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