Genetic diversity and a population structure analysis of accessions in the Chinese cowpea [Vigna unguiculata(L.)Walp.]germplasm collection  

作　　者：Honglin Chen Hong Chen Liangliang Hu Lixia Wang Suhua Wang Ming Li Wang Xuzhen Cheng 

机构地区：[1]National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences [2]Development Center of Science and Technology, Ministry of Agriculture, PR China [3]United States Department of Agriculture, Agricultural Research Service, Plant Genetic Resources Conservation Unit

出　　处：《The Crop Journal》2017年第5期363-372,共10页作物学报（英文版）

基　　金：funded by the Agricultural Science and Technology Innovation Program (ASTIP) of CAAS;the China Agriculture Research System (CARS-09)

摘　　要：Cowpea(Vigna imguicuiata) 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.Cowpea(Vigna imguicuiata) 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.

关 键 词：Vigna unguiculata (L.) Walp CULTIVATED COWPEA collection MICROSATELLITE marker Genetic diversity POPULATION structure 

分 类 号：S643.4[农业科学—蔬菜学]