Population genomics of pearl millet (Pennisetum glaucum (L.) R. Br.): Comparative analysis of global accessions and Senegalese landraces

Abstract

BackgroundPearl millet is a staple food for people in arid and semi-arid regions of Africa and South 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 conservation and genetic improvement of this crop. Here we characterized two pearl millet diversity panels, (i) a set of global accessions from Africa, Asia, and the America, and (ii) a collection of landraces from multiple agro-ecological zones in Senegal.ResultsWe identified 83,875 single nucleotide polymorphisms (SNPs) in 500 pearl millet accessions, comprised of 252 global accessions and 248 Senegalese landraces, using genotyping by sequencing (GBS) of PstI-MspI reduced representation libraries. We used these SNPs to characterize genomic diversity and population structure among the accessions. The Senegalese landraces had the highest levels of genetic diversity (π), while accessions from southern Africa and Asia showed lower diversity levels. Principal component analyses and ancestry estimation indicated clear population structure between the Senegalese landraces and the global accessions, and among countries in the global accessions. In contrast, little population structure was observed across in the Senegalese landraces collections. We ordered SNPs on the pearl millet genetic map and observed much faster linkage disequilibrium (LD) decay in Senegalese landraces compared to global accessions. A comparison of pearl millet GBS linkage map with the foxtail millet (Setaria italica) and sorghum (Sorghum bicolor) genomes indicated extensive regions of synteny, as well as some large-scale rearrangements in the pearl millet lineage.ConclusionsWe identified 83,875 SNPs as a genomic resource for pearl millet improvement. The high genetic diversity in Senegal relative to other regions of Africa and Asia supports a West African origin of this crop, followed by wide diffusion. The rapid LD decay and lack of confounding population structure along agro-ecological zones in Senegalese pearl millet will facilitate future association mapping studies. Comparative population genomics will provide insights into panicoid crop evolution and support improvement of these climate-resilient crops.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-2255-0) contains supplementary material, which is available to authorized users.

New Genetic Insights into Pearl Millet Diversity As Revealed by Characterization of Early- and Late-Flowering Landraces from Senegal

“…Recently, phenotyping (Sy et al, 2015) and genotyping by sequencing (Hu et al, 2015) studies were carried out on a set of Senegalese pearl millet landraces. Sampling was restricted to only one agro-ecological area of Senegal, the Groundnut Basin, and included only nine so-called intermediate-flowering landraces (flower between 75 to 100 days after sowing).…”

“…Based on phenology, head architecture and grain color, these accessions were classified into three cultivar groups, indicating a morphological diversity between early flowering landraces (Sy et al, 2015). Using 83,875 single nucleotide polymorphisms (SNPs) on the same set of accessions in addition to 252 global accessions, a higher genetic diversity was observed in Senegal accessions compared to millet accessions in India, South and Western Africa (Hu et al, 2015). Any local structure was evidenced, therefore studies of loci that control the cycle length would be necessary to assess more accurately the evolution of cultivated millet varieties (Dussert et al, 2015).…”

Exploration of Genetic and Genomic Resources for Abiotic and Biotic Stress Tolerance in Pearl Millet

“…Sehgal et al (2012) used available pearl millet ESTs and developed 75 SNP and CISP markers and demonstrated their use in identifying candidate genes underlying a major DT-QTL using four genotypes namely, H 77/833-2, PRLT 2/89-33, ICMR 01029 and ICMR 01004, representing parents of two mapping populations. There is another recent research on identification of 83,875 SNP markers using genotyping by sequencing (GBS) of PstI-MspI reduced representation libraries in 500 genotypes of pearl millet, comprised of 252 global accessions and 248 Senegalese landraces, which exhibited high genetic diversity relative to other genotypes of Africa and Asia (Hu et al, 2015). Further ISSR-derived sequence characterized amplified region (SCAR) markers were developed to screen out polymorphism in a pair of pearl millet genotypes ICMR-01007 (P1) and ICMR-01004 (P2) and their population for downy mildew resistance.…”

Setaria viridis as a Model System to Advance Millet Genetics and Genomics

“…With a closer phylogenetic relationship, more shared synteny and no complicated duplication history, S. viridis is generally a better reference than sorghum or maize for both purposes. For example, Hu et al (2015) examined a diverse panel of pearl millet and showed that shared markers and size of syntenic regions between Setaria and pearl millet is more than double of those between sorghum and pearl millet. In addition, S. viridis allelic variation can be directly introgressed into foxtail millet through interspecific crosses.…”