Pearl millet genomic diversity

Genetic Diversity, Population Structure, and Linkage Disequilibrium of Pearl Millet Inbred Lines and Germplasm AccessionsPearl millet (Pennisetum glaucum (L.) R. Br.) is one of the most extensively cultivated cereals in the world, after rice, wheat, maize, barley and sorghum. It is the main component of traditional farming systems and a staple food in the arid and semi-arid regions of Africa and South Asia. However, its genetic improvement is lagging behind other major cereals and the yield is still low. Genotyping-by-sequencing (GBS) single nucleotide polymorphism (SNP) markers were screened on a total of 400 inbred pearl millet lines and germplasm accessions from different geographic regions to assess genetic diversity, population structure and linkage disequilibrium (LD). By mapping the GBS reads with SNPs to the reference genome sequence, we discovered 82,112 genome-wide SNPs. The SNP density was higher in the telomeric regions of all seven chromosomes than in peri-centromeric regions. Model-based clustering analysis of the population revealed a hierarchical genetic structure of six subgroups that mostly overlap with the geographic origins or sources of the genotypes but with differing levels of admixtures. A neighbor-joining phylogeny analysis of the population revealed that germplasm from West Africa rooted the dendrogram with much diversity within each subgroup. Greater LD decay was observed in the West African sub-population than in the other sub-populations, indicating a long history of recombination among landraces from West Africa. Also, selection signature analysis detected significantly different selection histories among subpopulations.Key words: pearl millet, genetic diversity, genotyping-by-sequencing, high throughput markers《珍珠粟自交系与种质资源的遗传多样性、群体结构及连锁不平衡》 珍珠粟（*Pennisetum glaucum* (L.) R. Br.）是全球种植规模最为广泛的谷类作物之一，仅次于水稻、小麦、玉米、大麦与高粱。它既是传统耕作体系的核心组成部分，也是非洲与南亚干旱半干旱地区的主粮作物。然而，其遗传改良进度显著落后于其他主要谷类作物，单产仍处于较低水平。 本研究针对来自不同地理区域的共计400份珍珠粟自交系与种质资源，采用测序分型（Genotyping-by-sequencing, GBS）单核苷酸多态性（Single Nucleotide Polymorphism, SNP）标记开展筛选，以解析其遗传多样性、群体结构与连锁不平衡（Linkage Disequilibrium, LD）。通过将携带SNP标记的GBS测序reads比对至参考基因组序列，本研究共发掘出82112个全基因组范围的SNP位点。所有7条染色体的端粒区域SNP密度均高于着丝粒周边区域。 基于模型的群体聚类分析显示，该群体存在6个亚群的层级遗传结构，各亚群大体与基因型的地理起源或种质来源相契合，但存在不同程度的遗传混合。邻接树系统发育分析表明，西非来源的种质构成了系统发育树的基部类群，且各亚群内部均蕴藏丰富的遗传多样性。西非亚群的连锁不平衡衰减速率快于其他亚群，这反映出西非地方品种间存在长期的重组演化历史。此外，选择信号分析检测到不同亚群间存在显著差异的选择历史。 关键词：珍珠粟；遗传多样性；测序分型；高通量分子标记