Data from: 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.