Population Structure and Genetic Diversity in Korean Cowpea Germplasm Based on SNP Markers
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...
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MDPI AG
2020-09-01
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| Online Access: | https://www.mdpi.com/2223-7747/9/9/1190 |
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| author | Eunju Seo Kipoong Kim Tae-Hwan Jun Jinsil Choi Seong-Hoon Kim María Muñoz-Amatriaín Hokeun Sun Bo-Keun Ha |
| author_facet | Eunju Seo Kipoong Kim Tae-Hwan Jun Jinsil Choi Seong-Hoon Kim María Muñoz-Amatriaín Hokeun Sun Bo-Keun Ha |
| author_sort | Eunju Seo |
| collection | DOAJ |
| description | 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. |
| first_indexed | 2024-03-10T16:22:49Z |
| format | Article |
| id | doaj.art-ba583414bd1b4829b4dcf1245440bdc8 |
| institution | Directory Open Access Journal |
| issn | 2223-7747 |
| language | English |
| last_indexed | 2024-03-10T16:22:49Z |
| publishDate | 2020-09-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Plants |
| spelling | doaj.art-ba583414bd1b4829b4dcf1245440bdc82023-11-20T13:29:43ZengMDPI AGPlants2223-77472020-09-0199119010.3390/plants9091190Population Structure and Genetic Diversity in Korean Cowpea Germplasm Based on SNP MarkersEunju Seo0Kipoong Kim1Tae-Hwan Jun2Jinsil Choi3Seong-Hoon Kim4María Muñoz-Amatriaín5Hokeun Sun6Bo-Keun Ha7Department of Applied Plant Science, Chonnam National University, Gwangju 61186, KoreaDepartment of Statistics, Pusan National University, Busan 46241, KoreaDepartment of Plant Bioscience, Pusan National University, Busan 46241, KoreaJeollanamdo Agricultural Research and Extension Services, Naju 58213, KoreaNational Agrobiodiversity Center, National Institute of Agricultural Sciences, RDA, Jeonju 54874, KoreaDepartment of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523, USADepartment of Statistics, Pusan National University, Busan 46241, KoreaDepartment of Applied Plant Science, Chonnam National University, Gwangju 61186, KoreaCowpea 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.https://www.mdpi.com/2223-7747/9/9/1190cowpeagenetic diversitypopulation structuresingle-nucleotide polymorphism |
| spellingShingle | Eunju Seo Kipoong Kim Tae-Hwan Jun Jinsil Choi Seong-Hoon Kim María Muñoz-Amatriaín Hokeun Sun Bo-Keun Ha Population Structure and Genetic Diversity in Korean Cowpea Germplasm Based on SNP Markers Plants cowpea genetic diversity population structure single-nucleotide polymorphism |
| title | Population Structure and Genetic Diversity in Korean Cowpea Germplasm Based on SNP Markers |
| title_full | Population Structure and Genetic Diversity in Korean Cowpea Germplasm Based on SNP Markers |
| title_fullStr | Population Structure and Genetic Diversity in Korean Cowpea Germplasm Based on SNP Markers |
| title_full_unstemmed | Population Structure and Genetic Diversity in Korean Cowpea Germplasm Based on SNP Markers |
| title_short | Population Structure and Genetic Diversity in Korean Cowpea Germplasm Based on SNP Markers |
| title_sort | population structure and genetic diversity in korean cowpea germplasm based on snp markers |
| topic | cowpea genetic diversity population structure single-nucleotide polymorphism |
| url | https://www.mdpi.com/2223-7747/9/9/1190 |
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