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.

Population genomics of sorghum (Sorghum bicolor) across diverse agroclimatic zones of Niger.

Improving adaptation of staple crops in developing countries is important to ensure food security. In the West African country of Niger, the staple crop sorghum (Sorghum bicolor) is cultivated across diverse agroclimatic zones, but the genetic basis of local adaptation has not been described. The objectives of this study were to characterize the genomic diversity of sorghum from Niger and to identify genomic regions conferring local adaptation to agroclimatic zones and farmer preferences. We analyzed 516 Nigerien accessions for which local variety name, botanical race, and geographic origin were known. We discovered 144 299 single nucleotide polymorphisms (SNPs) using genotyping-by-sequencing (GBS). We performed discriminant analysis of principal components (DAPC), which identified six genetic groups, and performed a genome scan for loci with high discriminant loadings. The highest discriminant coefficients were on chromosome 9, near the putative ortholog of maize flowering time adaptation gene Vgt1. Next, we characterized differentiation among local varieties and used a genome scan of pairwise FST values to identify SNPs associated with specific local varieties. Comparison of varieties named for light- versus dark-grain identified differentiation near Tannin1, the major gene responsible for grain tannins. These findings could facilitate genomics-assisted breeding of locally adapted and farmer-preferred sorghum varieties for Niger.

Diversity of wild and cultivated pearl millet accessions (Pennisetum glaucum [L.] R. Br.) in Niger assessed by microsatellite markers.

Genetic diversity of crop species in sub-Sahelian Africa is still poorly documented. Among such crops, pearl millet is one of the most important staple species. In Niger, pearl millet covers more than 65% of the total cultivated area. Analyzing pearl millet genetic diversity, its origin and its dynamics is important for in situ and ex situ germplasm conservation and to increase knowledge useful for breeding programs. We developed new genetic markers and a high-throughput technique for the genetic analysis of pearl millet. Using 25 microsatellite markers, we analyzed genetic diversity in 46 wild and 421 cultivated accessions of pearl millet in Niger. We showed a significantly lower number of alleles and lower gene diversity in cultivated pearl millet accessions than in wild accessions. This result contrasts with a previous study using iso-enzyme markers showing similar genetic diversity between cultivated and wild pearl millet populations. We found a strong differentiation between the cultivated and wild groups in Niger. Analyses of introgressions between cultivated and wild accessions showed modest but statistically supported evidence of introgressions. Wild accessions in the central region of Niger showed introgressions of cultivated alleles. Accessions of cultivated pearl millet showed introgressions of wild alleles in the western, central, and eastern parts of Niger.