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本地适应能力，是保障粮食安全的关键举措。西非国家尼日尔的主粮作物高粱（Sorghum bicolor）已在多样的农业气候区广泛种植，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，并鉴定出可适配不同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，这些资源均附带已知的本地品种名称、植物学类群及地理起源信息。通过测序分型（genotyping-by-sequencing, GBS）技术，本研究共鉴定出144299个单核苷酸多态性（single nucleotide polymorphisms, SNPs）。本研究开展了主成分判别分析（discriminant analysis of principal components, DAPC），成功鉴定出6个遗传类群；同时针对判别载荷较高的位点进行了全基因组扫描。判别系数最高的位点位于9号染色体，紧邻玉米开花时间适应基因Vgt1的推定同源基因。随后，本研究解析了不同本地品种间的遗传分化，并通过基于成对FST值的全基因组扫描，鉴定出与特定本地品种相关联的单核苷酸多态性位点。针对以籽粒颜色命名的浅色与深色品种的对比分析，发现Tannin1基因（控制籽粒单宁含量的主效基因）附近存在显著遗传分化。本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品种基因组辅助育种提供助力。