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

Abstract

Pearl 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)-based single nucleotide polymorphism (SNP) markers were screened on a total of 400 inbred lines and germplasm 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, we discovered 82,112 genome-wide SNPs. The telomeric regions of all seven chromosomes have the higher SNP density 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. This results have potential application in the development genomic-assisted breeding in pearl millet and heterotic grouping of the lines for improved hybrid performance.