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ARS Home » Southeast Area » Griffin, Georgia » Plant Genetic Resources Conservation Unit » Research » Publications at this Location » Publication #348369
Title: Genetic diversity and population structure analysis of accessions in the Chinese cowpea [Vigna unguiculata (L.) Walp.] germplasm collection

Author
item CHEN, HONGLIN - Chinese Academy Of Agricultural Sciences
item CHEN, HONG - Ministry Of Agriculture - China
item HU, LIANGLIANG - Chinese Academy Of Agricultural Sciences
item WANG, LIXIA - Chinese Academy Of Agricultural Sciences
item WANG, SUHUA - Chinese Academy Of Agricultural Sciences
item Wang, Ming
item CHENG, XUZHEN - Chinese Academy Of Agricultural Sciences

Submitted to: The Crop Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/18/2017
Publication Date: 4/30/2017
Citation: Chen, H., Chen, H., Hu, L., Wang, L., Wang, S., Wang, M.L., Cheng, X. 2017. Genetic diversity and population structure analysis of accessions in the Chinese cowpea [Vigna unguiculata (L.) Walp.] germplasm collection. The Crop Journal. 5(5):363-372. https://doi.org/10.1016/j.cj.2017.04.002.
DOI: https://doi.org/10.1016/j.cj.2017.04.002

Interpretive Summary: Cowpea is an important grain/vegetable legume crop in the world but the information on assessment of its genetic diversity is very limited. In this study, a total of 300 DNA markers were developed from cowpea. Fifty-four good markers were selected for distinguishing different accessions. They were used for assessing genetic diversity and population structure of 105 selected cowpea accessions. The low level of detected genetic diversity may be attributed to a severe genetic bottleneck that occurred during the cowpea domestication process. The accessions were classified into four subgroups that correlated well with their geographic origins or collection sites. The classification results from different methods were consistent and can be used as a guide for future germplasm collection and selection of accessions as breeding materials for cultivar improvement. The newly developed DNA markers described in this study will be valuable genomic resources for the assessment of genetic diversity, population structure, evaluation of germplasm accessions, construction of genetic maps, identification of genes of interest, and application of marker-assisted selection in cowpea breeding programs.

Technical Abstract: Cowpea (Vigna unguiculata) is an important legume crop with diverse uses. The species is presently a minor crop, and evaluation of its genetic diversity has been very limited. In this study, a total of 200 genic and 100 genomic simple sequence repeat (SSR) markers were developed from cowpea unigene and genome sequences, respectively. Among them, 27 genic and 27 genomic SSR markers were polymorphic and were used for assessment of genetic diversity and population structure in 105 selected cowpea accessions. A total of 155 alleles and 2.9 alleles per marker were identified, and the average polymorphic information content (PIC) value was 0.3615. The average PIC of genomic SSRs (0.3996) was higher than that of genic SSRs (0.3235), and most of the polymorphic genomic SSRs were composed of di- and trinucleotide repeats (51.9% and 37.0% of all loci, respectively). The low level of detected genetic diversity may be attributed to a severe genetic bottleneck that occurred during the cowpea domestication process. The accessions were classified by structure and cluster analysis into four subgroups that correlated well with their geographic origins or collection sites. The classification results were also consistent with the results from principal coordinate analysis and can be used as a guide during future germplasm collection and selection of accessions as breeding materials for cultivar improvement. The newly developed genic and genomic SSR markers described in this study will be valuable genomic resources for the assessment of genetic diversity, population structure, evaluation of germplasm accessions, construction of genetic maps, identification of genes of interest, and application of marker-assisted selection in cowpea breeding programs.