Genetic Diversity, Population Structure, and Linkage Disequilibrium of Pearl Millet

Abstract

Core Ideas 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.