Diversity, population structure, and linkage disequilibrium among cowpea accessions

Publication Type

Journal Article

Name of Author

• Sodedji Frejus Ariel Kpedetin, University Felix Houphouët-Boigny (U-FHB), Côte d'IvoireFollow
• Symphorien Agbahoungba, Korea Institute of Science and Technology (KIST)
• Eric Echikintho Agoyi, University of Abomey–Calavi (UAC),Cotonou, Benin
• Médard Konoutan Kafoutchoni, University of Abomey–Calavi (UAC),Cotonou, Benin
• Jaeyoung Choi, Korea Institute of Science and Technology (KIST)
• Simon-Pierre Assanvo Nguetta, University Felix Houphouët-Boigny (U-FHB), Côte d'Ivoire
• Achille Ephrem Assogbadjo, Korea Institute of Science and Technology (KIST)
• Ho-Youn Kim, University of Abomey–Calavi (UAC),Cotonou, Benin

Publication Date (Issue Year)

2021

Journal Name

The Plant Genome

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 basedon its diversity are required for its improvement. The present study aims to investigatethe genetic diversity, population structure, and linkage disequilibrium (LD) among274  cowpea  accessions  from  different  origins.  A  total  of  3,127  single  nucleotidepolymorphism (SNP) markers generated using diversity array technology (DArT)was used. Population structure, neighbor-joining clustering, and principal componentanalyses indicated three subpopulations within the germplasm. Results of STRUC-TURE  analysis  and  discriminant  analysis  of  principal  components  (DAPC)  werecomplementary 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  allsubpopulations. The subpopulations had fixation indexes of 0.48–0.56. Analysis ofmolecular variance revealed that within subpopulation variation accounted for 81%of observed genetic variation in the germplasm. The subpopulations mainly consistedof inbred lines (inbreeding coefficient=1) with common alleles, although the great physical distances between markers. The LD decay distance varied among chro-mosomes with the average distance of 80–100 kb across the genome. Thus, cropimprovement is possible, and the LD will facilitate genome-wide association studieson quality attributes and critical agronomic traits in cowpea.

Keywords

Diversity, population structure, linkage disequilibrium, cowpea accessions

Rsif Scholar Name

Sodedji Frejus Ariel Kpedetin

Rsif Scholar Nationality

Benin

Cohort

Cohort 1

Thematic Area

Climate Change

Africa Host University (AHU)

University Felix Houphouët-Boigny (U-FHB), Côte d'Ivoire

Funding Statement

The World Academy of Sciences,Grant/Award Number: grant 18-238RG/BIO/AF/AC_G-FR3240303667

Recommended Citation

Kpedetin, S. F., Agbahoungba, S., Agoyi, E. E., Kafoutchoni, M. K., Choi, J., Nguetta, S. A., Assogbadjo, A. E., & Kim, H. (2021). Diversity, population structure, and linkage disequilibrium among cowpea accessions. The Plant Genome, 14 (3), e20113. https://doi.org/10.1002/TPG2.20113