Diversity, population structure, and linkage disequilibrium among cowpea accessions

Abstract Cowpea [Vigna unguiculata (L.) Walp] is a globally important food security crop. However, it is susceptible to pest and disease; hence, constant breeding efforts based on its diversity are required for its improvement. The present study aims to investigate the genetic diversity, population...

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Autores principales:	Frejus Ariel Kpedetin Sodedji, Symphorien Agbahoungba, Eric Echikintho Agoyi, Médard Konoutan Kafoutchoni, Jaeyoung Choi, Simon‐Pierre Assanvo Nguetta, Achille Ephrem Assogbadjo, Ho‐Youn Kim
Formato:	article
Lenguaje:	EN
Publicado:	Wiley 2021
Materias:	Plant culture SB1-1110 Genetics QH426-470
Acceso en línea:	https://doaj.org/article/98fbc6ec001a48e8b352ab414894c30c
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spelling	oai:doaj.org-article:98fbc6ec001a48e8b352ab414894c30c2021-12-05T07:50:12ZDiversity, population structure, and linkage disequilibrium among cowpea accessions1940-337210.1002/tpg2.20113https://doaj.org/article/98fbc6ec001a48e8b352ab414894c30c2021-11-01T00:00:00Zhttps://doi.org/10.1002/tpg2.20113https://doaj.org/toc/1940-3372Abstract Cowpea [Vigna unguiculata (L.) Walp] is a globally important food security crop. However, it is susceptible to pest and disease; hence, constant breeding efforts based on its diversity are required for its improvement. The present study aims to investigate the genetic diversity, population structure, and linkage disequilibrium (LD) among 274 cowpea accessions from different origins. A total of 3,127 single nucleotide polymorphism (SNP) markers generated using diversity array technology (DArT) was used. Population structure, neighbor‐joining clustering, and principal component analyses indicated three subpopulations within the germplasm. Results of STRUCTURE analysis and discriminant analysis of principal components (DAPC) were complementary in assessing the structuration of the diversity among the germplasm, with the grouping of the accessions improved in DAPC. Genetic distances of 0.005–0.44 were observed among accessions. Accessions from western and central Africa, eastern and central Africa, and Asia were predominant and distributed across all subpopulations. The subpopulations had fixation indexes of 0.48–0.56. Analysis of molecular variance revealed that within subpopulation variation accounted for 81% of observed genetic variation in the germplasm. The subpopulations mainly consisted of inbred lines (inbreeding coefficient = 1) with common alleles, although they were from different geographical regions. This reflects considerable seed movement and germplasm exchange between regions. The LD was characterized by low decay for great physical distances between markers. The LD decay distance varied among chromosomes with the average distance of 80–100 kb across the genome. Thus, crop improvement is possible, and the LD will facilitate genome‐wide association studies on quality attributes and critical agronomic traits in cowpea.Frejus Ariel Kpedetin SodedjiSymphorien AgbahoungbaEric Echikintho AgoyiMédard Konoutan KafoutchoniJaeyoung ChoiSimon‐Pierre Assanvo NguettaAchille Ephrem AssogbadjoHo‐Youn KimWileyarticlePlant cultureSB1-1110GeneticsQH426-470ENThe Plant Genome, Vol 14, Iss 3, Pp n/a-n/a (2021)
institution	DOAJ
collection	DOAJ
language	EN
topic	Plant culture SB1-1110 Genetics QH426-470
spellingShingle	Plant culture SB1-1110 Genetics QH426-470 Frejus Ariel Kpedetin Sodedji Symphorien Agbahoungba Eric Echikintho Agoyi Médard Konoutan Kafoutchoni Jaeyoung Choi Simon‐Pierre Assanvo Nguetta Achille Ephrem Assogbadjo Ho‐Youn Kim Diversity, population structure, and linkage disequilibrium among cowpea accessions
description	Abstract Cowpea [Vigna unguiculata (L.) Walp] is a globally important food security crop. However, it is susceptible to pest and disease; hence, constant breeding efforts based on its diversity are required for its improvement. The present study aims to investigate the genetic diversity, population structure, and linkage disequilibrium (LD) among 274 cowpea accessions from different origins. A total of 3,127 single nucleotide polymorphism (SNP) markers generated using diversity array technology (DArT) was used. Population structure, neighbor‐joining clustering, and principal component analyses indicated three subpopulations within the germplasm. Results of STRUCTURE analysis and discriminant analysis of principal components (DAPC) were complementary in assessing the structuration of the diversity among the germplasm, with the grouping of the accessions improved in DAPC. Genetic distances of 0.005–0.44 were observed among accessions. Accessions from western and central Africa, eastern and central Africa, and Asia were predominant and distributed across all subpopulations. The subpopulations had fixation indexes of 0.48–0.56. Analysis of molecular variance revealed that within subpopulation variation accounted for 81% of observed genetic variation in the germplasm. The subpopulations mainly consisted of inbred lines (inbreeding coefficient = 1) with common alleles, although they were from different geographical regions. This reflects considerable seed movement and germplasm exchange between regions. The LD was characterized by low decay for great physical distances between markers. The LD decay distance varied among chromosomes with the average distance of 80–100 kb across the genome. Thus, crop improvement is possible, and the LD will facilitate genome‐wide association studies on quality attributes and critical agronomic traits in cowpea.
format	article
author	Frejus Ariel Kpedetin Sodedji Symphorien Agbahoungba Eric Echikintho Agoyi Médard Konoutan Kafoutchoni Jaeyoung Choi Simon‐Pierre Assanvo Nguetta Achille Ephrem Assogbadjo Ho‐Youn Kim
author_facet	Frejus Ariel Kpedetin Sodedji Symphorien Agbahoungba Eric Echikintho Agoyi Médard Konoutan Kafoutchoni Jaeyoung Choi Simon‐Pierre Assanvo Nguetta Achille Ephrem Assogbadjo Ho‐Youn Kim
author_sort	Frejus Ariel Kpedetin Sodedji
title	Diversity, population structure, and linkage disequilibrium among cowpea accessions
title_short	Diversity, population structure, and linkage disequilibrium among cowpea accessions
title_full	Diversity, population structure, and linkage disequilibrium among cowpea accessions
title_fullStr	Diversity, population structure, and linkage disequilibrium among cowpea accessions
title_full_unstemmed	Diversity, population structure, and linkage disequilibrium among cowpea accessions
title_sort	diversity, population structure, and linkage disequilibrium among cowpea accessions
publisher	Wiley
publishDate	2021
url	https://doaj.org/article/98fbc6ec001a48e8b352ab414894c30c
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Diversity, population structure, and linkage disequilibrium among cowpea accessions

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