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 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 (r2 <
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 West
Africa 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.