Population Structure and Genetic Diversity in Korean Cowpea Germplasm Based on SNP Markers.

Eunju Seo,Hokeun Sun,Tae-Hwan Jun,María Muñoz-Amatriaín,Kipoong Kim,Seong-Hoon Kim,Bo-Keun Ha,Jinsil Choi

doi:10.3390/plants9091190

Abstract

Cowpea is one of the most essential legume crops providing inexpensive dietary protein and nutrients. The aim of this study was to understand the genetic diversity and population structure of global and Korean cowpea germplasms. A total of 384 cowpea accessions from 21 countries were genotyped with the Cowpea iSelect Consortium Array containing 51,128 single-nucleotide polymorphisms (SNPs). After SNP filtering, a genetic diversity study was carried out using 35,116 SNPs within 376 cowpea accessions, including 229 Korean accessions. Based on structure and principal component analysis, a total of 376 global accessions were divided into four major populations. Accessions in group 1 were from Asia and Europe, those in groups 2 and 4 were from Korea, and those in group 3 were from West Africa. In addition, 229 Korean accessions were divided into three major populations (Q1, Jeonra province; Q2, Gangwon province; Q3, a mixture of provinces). Additionally, the neighbor-joining tree indicated similar results. Further genetic diversity analysis within the global and Korean population groups indicated low heterozygosity, a low polymorphism information content, and a high inbreeding coefficient in the Korean cowpea accessions. The population structure analysis will provide useful knowledge to support the genetic potential of the cowpea breeding program, especially in Korea.

Highlights

Cowpea provides a cheap source of dietary protein and essential nutrients for the people in sub-Saharan Africa, East Asia, and other developing countries [1]
Was applied to call genotypes within GenomeStudio v.2.0 software (Illumina, Inc., San Diego, CA, USA), and on average, a 95% single-nucleotide polymorphisms (SNPs) call rate was obtained across all accessions
After the SNP data were filtered for a missing rate of >10%, a minor allele frequency (MAF) of

Summary

Introduction

Cowpea provides a cheap source of dietary protein and essential nutrients for the people in sub-Saharan Africa, East Asia, and other developing countries [1]. According to the FAO, cowpea is extensively grown by millions of African farmers and is a great source of essential food for many urban consumers. It contains high levels of carbohydrates (~64%), protein (~25%), vitamins, and minerals, such as iron, calcium, thiamin, and folic acid [2,3]. Aside from its suitability for human consumption, cowpea has high nutritional value required for animal fodder [4,5]. It is tolerant to low soil fertility because of its ability to fix nitrogen [6,7]

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