSRs related to important “stress tolerance” traits based on functional annotation evidence, were selected for wet PCR-validation in C. balansae and other Cedrela species inhabiting in northwest and northeast of Argentina (C. fissilis, C. saltensis and C. angustifolia). Successful transferability was between 77% and 93% and thanks to this study, 32 polymorphic functional SSRs for all analyzed Cedrela species are now available. The gene catalog and molecular markers obtained here represent a starting point for further research, which will assist genetic breeding programs in the Cedrela genus and will contribute to identifying key populations for its preservation. Fil: Torales, Susana. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación de Recursos Naturales. Instituto de Recursos Biológicos; Argentina Fil: Rivarola, Maximo Lisandro. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina Fil: Gonzalez, Sergio. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina Fil: Inza, María Virginia. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación de Recursos Naturales. Instituto de Recursos Biológicos; Argentina Fil: Pomponio, María Florencia. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación de Recursos Naturales. Instituto de Recursos Biológicos; Argentina Fil: Fernández, Paula. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina Fil: Acuña, Cintia Vanesa. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Zelener, Noga. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación de Recursos Naturales. Instituto de Recursos Biológicos; Argentina Fil: Fornes, Luis Fernando. Instituto Nacional de Tecnología Agropecuaria. Centro Regional Tucuman-Santiago del Estero; Argentina Fil: Hopp, Horacio Esteban. Universidad de Belgrano. Facultad de Ciencias Exactas y Naturales; Argentina. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina Fil: Paniego, Norma Beatriz. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina. Consejo Nacional de Investigaciones Científicas y Técnicas; Argentina Fil: Marcucci Poltri, Susana Noemí. Instituto Nacional de Tecnología Agropecuaria. Centro de Investigación en Ciencias Veterinarias y Agronómicas. Instituto de Biotecnología; Argentina

Published
2018
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