Uncovering the genomic basis of climate adaptation in traditional crop varieties can provide insight into plant evolution and facilitate breeding for climate resilience. In the African cereal sorghum (Sorghum bicolor L. [Moench]), the genomic basis of adaptation to the semiarid Sahelian zone versus the subhumid Soudanian zone is largely unknown. To address this issue, we characterized a large panel of 421 georeferenced sorghum landrace accessions from Senegal and adjacent locations at 213,916 single‐nucleotide polymorphisms (SNPs) using genotyping‐by‐sequencing. Seven subpopulations distributed along the north‐south precipitation gradient were identified. Redundancy analysis found that climate variables explained up to 8% of SNP variation, with climate collinear with space explaining most of this variation (6%). Genome scans of nucleotide diversity suggest positive selection on chromosome 2, 4, 5, 7, and 10 in durra sorghums, with successive adaptation during diffusion along the Sahel. Putative selective sweeps were identified, several of which colocalize with stay‐green drought tolerance (Stg) loci, and a priori candidate genes for photoperiodic flowering and inflorescence morphology. Genome‐wide association studies of photoperiod sensitivity and panicle compactness identified 35 and 13 associations that colocalize with a priori candidate genes, respectively. Climate‐associated SNPs colocalize with Stg3a, Stg1, Stg2, and Ma6 and have allelic distribution consistent with adaptation across Sahelian and Soudanian zones. Taken together, the findings suggest an oligogenic basis of adaptation to Sahelian versus Soudanian climates, underpinned by variation in conserved floral regulatory pathways and other systems that are less understood in cereals.

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;

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Drought is a major constraint on plant productivity globally. Sorghum [Sorghum bicolor (L.) Moench] landraces have evolved in drought‐prone regions, but the genetics of their adaptation is poorly understood. Here we sought to identify novel drought‐tolerance loci and test hypotheses on the role of known loci including those underlying stay‐green (Stg) postflowering drought tolerance. We phenotyped 590 diverse sorghum accessions from West Africa in 10 environments, under field‐based managed drought stress [preflowering water stress (WS1), postflowering water stress (WS2), and well‐watered (WW)] and rainfed (RF) conditions over 4 yr. Days to 50% flowering (DFLo), aboveground dry biomass (DBM), plant height (PH), and plant grain yield components (including grain weight [GrW], panicle weight [PW] and grain number [GrN] per plant, and 1000‐grain weight [TGrW]) were measured, and genome‐wide association studies (GWAS) was conducted. Broad‐sense heritability for biomass and plant grain yield was high (33–92%) across environments. There was a significant correlation between stress tolerance index (STI) for GrW per plant across WS1 and WS2. Genome‐wide association studies revealed that SbZfl1 and SbCN12, orthologs of maize (Zea mays L.) flowering genes, likely underlie flowering time variation under these conditions. Genome‐wide association studies further identified associations (n = 134; common between two GWAS models) for STI and drought effects on plant yield components including 16 putative pleiotropic associations. Thirty of the associations colocalized with Stg1, Stg2, Stg3, and Stg4 loci and had large effects. Seven lead associations, including some within Stg1, overlapped with positive selection outliers. Our findings reveal previously undescribed natural genetic variation for drought‐tolerance‐related traits and suggest a broad role of Stg loci in drought adaptation of sorghum.

Drought is a major constraint on plant productivity globally. Sorghum (Sorghum bicolor) landraces have evolved in drought-prone regions, but the genetics of their adaptation is not yet understood. Loci underlying stay-green post-flowering drought tolerance (Stg), have been identified in a temperate breeding line, but their role in drought adaptation of tropical sorghum is to be elucidated. We phenotyped 590 diverse sorghum accessions from West Africa under field-based managed drought stress, pre-flowering (WS1) and post-flowering (WS2) over several years and conducted genome-wide association studies (GWAS). Broad-sense heritability for grain and biomass yield components was high (33-92%) across environments. There was a significant correlation between stress tolerance index (STI) for grain weight across WS1 and WS2. GWAS revealed that SbZfl1 and SbCN12, orthologs of maize flowering genes, likely underlie flowering time variation under these conditions. GWAS further identified associations (n = 134) for STI and drought effects on yield components, including 16 putative pleiotropic associations. Thirty of the associations colocalized with Stg1-4 loci and had large effects. Seven lead associations, including some within Stg1, overlapped with positive selection outliers. Our findings reveal natural genetic variation for drought tolerance-related traits, and suggest a broad role of Stg loci in drought adaptation of sorghum.

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Combining resistance to grain mold with high grain yield in tannin-free white-grained photoperiod-insensitive sorghum is of major interest for farmers in Senegal. In this study, GGE biplot analysis was used to assess the performance, adaptability, and stability of eleven sorghum parental lines and their hybrid combinations for yield and grain mold resistance under Senegalese environments. Eleven inbred lines along with their 22 hybrid combinations and one check were evaluated across three sites during the 2015 and 2016 rainy seasons under natural grain mold infestation. The results of this study showed strong genetic variability among studied genotypes for all measured traits. The highly significant G × E interaction effects for grain yield and panicle grain mold rating score (PGMR) indicated that both traits are influenced by genetics and to some extent by environment. Broad-sense heritability computed was high for all these traits except PGMR, showing a high environmental pressure on this later. The study showed that grain mold pressure in the studied sites decreased following a South-North gradient similar to the rainfall pattern, with the south region wetter, explaining the high disease pressure in Darou and Sinthiou Maleme contrary to Bambey. The GGE biplot analysis performed showed that the first two principal components explained 85.84% of the total variation of GGE sum of squares for grain yield. The which-won-where view of the GGE biplot for grain yield showed that the hybrid HB16 was the most adapted for Bambey area. The ranking of genotypes based on both yield performance and stability showed that HB16, HB5, HB21, HB18, and HB7 were the best hybrids combining high grain yield, high stability performance, and tolerance to grain mold disease across the test environments. These hybrids outperformed the best yielding inbred line P29 (2196.7 kg ha−1) with grain yield advantages ranging 17–60%. Therefore, these hybrids could be recommended to farmers in order to improve sorghum yield in Senegal.