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ARS Home » Plains Area » Manhattan, Kansas » Center for Grain and Animal Health Research » Hard Winter Wheat Genetics Research » Research » Publications at this Location » Publication #366388

Research Project: Genetic Improvement of Biotic and Abiotic Stress Tolerance and Nutritional Quality in Hard Winter Wheat

Location: Hard Winter Wheat Genetics Research

Title: Genetic diversity, population structure, and linkage disequilibrium of pearl millet

item SERBA, DESALEGN - Kansas State University
item MULETA, KEBEDE - Kansas State University
item St Amand, Paul
item BERNANDO, AMY - Kansas State University
item Bai, Guihua
item PERUMAL, RAMASAMY - Kansas State University
item BASHIR, ELFADIL - Kansas State University
item MORRIS, GEOFFREY - Kansas State University

Submitted to: The Plant Genome
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/5/2019
Publication Date: 5/13/2019
Citation: Serba, D.D., Muleta, K., St Amand, P.C., Bernando, A., Bai, G., Perumal, R., Bashir, E., Morris, G. 2019. Genetic diversity, population structure, and linkage disequilibrium of pearl millet. The Plant Genome.

Interpretive Summary: Pearl millet is the sixth most popular cultivated cereal in the world. We assessed 400 pearl millet lines from different eographic regions using genome-wide DNA markers and separated these lines to six subgroups that mostly corresponded with the geographic origins. West African subgroups have high genetic diversity which s consistent with West Africa being the center of origin for pearl millet. Markers from the West African populations also indicated a long history of selection and recombination among cultivated landraces. Selection signature analysis identified significantly different selection histories among subgroups. This research provides useful information for effective use of these pearl millet populations in breeding programs.

Technical 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. enotyping-by-sequencing (GBS)-based single nucleotide polymorphism (SNP) markers were screened on a total of 400 inbred and germplasm pearl millet lines from different geographic regions to assess genetic diversity, population structure and linkage disequilibrium (LD). For 82,112 genome-wide SNPs we identified, the telomeric regions of all the seven chromosomes showed 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.