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.
Highlights
Pearl 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
Genome-wide Single-nucleotide polymorphism (SNP) data from global germplasm Two pearl millet germplasm sets were genotyped with genotyping by sequencing (GBS) in present study
All accessions were landraces, excepted 11 improved or introduced accessions, including six introduced lines from Mali, Niger, and Mauritania (Additional file 1: Table S1). While these Agricultural regions of Senegal are all part of the major pearl millet growing zone in Senegal, the annual precipitation ranges from 400 mm year−1 (Louga) to 770 mm year−1 (Tamba). Another set was 262 global pearl millet accessions selected from United States Department of Agriculture (USDA) National Plant Germplasm System (NPGS)
Summary
Pearl 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. Ensuring food security in the world’s arid and semi-arid regions is a great challenge due to rapid population growth and strong effects of climate change in these regions [1] Food security in these regions would be strengthened by higher crop yields, greater yield stability, and increased macro- and micro-nutrient quality of staple crops [2]. Pearl millet is an important cereal crop for arid and semi-arid regions of Africa and south Asia due to its high nutritional value and its exceptional tolerance to drought and high temperature. The potential of pearl millet for climate-resilient agriculture has yet to be fully realized [5, 6]
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