Kansas State Univ., Agricultural Research Center-Hays, Hays, 1232 240th Avenue, Hays, KS, 67601, USA.
Hard Winter Wheat Genetics Research Unit, USDA-ARS, Manhattan, KS.
Plant Genome. 2019 Nov;12(3):1-12. doi: 10.3835/plantgenome2018.11.0091.
Mapping of GBS reads of 398 accessions to the draft genome sequence identified 82,112 SNPs Model-based clustering analysis revealed a hierarchical genetic structure of six subgroups Greater LD decay in the west-African subpopulation is likely due to long history of recombination Genetic differentiation analysis among subpopulations revealed variation in selection signatures Pearl millet [Cenchrus americanus (L.) Morrone syn. Pennisetum glaucum (L.) R. Br.] is one of the most extensively cultivated cereals in the world, after wheat (Triticum aestivum L.), maize (Zea mays L.), rice (Oryza sativa L.), barley (Hordeum vulgare L.), and sorghum [Sorghum bicolor (L.) Moench]. It is the main component of traditional farming systems and a staple food in the arid and semiarid regions of Africa and southern Asia. However, its genetic improvement is lagging behind other major cereals and the yield is still low. Genotyping-by-sequencing (GBS)-based single-nucleotide polymorphism (SNP) markers were screened on a total of 398 accessions from different geographic regions to assess genetic diversity, population structure, and linkage disequilibrium (LD). By mapping the GBS reads to the reference genome sequence, 82,112 genome-wide SNPs were discovered. The telomeric regions of the chromosomes have the higher SNP density than in pericentromeric 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 revealed that germplasm from western Africa rooted the dendrogram with much diversity within each subgroup. Greater LD decay was observed in the west-African subpopulation than in the other subpopulations, indicating a long history of recombination among landraces. Also, genome scan of genetic differentiatation detected different selection histories among subpopulations. These results have potential application in the development of genomic-assisted breeding in pearl millet and heterotic grouping of the lines for improved hybrid performance.
将 398 个品系的 GBS 序列映射到基因组草图序列上，共鉴定出 82112 个 SNP。基于模型的聚类分析揭示了六个亚群的层次遗传结构，六个亚群的遗传分化分析表明选择标记的变异。珍珠粟 [Cenchrus americanus (L.) Morrone syn. Pennisetum glaucum (L.) R. Br.] 是继小麦（Triticum aestivum L.）、玉米（Zea mays L.）、水稻（Oryza sativa L.）、大麦（Hordeum vulgare L.）和高粱 [Sorghum bicolor (L.) Moench] 之后，世界上种植最广泛的谷物之一。它是传统农业系统的主要组成部分，也是非洲和南亚干旱和半干旱地区的主食。然而，其遗传改良落后于其他主要谷物，产量仍然较低。在来自不同地理区域的 398 个品系上筛选了基于测序的基因型（GBS）的单核苷酸多态性（SNP）标记，以评估遗传多样性、群体结构和连锁不平衡（LD）。通过将 GBS 序列映射到参考基因组序列上，发现了 82112 个全基因组 SNP。染色体的端粒区域的 SNP 密度高于着丝粒区域。群体的基于模型的聚类分析揭示了六个亚群的层次遗传结构，这些亚群主要与基因型的地理起源或来源重叠，但混合程度不同。系统发育树分析表明，来自西非的种质以每个亚群内的多样性为基础扎根于系统发育树。与其他亚群相比，西非亚群观察到更大的 LD 衰减，表明在地方品种之间存在悠久的重组历史。此外，遗传分化的基因组扫描检测到不同亚群之间的不同选择历史。这些结果在珍珠粟的基因组辅助育种和杂种优势群的杂种性能改良方面具有潜在的应用价值。
