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Conférence en ligne aux Journées Francophones de Nutrition - JFN du 10 au 12/11/2021.; International audience; In urban and peri-urban areas, where waste management is more than ever a major issue, insect farming may be an ecological way to recycle bio-waste in a circular bioeconomy approach. Indeed, someinsect species such as Hermetia illucens can grow on many types of organic substrates and can convert them into valuable byproducts(1). There may be a wide variety of insect bioconversion products since larvae are a natural source of micronutrients, amino acids and antimicrobial compounds. They are also rich in proteins which can be used for animal feed, in fats used for the production of biodiesel, in chitin used in various industries, and they produce a type of manure called frass that can be used as biofertilizer(2). However, besides its ecological and nutritional benefits, risks of insectbased bioconversion should be identified and monitored. Indeed, some chemical contaminants may be found in insect farming environment, in their feeding substrates or can be produced during processing methods(3). Moreover, microbiological contaminants may be found in the farming insect chain(4). Therefore, it is necessary to assess the impact of these contaminants on insect survival and to determine their fate in the insect. It is also important to assess the environmental, social and economic impact of insect-based bioconversion and to determine the consumer acceptability of these new processes and products

Flowering date is an important trait in Prunus fruit species, especially for their adaptation in a global warming context. Numerous quantitative trait loci (QTLs) have been identified and a major one was previously located on LG4. The objectives of this study were to fine-map this QTL in sweet cherry, to identify robust candidate genes by using the new sweet cherry genome sequence of the cultivar “Regina” and to define markers usable in marker-assisted selection (MAS). We performed QTL analyses on two populations derived from crosses using cultivars “Regina” and “Garnet” as parents. The first one (n = 117) was phenotyped over ten years, while the second one (n = 1386) was evaluated during three years. Kompetitive allele specific PCR (KASP) markers located within the QTL region on LG4 were developed and mapped within this region, consisting in the first fine mapping in sweet cherry. The QTL interval was narrowed from 380 kb to 68 kb and candidate genes were identified by using the genome sequence of “Regina”. Their expression was analyzed from bud dormancy period to flowering in cultivars “Regina” and “Garnet”. Several genes, such as PavBOI-E3, PavSR45a and PavSAUR71, were differentially expressed in these two cultivars and could be then considered as promising candidate genes. Two KASP markers were validated using a population derived from a cross between cultivars “Regina” and “Lapins” and two collections, including landraces and modern cultivars. Thanks to the high synteny within the Prunus genus, these results give new insights into the control of flowering date in Prunus species and pave the way for the development of molecular breeding strategies., This work was supported by the “Région Nouvelle-Aquitaine” in the project “CerGEn” reference 2018-1R20203, numbers 00019006 and 00019007. INRAE BAP division and the “Région Nouvelle-Aquitaine” co-funded the PhD scholarship of C.B and funded the Postdoctoral fellowship of A.D. The “Groupement d’Intérêt Scientifique Fruits”, GIS Fruits (https://www.gis-fruits.org/), funded the Master thesis scholarship of N.H.Z.E.

International audience

International audience; Sweet cherry (Prunus avium L.) is a diploid species with an estimated genome size of 338 MB (Arumuganathan et al. 1991). It is mostly selfincompatible, and therefore has a heterozygous genetic background. We have sequenced the genome of the 'Regina' sweet cherry variety, which is a late blooming cultivar. Here we present whole-chromosomes assembly and phasing using a combination of long read sequencing, proximity ligation (HiC) data and GBS markers.Regina PacBio long reads were de novo assembled using FALCON UNZIP. A first assembly using optical mapping and high density genetic linkage maps with GBS data resulted in a genome of 264,8 Mb (78,4 % of estimated genome size) distributed on 8 linkage groups with a scaffold N50~6Mb (Regina V1). A new assembly (ReginaV2) combining Falcon Unzip assembly of PacBio long reads, proximity ligation (HiC) data and GBS markers has been done with Falcon Phased and the Proximo pipeline of Phase Genomics. It produced complete, fully phased, diploid chromosome scale scaffolds with a genome coverage of~90%, a N50 of~37 Mb and a complete BUSCO score of 95,6%. Structural and functional annotations of Regina V2 are in progress. Obtaining these phased chromosomes will allow very detailed studies of the allelic effects on the traits studied, in particular by making it possible to study the allelic expressions of candidate genes.

The preservation of maximum diversity within the smallest number of accessions is one of the challenges of germplasm management, and the assessment of the population structure, the relationships between the accessions, and the construction of core collections are the key steps. The choice of suitable molecular markers is often the starting point. In this study, we analyzed a part of the INRAE walnut germplasm collection, which is highly diverse and unique in Europe, consisting of 150 accessions from American, European, and Asian continents. Based on genotypic data already available, using 13 SSRs or 364,275 SNPs, we showed that the first level of structure is detected equally. We also highlighted empirically that approximately 100 SNPs are needed to obtain similar clustering to 13 SSRs in Principal Coordinate Analysis (PCoA). We constructed eight core collections following two strategies (percentage of total allelic diversity or number of accessions) and two construction methods based on different algorithms (“maximum length subtree” and “entry-to-nearest-entry” methods). We showed that core collections based on few SSR markers are able to capture at least 99.5% of the SNP allelic diversity, irrespective of the construction method used. Then, core collections based on each marker type are highly similar, using both construction methods. All these steps are crucial to identify the suitable tools and methods to improve plant genetic resources management.

Premise: Few studies have addressed the evolutionary history of tree species from African savannahs. Afzelia contains economically important timber species, including two species widely distributed in African savannahs: A. africana in the Sudanian region and A. quanzensis in the Zambezian region. We aimed to infer whether these species underwent range fragmentation and/or demographic changes, possibly reflecting how savannahs responded to Quaternary climate changes. Methods: We characterized the genetic diversity and structure of these species across their distribution ranges using nuclear microsatellites (SSRs) and genotyping-by-sequencing (GBS) markers. Six SSR loci were genotyped in 241 A. africana and 113 A. quanzensis individuals, while 2800 high-quality single nucleotide polymorphisms (SNPs) were identified in 30 A. africana individuals. Results: Both species appeared to be mainly outcrossing. The kinship between individuals decayed with the logarithm of the distance at similar rates across species and markers, leading to relatively small Sp statistics (0.0056 for SSR and 0.0054 for SNP in A. africana, 0.0075 for SSR in A. quanzensis). The patterns were consistent with isolation by distance expectations in the absence of large-scale geographic gradients. Bayesian clustering of SSR genotypes did not detect genetic clusters within species. In contrast, SNP data resolved intraspecific genetic clusters in A. africana, illustrating the higher resolving power of GBS. However, these clusters revealed low levels of differentiation and no clear geographical entities, so that they were interpreted as resulting from the isolation by distance pattern rather than from past population fragmentation. Conclusions: These results suggest that populations have remained connected throughout the large, continuous savannah landscapes. The absence of clear phylogeographic discontinuities, also found in a few other African savannah trees, indicates that their distribution ranges have not been significantly fragmented during the climatic oscillations of the Pleistocene, in contrast to patterns commonly found in African rainforest trees., SCOPUS: ar.j, info:eu-repo/semantics/published

International audience; In perennial fruit species, phenology and fruit quality traits are highly dependent on environmental conditions. In the context of climate change, a rise of fall and winter temperatures leads to a slowing down of the dormancy release which may result in a dramatic decrease of the production. Also, a rise of spring temperatures induces a significant advance of blooming date, increasing risks of damages by the frost. Moreover, the higher frequency of spring rainy periods has serious consequences for fruit quality, particularly on fruit cracking. The objective of our study is to identify the genetic determinism of the cherry tree response to the climate change. Several F1 sweet cherry progenies and a germplasm collection were evaluated for phenological traits and fruit quality. One of the mapping progenies, Regina × Lapins, was evaluated in five sites in order to study the genotype × environment interactions. The progenies were genotyped with the SNP RosBREED arrays and the collection using a genotyping-by-sequencing (GBS) approach. QTL detection and GWAS were performed allowing the identification of the genomic regions associated with the phenological and the fruit quality traits. The comparison of the genomic regions identified by the two analyses was achieved. For both datasets, we revealed that a genomic region at the end of Chromosome 1 controls both flowering and chilling requirements in sweet cherry, consistent with the observed strong phenotypical correlation between these traits. For the first time, marker-trait associations on several chromosomes were found for traits related to sweet cherry fruit quality.

International audience

Additional file 11: Figure S4. Density plots showing the two-year data related to phenological traits in Julian days for the 78 accessions of the F1 progeny.

Additional file 8: Figure S1. Scatter plots showing the two-year data related to phenological traits in Julian days for the 170 accessions of the GWAS panel.

Premise Few studies have addressed the evolutionary history of tree species from African savannahs. Afzelia contains economically important timber species, including two species widely distributed in African savannahs: A. africana in the Sudanian region and A. quanzensis in the Zambezian region. We aimed to infer whether these species underwent range fragmentation and/or demographic changes, possibly reflecting how savannahs responded to Quaternary climate changes. Methods We characterized the genetic diversity and structure of these species across their distribution ranges using nuclear microsatellites (SSRs) and genotyping-by-sequencing (GBS) markers. Six SSR loci were genotyped in 241 A. africana and 113 A. quanzensis individuals, while 2800 high-quality single nucleotide polymorphisms (SNPs) were identified in 30 A. africana individuals. Results Both species appeared to be mainly outcrossing. The kinship between individuals decayed with the logarithm of the distance at similar rates across species and markers, leading to relatively small Sp statistics (0.0056 for SSR and 0.0054 for SNP in A. africana, 0.0075 for SSR in A. quanzensis). The patterns were consistent with isolation by distance expectations in the absence of large-scale geographic gradients. Bayesian clustering of SSR genotypes did not detect genetic clusters within species. In contrast, SNP data resolved intraspecific genetic clusters in A. africana, illustrating the higher resolving power of GBS. However, these clusters revealed low levels of differentiation and no clear geographical entities, so that they were interpreted as resulting from the isolation by distance pattern rather than from past population fragmentation. Conclusions These results suggest that populations have remained connected throughout the large, continuous savannah landscapes. The absence of clear phylogeographic discontinuities, also found in a few other African savannah trees, indicates that their distribution ranges have not been significantly fragmented during the climatic oscillations of the Pleistocene, in contrast to patterns commonly found in African rainforest trees.

Additional file 9: Figure S2. Density plots showing the two-year data related to phenological traits in Julian days for the 170 accessions of the GWAS panel.

BackgroundUnravelling the genetic architecture of agronomic traits in walnut such as budbreak date and bearing habit, is crucial for climate change adaptation and yield improvement. A Genome-Wide Association Study (GWAS) using multi-locus models was conducted in a panel of 170 walnut accessions genotyped using the Axiom™J. regia700 K SNP array, with phenological data from 2018, 2019 and legacy data. These accessions come from the INRAE walnut germplasm collection which is the result of important prospecting work performed in many countries around the world. In parallel, an F1progeny of 78 individuals segregating for phenology-related traits, was genotyped with the same array and phenotyped for the same traits, to construct linkage maps and perform Quantitative Trait Loci (QTLs) detection.ResultsUsing GWAS, we found strong associations of SNPs located at the beginning of chromosome 1 with both budbreak and female flowering dates. These findings were supported by QTLs detected in the same genomic region. Highly significant associated SNPs were also detected using GWAS for heterodichogamy and lateral bearing habit, both on chromosome 11. We developed a Kompetitive Allele Specific PCR (KASP) marker for budbreak date in walnut, and validated it using plant material from the Walnut Improvement Program of the University of California, Davis, demonstrating its effectiveness for marker-assisted selection in Persian walnut. We found several candidate genes involved in flowering events in walnut, including a gene related to heterodichogamy encoding a sugar catabolism enzyme and a cell division related gene linked to female flowering date.ConclusionsThis study enhances knowledge of the genetic architecture of important agronomic traits related to male and female flowering processes and lateral bearing in walnut. The new marker available for budbreak date, one of the most important traits for good fruiting, will facilitate the selection and development of new walnut cultivars suitable for specific climates.

The dating of diversification events, including transitions between biomes, is key to elucidate the processes that underlie the assembly and evolution of tropical biodiversity. Afzelia is a widespread genus of tropical trees, threatened by exploitation for its valuable timber, that presents an interesting system to investigate diversification events in Africa. Africa hosts diploid Afzelia species in the savannahs north and south of the Guineo-Congolian rainforest and autotetraploid species confined to the rainforest. Species delimitation and phylogenetic relationships among the diploid and tetraploid species remained unresolved in previous studies using small amounts of DNA sequence data. We used genotyping-by-sequencing in the five widespread Afzelia species in Africa, the savannah species A. africana and A. quanzensis and the rainforest species A. bipindensis, A. pachyloba, and A. bella. Maximum likelihood and coalescent approaches resolved all species as monophyletic and placed the savannah and rainforest taxa into two separate clades corresponding to contrasted ploidy levels. Our data are thus compatible with a single biome shift in Afzelia in Africa, although we were unable to conclude on its direction. SNAPP calibrated species trees show that the savannah diploids started to diversify early, at 12 (9.09–14.89) Ma, which contrasts with a recent and rapid diversification of the rainforest tetraploid clade, starting at 4.22 (3.12 – 5.36) Ma. This finding of older diversification in a tropical savannah clade vs. its sister rainforest clade is exceptional; it stands in opposition to the predominant observation of young ages for savannahs lineages in tropical regions during the relatively recent expansion of the savannah biome., SCOPUS: ar.j, info:eu-repo/semantics/published

The preservation of the maximum of diversity within the smallest number of accessions is one of the challenges of germplasm management. To construct core-collections, the assessment of the population structure and the relationships between the accessions represents a key step and the choice of suitable molecular markers is the starting point. Since the expansion of available SNP-based genomics tools, a debate has emerged regarding the usefulness of the widely used microsatellites (SSRs) markers. In this study, we analysed a part of the INRAE walnut germplasm collection of 150 accessions, unique in Europe for walnut biodiversity conservation, by comparing the power of both types of marker. We found that the first level of structure is equally detected using 13 SSRs or the Axiom™ J. regia 700K SNP array, and is in relation with the geographical origin of the accessions. For K=2, there was no exchange of accession between the two groups when both markers were compared. We also highlighted empirically that approximately 100 SNPs are needed to obtain similar clustering to SSRs in Principal Coordinate Analysis (PCoA). The neighbor-joining trees constructed were also consistent between both types of marker. The main differences lied in the upper levels of structure from K=3 to K=6, more powerful using the SNPs, and in the percentage of the explained variation in PCoA for K=2, higher using SSRs. We then constructed core-collections of 50 accessions, a crucial step in genetic resources management to reduce the costs and preserve the allelic diversity. Using two different construction methods, both SSR and SNP markers were suitable and able to keep at least 88.57% of the alleles. 32/50 accessions were in common between the two markers, for both methods. We concluded that the use of either marker is dependent on the researcher’s goal.

The dating of diversification events, including transitions between biomes, is key to elucidate the processes that underlie the assembly and evolution of tropical biodiversity. Afzelia is a widespread genus of tropical trees, threatened by exploitation for its valuable timber, that presents an interesting system to investigate diversification events in Africa. Africa hosts diploid Afzelia species in the savannahs north and south of the Guineo-Congolian rainforest and autotetraploid species confined to the rainforest. Species delimitation and phylogenetic relationships among the diploid and tetraploid species remained unresolved in previous studies using small amounts of DNA sequence data. We used genotyping-by-sequencing in the five widespread Afzelia species in Africa, the savannah species A. africana and A. quanzensis and the rainforest species A. bipindensis, A. pachyloba, and A. bella. Maximum likelihood and coalescent approaches resolved all species as monophyletic and placed the savannah and rainforest taxa into two separate clades corresponding to contrasted ploidy levels. Our data are thus compatible with a single biome shift in Afzelia in Africa, although we were unable to conclude on its direction. SNAPP calibrated species trees show that the savannah diploids started to diversify early, at 12 (9.09–14.89) Ma, which contrasts with a recent and rapid diversification of the rainforest tetraploid clade, starting at 4.22 (3.12 – 5.36) Ma. This finding of older diversification in a tropical savannah clade vs. its sister rainforest clade is exceptional; it stands in opposition to the predominant observation of young ages for savannahs lineages in tropical regions during the relatively recent expansion of the savannah biome.

Background: Unravelling the genetic architecture of agronomic traits in walnut such as budbreak date and bearing habit, is crucial for climate change adaptation and yield improvement. A Genome-Wide Association Study (GWAS) using multi-locus models was conducted in a panel of 170 walnut accessions genotyped using the Axiom™ J. regia 700K SNP array, with phenological data from several years. These accessions come from the INRAE walnut germplasm collection which is the result of important prospecting work performed in many countries around the world. In parallel, an F1 progeny of 78 individuals segregating for phenology-related traits, was genotyped with the same array and phenotyped for the same traits, to construct linkage maps and perform Quantitative Trait Loci (QTLs) detection. Results: Using GWAS, we found strong associations of SNPs located at the beginning of chromosome 1 with both budbreak and female flowering dates. These findings were supported by QTLs detected in the same genomic region. Highly significant associated SNPs were also detected using GWAS for heterodichogamy and lateral bearing habit, both on chromosome 11. We developed a Kompetitive Allele Specific PCR (KASP) marker for budbreak date in walnut, and validated it using plant material from the Walnut Improvement Program of the University of California, Davis, demonstrating its effectiveness for marker-assisted selection in Persian walnut. We found several candidate genes involved in flowering events in walnut, including a gene related to heterodichogamy encoding a sugar catabolism enzyme and a cell division related gene linked to female flowering date. Conclusions: This study enhances knowledge of the genetic architecture of important agronomic traits related to male and female flowering processes and lateral bearing in walnut. The new marker available for budbreak date, the first key trait for good fruiting, will facilitate the selection and development of new walnut cultivars suitable for specific climates.

International audience

Polyploidy has rarely been documented in rain forest trees but it has recently been found in African species of the genus Afzelia (Leguminosae), which is composed of four tetraploid rain forest species and two diploid dry forest species. The genus Afzelia thus provides an opportunity to examine how and when polyploidy and habitat shift occurred in Africa, and whether they are associated. In this study, we combined three plastid markers (psbA, trnL, ndhF), two nuclear markers (ribosomal ITS and the single-copy PEPC E7 gene), plastomes (obtained by High Throughput Sequencing) and morphological traits, with an extensive taxonomic and geographic sampling to explore the evolutionary history of Afzelia. Both nuclear DNA and morphological vegetative characters separated diploid from tetraploid lineages. Although the two African diploid species were well differentiated genetically and morphologically, the relationships among the tetraploid species were not resolved. In contrast to the nuclear markers, plastid markers revealed that one of the diploid species forms a well-supported clade with the tetraploids, suggesting historical hybridisation, possibly in relation with genome duplication (polyploidization) and habitat shift from dry to rain forests. Molecular dating based on fossil-anchored gene phylogenies indicates that extant Afzelia started diverging c. 14.5 or 20 Ma while extant tetraploid species started diverging c. 7.0 or 9.4 Ma according to plastid and nuclear DNA, respectively. Additional studies of tropical polyploid plants are needed to assess whether the ploidy-habitat association observed in African Afzelia would reflect a role of polyploidization in niche divergence in the tropics.

Few studies have addressed the evolutionary history of tree species from African savannahs at large geographic scales, particularly in the southern hemisphere (Zambezian region).Afzelia(Fabaceae: Caesalpinioideae) contains economically important timber species, including two species widely distributed in African savannahs:A. africanain the Sudanian region andA. quanzensisin the Zambezian region. To characterize the population genetic diversity and structure of these two species across their distribution ranges, we used nuclear microsatellites (simple sequence repeats, SSRs) and genotyping-by-sequencing (GBS) markers. Six SSR loci were genotyped in 241A. africanaand 113A. quanzensisindividuals, while 2,800 and 3,841 high-quality single nucleotide polymorphisms (SNPs) were identified in 30A. africanaand 12A. quanzensisindividuals, respectively. Both species appeared to be outcrossing (selfing rate ~ 0%). The spatial genetic structure was consistent with isolation-by-distance expectations based on both SSR and SNP data, suggesting that gene dispersal is spatially restricted in both species (bLd (SSR)= −0.005and −0.007andbLd (SNP)= −0.008and −0.006 forA. africanaandA. quanzensis, respectively). Bayesian clustering of SSR genotypes failed to identify genetic structure within species. In contrast, SNP data resolved intraspecific genetic clusters in both species, illustrating the higher resolving power of GBS at shallow levels of divergence. However, the clusters identified by SNPs revealed low levels of differentiation and no clear geographical entities. These results suggest that, although gene flow has been restricted over short distances in both species, populations have remained connected throughout the large, continuous Savannah landscapes. The absence of clear phylogeographic discontinuities, also found in a few other African savannah trees, indicates that their distribution ranges have not been significantly fragmented during past climate changes, in contrast to patterns commonly found in African rainforest trees.

Few studies have addressed the evolutionary history of tree species from African savannahs at large geographic scales, particularly in the southern hemisphere (Zambezian region). Afzelia (Fabaceae: Caesalpinioideae) contains economically important timber species, including two species widely distributed in African savannahs: A. africana in the Sudanian region and A. quanzensis in the Zambezian region. To characterize the population genetic diversity and structure of these two species across their distribution ranges, we used nuclear microsatellites (simple sequence repeats, SSRs) and genotyping-by-sequencing (GBS) markers. Six SSR loci were genotyped in 241 A. africana and 113 A. quanzensis individuals, while 2,800 and 3,841 high-quality single nucleotide polymorphisms (SNPs) were identified in 30 A. africana and 12 A. quanzensis individuals, respectively. Both species appeared to be outcrossing (selfing rate ~ 0%). The spatial genetic structure was consistent with isolation-by-distance expectations based on both SSR and SNP data, suggesting that gene dispersal is spatially restricted in both species (bLd (SSR)= −0.005 and −0.007 and bLd (SNP)= −0.008 and −0.006 for A. africana and A. quanzensis, respectively). Bayesian clustering of SSR genotypes failed to identify genetic structure within species. In contrast, SNP data resolved intraspecific genetic clusters in both species, illustrating the higher resolving power of GBS at shallow levels of divergence. However, the clusters identified by SNPs revealed low levels of differentiation and no clear geographical entities. These results suggest that, although gene flow has been restricted over short distances in both species, populations have remained connected throughout the large, continuous Savannah landscapes. The absence of clear phylogeographic discontinuities, also found in a few other African savannah trees, indicates that their distribution ranges have not been significantly fragmented during past climate changes, in contrast to patterns commonly found in African rainforest trees.

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 agronomical importance, the genetic bases of their adaptations to natural and anthropogenic selective pressures 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. The release of the genome sequence, its phylogenetic proximity with other important C4 species (maize, switchgrass, sugarcane) and its low genome complexity contribute to the interest on S. bicolor on a more fundamental level. We leverage transcriptomic and genomic resources to address the adaptive consequences of the domestication process. Despite gene flow with the wild pool, a clear domestication syndrome is visible in cultivated sorghum (plant architecture, shattering, dormancy and seed weight). Gene expression and nucleotide variability were analyzed in 11 cultivated and 9 wild accessions. The cultivated compartment harbors 30% lower genetic diversity than the wild pool, which supports the occurrence of a genetic bottleneck in the domestication history of sorghum. Furthermore, the crop gene pool showed polymorphism patterns in coding regions indicative of lower efficacy of purifying selection, suggesting that sorghum suffers from the cost of domestication. 949 genes are significantly differentially expressed between the two compartments. Among them, genes involved in internode elongation and cytoskeleton organization are over-expressed, while genes linked to photosynthesis and reduction-oxidation processing of seed storage proteins are under-expressed in the cultivated accessions. Further analyses revealed that domestication reduced significantly the variability of the isoform expression balance (expression ratio of the alternative proteins coded by a single gene) in cultivated sorghum. Overall, these analyses pave the way towards the identification of key domestication genes valuable for genetic resources characterization and breeding purposes.

In temperate trees, optimal timing and quality of flowering directly depend on adequate winter dormancy progression, regulated by a combination of chilling and warm temperatures. Physiological, genetic and functional genomic studies have shown that hormones play a key role in bud dormancy establishment, maintenance and release. We combined physiological, transcriptional analyses, quantification of abscisic acid (ABA) and gibberellins (GAs), and modelling to further investigate how these signaling pathways are associated with dormancy progression in the flower buds of two sweet cherry cultivars.Our results demonstrated that GA-associated pathways have distinct functions and may be differentially related with dormancy. In addition, ABA levels rise at the onset of dormancy, associated with enhanced expression of ABA biosynthesisPavNCEDgenes, and decreased prior to dormancy release. Following the observations that ABA levels are correlated with dormancy depth, we identifiedPavUG71B6, a sweet cherryUDP-GLYCOSYLTRANSFERASEgene that up-regulates active catabolism of ABA to ABA-GE and may be associated with low ABA content in the early cultivar. Subsequently, we modelled ABA content and dormancy behavior in three cultivars based on the expression of a small set of genes regulating ABA levels. These results strongly suggest the central role of ABA pathway in the control of dormancy progression and open up new perspectives for the development of molecular-based phenological modelling.

Sorghum bicolor is the fifth cereal worldwide for grain production, constituting the staple food for a round 500 million people. The release of its genome sequence, its phylogenetic proximity with other important C4 species (maize, switchgrass, sugarcane) and its low genome complexity contribute to its interest on a more fundamental level. Sorghum bicolor wild relatives (ssp. verticilliflorum) and domesticated (ssp. bicolor) pools are inter-fertile and intense gene flow occurs. However, a clear domestication syndrome is visible (plant architecture, shattering, dormancy and seed weight). ln spite of its agronomical Importance, the evolutionary dynamics of sorghum domestication and the genetic bases of adaptations to natural and anthropogenic pressures are not well understood. Here we leverage transcriptomic and genomic resources to improve our knowledge on the evolutionary history of S. bicolor, with a particular focus on the consequences of the domestication process. As a first step, gene expression and nucleotide variability of the expressed genes were analyzed in 11 cultivated and 9 wild accessions selected to maximize the genetic coverage of these two pools. The cultivated compartment harbors 30% lower genetic diversity than the wild pool, which supports the occurrence of a genetic bottleneck in the domestication history of sorghum. More than 900 genes are significantly differentially expressed between the two compartments. Among them, genes involved in photosynthesis and in reduction-oxidation processing of seed storage proteins are over-represented. Further analyses revealed that domestication reduced significantly the variability of the isoform expression balance (expression ratio of the alternative proteins coded by a single gene) in cultivated sorghum. Scans for local adaptation and positive selection on large cultivated and wild panels genotyped with genotyping by sequencing approaches are ongoing. Overall, these analyses pave the way towards the identification of key domestication genes that cou Id be useful for conservation strategies but also for breeding purposes.

Polyploidy has rarely been documented in rain forest trees but it has recently been found in African species of the genus Afzelia (Leguminosae), which is composed of four tetraploid rain forest species and two diploid dry forest species. The genus Afzelia thus provides an opportunity to examine how and when polyploidy and habitat shift occurred in Africa, and whether they are associated. In this study, we combined three plastid markers (psbA, trnL, ndhF), two nuclear markers (ribosomal ITS and the single-copy PEPC E7 gene), plastomes (obtained by High Throughput Sequencing) and morphological traits, with an extensive taxonomic and geographic sampling to explore the evolutionary history of Afzelia. Both nuclear DNA and morphological vegetative characters separated diploid from tetraploid lineages. Although the two African diploid species were well differentiated genetically and morphologically, the relationships among the tetraploid species were not resolved. In contrast to the nuclear markers, plastid markers revealed that one of the diploid species forms a well-supported Glade with the tetraploids, suggesting historical hybridisation, possibly in relation with genome duplication (polyploidization) and habitat shift from dry to rain forests. Molecular dating based on fossil-anchored gene phylogenies indicates that extant Afzelia started diverging c. 14.5 or 20 Ma while extant tetraploid species started diverging c. 7.0 or 9.4 Ma according to plastid and nuclear DNA, respectively. Additional studies of tropical polyploid plants are needed to assess whether the ploidy-habitat association observed in African Afzelia would reflect a role of polyploidization in niche divergence in the tropics.

The long generation time and large effective size of widespread forest tree species can result in slow evolutionary rate and incomplete lineage sorting, complicating species delimitation. We addressed this issue with the African timber tree genus Milicia that comprises two morphologically similar and often confounded species: M. excelsa, widespread from West to East Africa, and M. regia, endemic to West Africa. We combined information from nuclear microsatellites (nSSRs), nuclear and plastid DNA sequences, and morphological systematics to identify significant evolutionary units and infer their evolutionary and biogeographical history. We detected five geographically coherent genetic clusters using nSSRs and three levels of genetic differentiation. First, one West African cluster matched perfectly with the morphospecies M. regia that formed a monophyletic clade at both DNA sequences. Second, a West African M. excelsa cluster formed a monophyletic group at plastid DNA and was more related to M. regia than to Central African M. excelsa, but shared many haplotypes with the latter at nuclear DNA. Third, three Central African clusters appeared little differentiated and shared most of their haplotypes. Although gene tree paraphyly could suggest a single species in Milicia following the phylogenetic species concept, the existence of mutual haplotypic exclusivity and nonadmixed genetic clusters in the contact area of the two taxa indicate strong reproductive isolation and, thus, two species following the biological species concept. Molecular dating of the first divergence events showed that speciation in Milicia is ancient (Tertiary), indicating that long-living tree taxa exhibiting genetic speciation may remain similar morphologically.