Libraries
 

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

Simple item page
dc.citationHu, Z., Mbacké, B., Perumal, R., Guèye, M. C., Sy, O., Bouchet, S., . . . Morris, G. P. (2015). Population genomics of pearl millet (Pennisetum glaucum (L.) R. Br.): Comparative analysis of global accessions and Senegalese landraces. Bmc Genomics. doi:10.1186/s12864-015-2255-0
dc.citation.doi10.1186/s12864-015-2255-0
dc.citation.issn1471-2164
dc.citation.issue1
dc.citation.jtitleBMC Genomics
dc.citation.spage1048
dc.citation.volume16
dc.contributor.authorHu, Z.
dc.contributor.authorMbacké, B.
dc.contributor.authorPerumal, Ramasamy
dc.contributor.authorGuèye, M. C.
dc.contributor.authorSy, O.
dc.contributor.authorBouchet, S.
dc.contributor.authorVara Prasad, P.V.
dc.contributor.authorMorris, Geoffrey P.
dc.contributor.authoreidperumal
dc.contributor.authoreidvara
dc.contributor.authoreidgpmorris
dc.date.accessioned2016-03-30T01:38:04Z
dc.date.available2016-03-30T01:38:04Z
dc.date.issued2015-12-09
dc.date.published2015
dc.descriptionCitation: Hu, Z., Mbacké, B., Perumal, R., Guèye, M. C., Sy, O., Bouchet, S., . . . Morris, G. P. (2015). Population genomics of pearl millet (Pennisetum glaucum (L.) R. Br.): Comparative analysis of global accessions and Senegalese landraces. Bmc Genomics. doi:10.1186/s12864-015-2255-0
dc.descriptionBackground: 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. 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. Results: We 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 (?), 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. Conclusions: We 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. © 2015 Hu et al.
dc.description.versionArticle: Version of Record
dc.identifier.urihttp://hdl.handle.net/2097/32206
dc.relation.urihttps://doi.org/10.1186/s12864-015-2255-0
dc.rightsAttribution 4.0 International (CC BY 4.0)
dc.rightsThis article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated.
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.rights.urihttp://creativecommons.org/licenses/by/4.0/
dc.subjectCrop Diversity
dc.subjectGenotype-By-Sequencing
dc.subjectPopulation Structure
dc.subjectPrincipal Component Analysis
dc.subjectSingle Nucleotide Polymorphism
dc.subjectClimate
dc.titlePopulation genomics of pearl millet (Pennisetum glaucum (L.) R. Br.): Comparative analysis of global accessions and Senegalese landraces
dc.typeText

Files

Original bundle

Now showing 1 - 1 of 1
Thumbnail Image
Name:
art%3A10.1186%2Fs12864-015-2255-0.pdf
Size:
2.94 MB
Format:
Adobe Portable Document Format
Download

Collections

Agronomy Faculty Research and Publications
facebook
twitter
youtube

Center for Scholarly Publishing

K-State Libraries

1117 Mid-Campus Drive North, Manhattan, KS 66506

785-532-3514|cads@k-state.edu