Rice production faces the challenge to be enhanced by 50% by year 2030 to meet the growth of the population in rice-eating countries. Whereas yield of cereal crops tend to reach plateaus and a yield is likely to be deeply affected by climate instability and resource scarcity in the coming decades, building rice cultivars harboring root systems that can maintain performance by capturing water and nutrient resources unevenly distributed is a major breeding target. Taking advantage of gathering a community of rice root biologists in a Global Rice Science Partnership workshop held in Montpellier, France, we present here the recent progresses accomplished in this area and focal points where an international network of laboratories should direct their efforts.

Pearl millet plays a major role in food security in arid and semi-arid areas of Africa and India. However, it lags behind the other cereal crops in terms of genetic improvement. The recent sequencing of its genome opens the way to the use of modern genomic tools for breeding. Our study aimed at identifying genetic components involved in early drought stress tolerance as a first step toward the development of improved pearl millet varieties or hybrids. A panel of 188 inbred lines from West Africa was phenotyped under early drought stress and well-irrigated conditions. We found a strong impact of drought stress on yield components. This impact was variable between inbred lines. We then performed an association analysis with a total of 392,493 SNPs identified using Genotyping-by-Sequencing (GBS). Correcting for genetic relatedness, genome wide association study identified QTLs for biomass production in early drought stress conditions and for stay-green trait. In particular, genes involved in the sirohaem and wax biosynthesis pathways were found to co-locate with two of these QTLs. Our results might contribute to breed pearl millet lines with improved yield under drought stress.

Sorghum is the fifth most important cereal crop world-wide and feeds millions of people in the Sahel. However, it often faces early-stage water deficit due to false onsets of rainy seasons resulting in production decrease. Therefore, developing early drought tolerant material becomes a necessity but requires a good knowledge of adaptation mechanisms, which remains to be elucidated. The present study aimed at assessing the effects of early drought stress on ten elite sorghum varieties tested over two years (2018–2019) at the National Agronomic Research Centre (CNRA) of Bambey (Senegal, West Africa). Two different water regimes (well-watered and drought stress) were applied during the dry season. Water stress was applied by withholding irrigation 25 days after sowing for one month, followed by optimal irrigation until maturity. Soil moisture measurements were performed and allowed to follow the level of stress (down to a fraction of transpirable soil water (FTSW) of 0.30 at the end of stress). An agro-physio-morphological monitoring was carried out during the experiment. Results showed highly significant effects of early drought stress in sorghum plants growth by decreasing leaf appearance, biomass, height but also yield set up. The combined analysis of variance revealed highly significant differences (p ≤ 0.01) between varieties in the different environments for most characters. Under water deficit, the variability was less strong on leaf appearance and plant height at the end of stress. The adaptation responses were related to the capacity of varieties to grow up fast and complete their cycle rather, increase the dead leaves weight, reduce photosynthesis rate, stomatal conductance, leaf transpiration and increase the roots length density. However, varieties V1, V2, V8 and V9 showed promising behavior under stress and could be suitable for further application in West Africa for sorghum breeding and farming.

To ensure food security in Africa and Asia, developing sorghum varieties with grain quality that matches consumer demand is a major breeding objective that requires a better understanding of the genetic control of grain quality traits. The objective of this targeted association study was to assess whether the polymorphism detected in six genes involved in synthesis pathways of starch (Sh2, Bt2, SssI, Ae1, and Wx) or grain storage proteins (O2) could explain the phenotypic variability of six grain quality traits [amylose content (AM), protein content (PR), lipid content (LI), hardness (HD), endosperm texture (ET), peak gelatinization temperature (PGT)], two yield component traits [thousand grain weight (TGW) and number of grains per panicle (NBG)], and yield itself (YLD). We used a core collection of 195 accessions which had been previously phenotyped and for which polymorphic sites had been identified in sequenced segments of the six genes. The associations between gene polymorphism and phenotypic traits were analyzed with Tassel. The percentages of admixture of each accession, estimated using 60 RFLP probes, were used as cofactors in the analyses, decreasing the proportion of false-positive tests (70%) due to population structure. The significant associations observed matched generally well the role of the enzymes encoded by the genes known to determine starch amount or type. Sh2, Bt2, Ae1, and Wx were associated with TGW. SssI and Ae1 were associated with PGT, a trait influenced by amylopectin amount. Sh2 was associated with AM while Wx was not, possibly because of the absence of waxy accessions in our collection. O2 and Wx were associated with HD and ET. No association was found between O2 and PR. These results were consistent with QTL or association data in sorghum and in orthologous zones of maize. This study represents the first targeted association mapping study for grain quality in sorghum and paves the way for marker-aided selection.

____________________________________________________________________________________________________________________________________________________________________________Abstract: The root length density (RLD) distribution in the soil is a key factor for water and nutrient uptake but its direct assessment is not easy. A field method is presented here to assess RLD of sorghum (Sorghum bicolor L. Moench) from the root intersection density (RID) and taking root orientations into account. The method was developed with four varieties cropped in 2006 in Bambey (Senegal) on a sandy soil, and validated on the basis of independent data obtained on two other varieties cropped in 2008 in Thiès in Senegal on a sandy loam soil. Sets of 1 × 10 -3 m 3 cubic undisturbed soil samples were collected at different positions and at three different dates for the four varieties during the first experiment. RIDs of thick and fine roots were assessed on the sides of the soil cubes and RLDs were measured in the volumes. Fine roots appeared to be isotropic when thick roots were horizontal near the surface and gradually became vertical in deeper horizons. RLD was tenfold lower for thick roots than for fine ones. This led to the development of a model to determine RLD from RID. The relationship for all roots was modeled as RLD = RID × CO, where the root orientation coefficient (CO) is equal to 1.97, indicating that the global root distribution is almost isotropic (CO = 2 for isotropic conditions). The model was validated on the basis of independent data from the second experiment. This model enables RLD mapping and description of RLD variability on sorghum from RID observations on trench profiles (with 10 × 10 cm or 5 × 5 cm surface area used for RID measurement).

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Local landrace and breeding germplasm is a useful source of genetic diversity for regional and global crop improvement initiatives. Sorghum (Sorghum bicolor L.Moench) in western Africa (WA) has diversified across a mosaic of cultures and end uses and along steep precipitation and photoperiod gradients. To facilitate germplasm utilization, a West African sorghum association panel (WASAP) of 756 accessions from national breeding programs of Niger, Mali, Senegal, and Togo was assembled and characterized. Genotyping-by-sequencing (GBS) was used to generate 159,101 high-quality biallelic single nucleotide polymorphisms (SNPs), with 43% in intergenic regions and 13% in genic regions. High genetic diversity was observed within the WASAP (π = .00045), only slightly less than in a global diversity panel (GDP) (π = .00055). Linkage disequilibrium (LD) decayed to background level (r 2 < .1) by ∼50 kb in the WASAP. Genome-wide diversity was structured both by botanical type and by populations within botanical type with eight ancestral populations identified. Most populations were distributed across multiple countries, suggesting several potential common gene pools across the national programs. Genome-wide association studies (GWAS) of days to flowering (DFLo) and plant height (PH) revealed eight and three significant quantitative trait loci (QTL), respectively, with major height QTL at canonical height loci Dw3 and SbHT7.1. Colocalization of two of eight major flowering time QTL with flowering genes previously described in U.S. germplasm (Ma6 and SbCN8) suggests that photoperiodic flowering in West African sorghum is conditioned by both known and novel genes. This genomic resource provides a foundation for genomics-enabled breeding of climate-resilient varieties in WA.

Running head: West African sorghum genomics resource Core ideas: 1. A West African sorghum panel (n = 756) was assembled from four national programs.2. Over 150,000 genome-wide nucleotide polymorphisms were genotyped by sequencing.3. Diversity was structured by subpopulation within botanical type and across countries. 4. Known genes and novel loci for flowering time and plant height were identified. AbstractLocal landrace and breeding germplasm is a useful source of genetic diversity for regional and global crop improvement initiatives. Sorghum ( Sorghum bicolor L. Moench) in West Africa has diversified across a mosaic of cultures and end-uses, and along steep precipitation and photoperiod gradients. To facilitate germplasm utilization, a West African sorghum association panel (WASAP) of 756 accessions from national breeding programs of Niger, Mali, Senegal, and Togo was assembled and characterized. Genotyping-by-sequencing was used to generate 159,101 high-quality biallelic SNPs, with 43% in intergenic regions and 13% in genic regions. High genetic diversity was observed within the WASAP (π = 0.00045), only slightly less than in a global diversity panel (π = 0.00055). Linkage disequilibrium decayed to background level ( r 2 < 0.1) by ~50 kb in the WASAP. Genome-wide diversity was structured both by botanical type, and by populations within botanical type, with eight ancestral populations identified. Most populations were distributed across multiple countries, suggesting several potential common gene pools across the national programs. Genome-wide association studies of days to flowering and plant height revealed eight and three significant quantitative trait loci (QTL), respectively, with major height QTL at canonical height loci Dw3 and SbHT7.1 . Colocalization of two of eight major flowering time QTL with flowering genes previously described in US germplasm ( Ma6 and SbCN8 ) suggests that photoperiodic flowering in WA sorghum is conditioned by both known and novel genes. This genomic resource provides a foundation for genomics-enabled breeding of climate-resilient varieties in West Africa. AbbreviationsBLUP, best linear unbiased prediction; CVE, cross-validation error; DFLo, days to flowering;