Genetic Diversity And Association Analysis Of Agronomic Traits In Cowpea

Cowpea(Vigna unguiculata L. Walp.), an annual herbaceous legume plant, are widely distributed in tropical and subtropical regions. All the plant parts that are used for food are nutritious, providing protein, vitamins, and minerals. Cowpea pods are consumed as vegetable, and its grain contains 23-25% protein and 50-67% starch. What’s more, cowpea is very efficient in nitrogen fixing, and play an important role in local agro-ecosystem. Cowpea has been considered to be cultivated from wild type 3000 years ago in Africa, After transferred to Asia, cowpea was evolved into two subspecies known as ssp. biflora and ssp. sesquipedalis that are important vegetable in East-south Asia. Now cowpea is the major food and fodder to the livelihoods of millions of relatively poor people in less developed countries in tropical and subtropical region. International Institute of Tropical Agriculture in Nigeria’s (IITA; http://old.iita.org) and United States Department of Agriculture (USDA) collected a large number of cowpea germplasm, which provides rich materials for genetic and breeding research. In this study, with the 716 germplasm resources (including 502 core germplasm from USDA) and 56 U.S. commercial varieties, the genetic diversity in cowpea resources were analyzed based on their phenotypes and genotypes, meantime, the whole genome association scanning were connected for 8 key breeding traits. The major results are followings:1. Seventeen agronomic traits of 768 cowpea resources were analyzed with USDA standard method. Phenotypic polymorphism analysis shown that among all traits, the major accessions have white pod, semi-round smooth white seed with black eye seed-type and erect semi-prostrate plant-type with semi-hastate leaf. Variance analysis showed that there were no significant differences in grain shape, pod-position, pod placement and plant type among each geographic group. The variances of remaining traits were different in certain extent among each geographic group. Clustering analysis showed the geographical groups have certain difference with no significant. Among each group, commercial cultivars were obviously different from those in other groups with the highest pod number and the seed weight, the lowest coefficient of variation (CV) and genetic diversity. Accessions from Africa and Asia have the highest genetic diversity with close genetic relationship. Within North America and Latin America groups, the phenotypes were similar and have closer relations with South and Central Asian compare with other out-continent groups. Therefore it can be inferred that cowpea may originate from Africa and undergo second domestication in Asia, then move into the American colonies by colonial expansion.2. Genotyping by sequencing was used to discover single nucleotide polymorphism (SNP) in cowpea and the postulated SNP alleles were used to estimate the level of genetic diversity, population structure and phylogenetic relationships. There were abundant genetic diversities among East Africa, West Africa and the Indian subcontinent; while those within East Asia, central Asia, Europe and commercial cultivars have lowest species diversity. The analysis of variance shown about 10% genetic variations were among geographical groups and 90% variation within groups. The accessions from Southeast Africa, North American and South Asian subcontinent grouped together. The accessions from Europe, East and Central west Asia have the close relationship. According to the phylogenetic analyses among each individual, region and country, the accession can be traced from off-original back to the two candidate original areas (West and East of Africa) to predict the migration and domestication history during the cowpea dispersal and development. The result will help breeders to understand, utilize, conserve, and manage the collection for more efficient service to international cowpea research.3. Eight important agronomic traits:pod number, pod position, pod length, plant height, plant type, seed weight, vines habits and maturity, were selected for association mapping by using 1048 SNP markers. The markers which are significantly associated with those traits under all 4 liner models were considered as the candidate associated markers. The marker scaffold22616 and scaffold8664 are associated with maturity; C35010719 is associated with plant high; C35084948 and scaffold72837 are associated with pod length; scaffold20520 is associated with pod number; C35004001, C35022001, scaffold26894 and scaffold95778 are associated seed weight. The mapping results could complement and enrich the information for gene mapping studies, and help improve harvest directly or indirectly in cowpea.