Genetic diversity and demographic history of Cajanus spp. illustrated from genome-wide SNPs.

Understanding genetic structure of Cajanus spp. is essential for achieving genetic improvement by quantitative trait loci (QTL) mapping or association studies and use of selected markers through genomic assisted breeding and genomic selection. After developing a comprehensive set of 1,616 single nuc...

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Autores principales:	Rachit K Saxena, Eric von Wettberg, Hari D Upadhyaya, Vanessa Sanchez, Serah Songok, Kulbhushan Saxena, Paul Kimurto, Rajeev K Varshney
Formato:	article
Lenguaje:	EN
Publicado:	Public Library of Science (PLoS) 2014
Materias:	Medicine R Science Q
Acceso en línea:	https://doaj.org/article/faa400671c8f47549db610d4e8685eee
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spelling	oai:doaj.org-article:faa400671c8f47549db610d4e8685eee2021-11-18T08:32:48ZGenetic diversity and demographic history of Cajanus spp. illustrated from genome-wide SNPs.1932-620310.1371/journal.pone.0088568https://doaj.org/article/faa400671c8f47549db610d4e8685eee2014-01-01T00:00:00Zhttps://www.ncbi.nlm.nih.gov/pmc/articles/pmid/24533111/?tool=EBIhttps://doaj.org/toc/1932-6203Understanding genetic structure of Cajanus spp. is essential for achieving genetic improvement by quantitative trait loci (QTL) mapping or association studies and use of selected markers through genomic assisted breeding and genomic selection. After developing a comprehensive set of 1,616 single nucleotide polymorphism (SNPs) and their conversion into cost effective KASPar assays for pigeonpea (Cajanus cajan), we studied levels of genetic variability both within and between diverse set of Cajanus lines including 56 breeding lines, 21 landraces and 107 accessions from 18 wild species. These results revealed a high frequency of polymorphic SNPs and relatively high level of cross-species transferability. Indeed, 75.8% of successful SNP assays revealed polymorphism, and more than 95% of these assays could be successfully transferred to related wild species. To show regional patterns of variation, we used STRUCTURE and Analysis of Molecular Variance (AMOVA) to partition variance among hierarchical sets of landraces and wild species at either the continental scale or within India. STRUCTURE separated most of the domesticated germplasm from wild ecotypes, and separates Australian and Asian wild species as has been found previously. Among Indian regions and states within regions, we found 36% of the variation between regions, and 64% within landraces or wilds within states. The highest level of polymorphism in wild relatives and landraces was found in Madhya Pradesh and Andhra Pradesh provinces of India representing the centre of origin and domestication of pigeonpea respectively.Rachit K SaxenaEric von WettbergHari D UpadhyayaVanessa SanchezSerah SongokKulbhushan SaxenaPaul KimurtoRajeev K VarshneyPublic Library of Science (PLoS)articleMedicineRScienceQENPLoS ONE, Vol 9, Iss 2, p e88568 (2014)
institution	DOAJ
collection	DOAJ
language	EN
topic	Medicine R Science Q
spellingShingle	Medicine R Science Q Rachit K Saxena Eric von Wettberg Hari D Upadhyaya Vanessa Sanchez Serah Songok Kulbhushan Saxena Paul Kimurto Rajeev K Varshney Genetic diversity and demographic history of Cajanus spp. illustrated from genome-wide SNPs.
description	Understanding genetic structure of Cajanus spp. is essential for achieving genetic improvement by quantitative trait loci (QTL) mapping or association studies and use of selected markers through genomic assisted breeding and genomic selection. After developing a comprehensive set of 1,616 single nucleotide polymorphism (SNPs) and their conversion into cost effective KASPar assays for pigeonpea (Cajanus cajan), we studied levels of genetic variability both within and between diverse set of Cajanus lines including 56 breeding lines, 21 landraces and 107 accessions from 18 wild species. These results revealed a high frequency of polymorphic SNPs and relatively high level of cross-species transferability. Indeed, 75.8% of successful SNP assays revealed polymorphism, and more than 95% of these assays could be successfully transferred to related wild species. To show regional patterns of variation, we used STRUCTURE and Analysis of Molecular Variance (AMOVA) to partition variance among hierarchical sets of landraces and wild species at either the continental scale or within India. STRUCTURE separated most of the domesticated germplasm from wild ecotypes, and separates Australian and Asian wild species as has been found previously. Among Indian regions and states within regions, we found 36% of the variation between regions, and 64% within landraces or wilds within states. The highest level of polymorphism in wild relatives and landraces was found in Madhya Pradesh and Andhra Pradesh provinces of India representing the centre of origin and domestication of pigeonpea respectively.
format	article
author	Rachit K Saxena Eric von Wettberg Hari D Upadhyaya Vanessa Sanchez Serah Songok Kulbhushan Saxena Paul Kimurto Rajeev K Varshney
author_facet	Rachit K Saxena Eric von Wettberg Hari D Upadhyaya Vanessa Sanchez Serah Songok Kulbhushan Saxena Paul Kimurto Rajeev K Varshney
author_sort	Rachit K Saxena
title	Genetic diversity and demographic history of Cajanus spp. illustrated from genome-wide SNPs.
title_short	Genetic diversity and demographic history of Cajanus spp. illustrated from genome-wide SNPs.
title_full	Genetic diversity and demographic history of Cajanus spp. illustrated from genome-wide SNPs.
title_fullStr	Genetic diversity and demographic history of Cajanus spp. illustrated from genome-wide SNPs.
title_full_unstemmed	Genetic diversity and demographic history of Cajanus spp. illustrated from genome-wide SNPs.
title_sort	genetic diversity and demographic history of cajanus spp. illustrated from genome-wide snps.
publisher	Public Library of Science (PLoS)
publishDate	2014
url	https://doaj.org/article/faa400671c8f47549db610d4e8685eee
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Genetic diversity and demographic history of Cajanus spp. illustrated from genome-wide SNPs.

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