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环境适应能力，对保障粮食安全至关重要。西非国家尼日尔的主粮作物高粱（Sorghum bicolor）广泛种植于多样的农业气候区，但目前尚未阐明其本地适应的遗传基础。本研究旨在解析尼日尔高粱的基因组多样性，并筛选出赋予其适应特定农业气候区以及契合农户种植偏好的基因组区域。本研究分析了516份尼日尔高粱种质资源，所有供试种质均已知其地方品种名称、植物学类群及地理起源。通过测序分型（genotyping-by-sequencing, GBS）技术，本研究共鉴定得到144299个单核苷酸多态性（single nucleotide polymorphisms, SNPs）位点。本研究开展了主成分判别分析（discriminant analysis of principal components, DAPC），将供试种质划分为6个遗传类群，并针对判别载荷较高的位点开展全基因组扫描。判别系数最高的位点位于9号染色体，靠近玉米开花时间适应基因Vgt1的推定同源基因。随后，本研究解析了不同地方品种间的遗传分化，并通过基于成对FST值的全基因组扫描，筛选出与特定地方品种相关联的SNPs位点。对以籽粒颜色命名的浅色与深色籽粒品种进行比较分析后发现，Tannin1基因附近存在显著遗传分化，该基因是调控籽粒单宁合成的主效基因。本研究结果可为尼日尔适配本地环境且契合农户种植偏好的高粱品种基因组辅助育种提供重要支撑。