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.提升发展中国家主粮作物的适应性对保障粮食安全至关重要。在西非国家尼日尔，主粮作物高粱（Sorghum bicolor）被广泛种植于多样的农业气候区中，但目前尚未阐明其本地适应的遗传基础。本研究的目标为表征尼日尔高粱的基因组多样性，并鉴定赋予其对农业气候区本地适应以及契合农户偏好的基因组区域。我们分析了516份尼日尔高粱种质，这些种质的本地品种名称、植物学类群以及地理起源均已明确。通过测序分型（genotyping-by-sequencing, GBS）技术，我们共鉴定得到144299个单核苷酸多态性（single nucleotide polymorphisms, SNPs）位点。我们开展了主成分判别分析（discriminant analysis of principal components, DAPC），鉴定出6个遗传类群，并对具有高判别载荷的位点进行了全基因组扫描。判别系数最高的区域位于第9号染色体，临近玉米开花时间适应基因Vgt1的推定同源基因。随后，我们表征了本地品种间的分化情况，并通过两两FST值的全基因组扫描，鉴定了与特定本地品种相关的单核苷酸多态性位点。对比以籽粒色泽命名的浅色与深色品种，我们发现单宁1（Tannin1）基因附近存在分化区域，该基因为控制籽粒单宁含量的主效基因。上述研究结果可为尼日尔适配本地环境且契合农户偏好的高粱基因组辅助育种工作提供助力。