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Most sorghum biomass accumulates in stem secondary cell walls (SCW). As sorghum stems are used as raw materials for various purposes such as feed, energy and fiber reinforced polymers, identifying the genes responsible for SCW establishment is highly important. Taking advantage of studies performed in model species, most of the structural genes contributing at the molecular level to the SCW biosynthesis in sorghum have been proposed while their regulatory factors have mostly not been determined. Validation of the role of several MYB and NAC transcription factors in SCW regulation in Arabidopsis and a few other species has been provided. In this study, we contributed to the recent efforts made in grasses to uncover the mechanisms underlying SCW establishment. We reported updated phylogenies of NAC and MYB in 9 different species and exploited findings from other species to highlight candidate regulators of SCW in sorghum. We acquired expression data during sorghum internode development and used co-expression analyses to determine groups of co-expressed genes that are likely to be involved in SCW establishment. We were able to identify two groups of co-expressed genes presenting multiple evidences of involvement in SCW building. Gene enrichment analysis of MYB and NAC genes provided evidence that while NAC SECONDARY WALL THICKENING PROMOTING FACTOR NST genes and SECONDARY WALL-ASSOCIATED NAC DOMAIN PROTEIN gene functions appear to be conserved in sorghum, NAC master regulators of SCW in sorghum may not be as tissue compartmentalized as in Arabidopsis. We showed that for every homolog of the key SCW MYB in Arabidopsis, a similar role is expected for sorghum. In addition, we unveiled sorghum MYB and NAC that have not been identified to date as being involved in cell wall regulation. Although specific validation of the MYB and NAC genes uncovered in this study is needed, we provide a network of sorghum genes involved in SCW both at the structural and regulatory levels.

Most sorghum biomass accumulates in stem secondary cell walls (SCW). As sorghum stems are used as raw materials for various purposes such as feed, energy and fiber reinforced polymers, identifying the genes responsible for SCW establishment is highly important. Taking advantage of studies performed in model species, most of the structural genes contributing at the molecular level to the SCW biosynthesis in sorghum have been proposed while their regulatory factors have mostly not been determined. Validation of the role of several MYB and NAC transcription factors in SCW regulation in Arabidopsis and a few other species has been provided. In this study, we contributed to the recent efforts made in grasses to uncover the mechanisms underlying SCW establishment. We reported updated phylogenies of NAC and MYB in 9 different species and exploited findings from other species to highlight candidate regulators of SCW in sorghum. We acquired expression data during sorghum internode development and used co-expression analyses to determine groups of co-expressed genes that are likely to be involved in SCW establishment. We were able to identify two groups of co-expressed genes presenting multiple evidences of involvement in SCW building. Gene enrichment analysis of MYB and NAC genes provided evidence that while NAC SECONDARY WALL THICKENING PROMOTING FACTOR NST genes and SECONDARY WALL-ASSOCIATED NAC DOMAIN PROTEIN gene functions appear to be conserved in sorghum, NAC master regulators of SCW in sorghum may not be as tissue compartmentalized as in Arabidopsis. We showed that for every homolog of the key SCW MYB in Arabidopsis, a similar role is expected for sorghum. In addition, we unveiled sorghum MYB and NAC that have not been identified to date as being involved in cell wall regulation. Although specific validation of the MYB and NAC genes uncovered in this study is needed, we provide a network of sorghum genes involved in SCW both at the structural and regulatory levels.

The Andropogonae tribe hosts some of the most efficient plant biomass accumulators on earth (sugarcane, switchgrass, miscanthus...). Among these, sorghum is a relevant candidate to support biomass value chain development for energy, biomaterials and innovative biorefinery approaches. Sorghum exhibits a large genetic variability for biomass composition providing the opportunities to support the development of different value chains. However, the access to fine-tuned varieties fitting the expectations of the various end-products is currently hampered by a limited understanding of the genetic architecture of the biomass and cell wall quality related traits. To tackle these limitations, an atlas of genomic regions that control the composition and properties of the vegetative biomass is under development. To fulfil this objective, we are integrating the results from i) GWAS analyses from three complementary broad based panels (i.e. worldwide collection (400 accessions), photoperiod sensitive (220) and photoperiod-insensitive (175) panels), ii) two Backcross Nested Association Mapping population (the first corresponding to 29 donor and 2 recurrent parents for a total of 1300 BC1F4 progenies and the second corresponding to 10 donors and 2 recurrent parents for a total of 2000 BC1F5) and iii) several connected biparental populations. All these populations were characterized either for their whole aboveground biomass composition or specifically for their stem composition using Van Soest methods. In addition, in vitro organic matter digestibility and cell wall digestibility were obtained using the Aufrere methods. Projection of the genomic regions identified on the different populations on the sorghum reference genome allowed to restrict the set of candidate genes. Meanwhile, dynamics of gene expression and biomass components accumulation patterns were analyzed on three contrasting genotypes to refine this list in combination with a comparative genomic approach taking advanta

The Andropogonae tribe hosts some of the most efficient plant biomass accumulators on earth (sugarcane, switchgrass, miscanthus...). Among these, sorghum is a relevant candidate to support biomass value chain development for energy, biomaterials and innovative biorefinery approaches. Sorghum exhibits a large genetic variability for biomass composition providing the opportunities to support the development of different value chains. However, the access to fine-tuned varieties fitting the expectations of the various end-products is currently hampered by a limited understanding of the genetic architecture of the biomass and cell wall quality related traits. To tackle these limitations, an atlas of genomic regions that control the composition and properties of the vegetative biomass is under development. To fulfil this objective, we are integrating the results from i) GWAS analyses from three complementary broad based panels (i.e. worldwide collection (400 accessions), photoperiod sensitive (220) and photoperiod-insensitive (175) panels), ii) two Backcross Nested Association Mapping population (the first corresponding to 29 donor and 2 recurrent parents for a total of 1300 BC1F4 progenies and the second corresponding to 10 donors and 2 recurrent parents for a total of 2000 BC1F5) and iii) several connected biparental populations. All these populations were characterized either for their whole aboveground biomass composition or specifically for their stem composition using Van Soest methods. In addition, in vitro organic matter digestibility and cell wall digestibility were obtained using the Aufrere methods. Projection of the genomic regions identified on the different populations on the sorghum reference genome allowed to restrict the set of candidate genes. Meanwhile, dynamics of gene expression and biomass components accumulation patterns were analyzed on three contrasting genotypes to refine this list in combination with a comparative genomic approach taking advanta

Broadening the genetic base of crops is crucial for developing varieties to respond to global agricultural challenges such as climate change. Here, we analysed a diverse panel of 371 domesticated lines of the model crop barley to explore the genetics of crop adaptation. We first collected exome sequence data and phenotypes of key life history traits from contrasting multi-environment common garden trials. Then we applied refined statistical methods, including some based on exomic haplotype states, for genotype-by-environment (G×E) modelling. Sub-populations defined from exomic profiles were coincident with barley's biology, geography and history, and explained a high proportion of trial phenotypic variance. Clear G×E interactions indicated adaptation profiles that varied for landraces and cultivars. Exploration of circadian clock-related genes, associated with the environmentally adaptive days to heading trait (crucial for the crop's spread from the Fertile Crescent), illustrated complexities in G×E effect directions, and the importance of latitudinally based genic context in the expression of large-effect alleles. Our analysis supports a gene-level scientific understanding of crop adaption and leads to practical opportunities for crop improvement, allowing the prioritisation of genomic regions and particular sets of lines for breeding efforts seeking to cope with climate change and other stresses.

To face global warming and fossil fuel depletion crisis, plant biomass will provide a renewable source of energy, materials and chemicals. Accordingly, agriculture will have to adapt not only to avoid competition between food-feed and non-food non-feed uses but also to ensure the economical and environmental sustainability of these productions. In this context, we are developing an integrative strategy merging genetics, breeding, material sciences, energy production, animal nutrition and socio economic analyses to accelerate the development of multipurpose sorghum value chains for both Mediterranean and tropical semi-arid conditions (West Africa). As a first step, new products (biocomposites) and uses (biomethane production) are being developed. Then the plant traits impacting the production and quality of the different end-products and uses are being identified taking advantage of the genetic diversity of sorghum. As a third step, the set-up of these key traits in the plant is being analyzed in order to describe their patterns of development / accumulation, their susceptibility to environmental constraints and provide some insights regarding their molecular determinism. Taking advantage of these functional information, the genomic regions impacting the key traits are being deciphered and used to develop new breeding tools and breeding strategies. In parallel, to maximize the probability to convert scientific results in local impacts, the different stakeholders of the value chains are being mobilized and territorial analyses aiming to assess the relevance of the different value chains are performed.

To face global warming and fossil fuel depletion crisis, plant biomass will provide a renewable source of energy, materials and chemicals. Accordingly, agriculture will have to adapt not only to avoid competition between food-feed and non-food non-feed uses but also to ensure the economical and environmental sustainability of these productions. In this context, we are developing an integrative strategy merging genetics, breeding, material sciences, energy production, animal nutrition and socio economic analyses to accelerate the development of multipurpose sorghum value chains for both Mediterranean and tropical semi-arid conditions (West Africa). As a first step, new products (biocomposites) and uses (biomethane production) are being developed. Then the plant traits impacting the production and quality of the different end-products and uses are being identified taking advantage of the genetic diversity of sorghum. As a third step, the set-up of these key traits in the plant is being analyzed in order to describe their patterns of development / accumulation, their susceptibility to environmental constraints and provide some insights regarding their molecular determinism. Taking advantage of these functional information, the genomic regions impacting the key traits are being deciphered and used to develop new breeding tools and breeding strategies. In parallel, to maximize the probability to convert scientific results in local impacts, the different stakeholders of the value chains are being mobilized and territorial analyses aiming to assess the relevance of the different value chains are performed.