Quantitative and population genomics suggest a broad role of stay-green loci in the drought adaptation of sorghum.

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.

A genomics resource for genetics, physiology, and breeding of West African sorghum.

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 (r2 < .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.

Genomic signatures of adaptation to Sahelian and Soudanian climates in sorghum landraces of Senegal.

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.