Population Genomics of Pearl Millet (Pennisetum glaucum (L.) R. Br.): Comparative Analysis of Global Accessions and Senegalese Landraces

Pearl millet is a staple food for people who live in arid and semi-arid climates regions in Africa and southern Asia due to its high drought tolerance and nutritional qualities. A better understanding of the genomic diversity and population structure of pearl millet germplasm is needed to support germplasm utilization and genetic improvement of this crop. We identified 83,875 single nucleotide polymorphisms (SNPs) in 500 pearl millet accessions, including 252 global accessions mainly from Africa, southern Asia, and the Americas and 248 Senegalese landraces from multiple agroecological zones in Senegal, using genotyping by sequencing (GBS) of PstI-MspI reduced representation libraries and those were used to characterize genomic diversity and population structure among the accessions. The Senegalese landraces had the highest levels of genetic diversity (pi), while accessions from southern Africa and Asia show lower diversity levels. Principal component analyses and ancestry estimation indicated clear population structure among global regions, and between Senegalese landraces and the global accessions. In contrast, little population structure was observed across in the Senegalese landraces collections. Faster linkage disequilibrium decay was observed in Senegalese landraces than that in global accessions. Comparative genomic analysis of pearl millet with foxtail millet (Setaria italica) and sorghum (Sorghum bicolor) indicated extensive regions of synteny between of them, as well as some large-scale rearrangements in pearl millet genome. This study will facilitate pearl millet germplasm conservation and improvement of these climate-resilient crops.