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ARS Home » Pacific West Area » Salinas, California » Crop Improvement and Protection Research » Research » Publications at this Location » Publication #336392
Title: Association mapping of aphid resistance in USDA cowpea (Vigna unguiculata L. Walp.) core collection using SNPs

Author
item QIN, JUN - University Of Arkansas
item SHI, AINONG - University Of Arkansas
item Mou, Beiquan
item BHATTARAI, GEHENDRA - University Of Arkansas
item YANG, WEI - University Of Arkansas
item WENG, YUEJIN - University Of Arkansas
item MOTES, DENNIS - University Of Arkansas

Submitted to: Euphytica
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/19/2016
Publication Date: 1/7/2017
Citation: Qin, J., Shi, A., Mou, B., Bhattarai, G., Yang, W., Weng, Y., Motes, D. 2017. Association mapping of aphid resistance in USDA cowpea (Vigna unguiculata L. Walp.) core collection using SNPs. Euphytica. 213:36. doi: 10.1007/s10681-016-1830-z.

Interpretive Summary: Cowpea (Vigna unguiculata L. Walp.) is an important legume crop and provides relatively cheap nutritious food to the resource-poor populations in the developing countries. Being resistant to drought and heat, cowpeas are widely grown in the drier tropics. For that reason, cowpea is extensively grown in Africa, South America, Southeast Asia, and in the southern United States. Cowpea is consumed both as a fresh vegetable and dry grain food. Besides food consumption cowpea is also used as cover crops and animal fodder. Cowpea aphid (CPA; Aphis craccivora) is a destructive insect pest of cowpea, as well as other legume crops including alfalfa, beans, chickpea, lentils, lupins and peanuts. The utilization of aphid resistance in cowpea breeding is one of the most efficient and environmental friendly methods to control aphids. Using molecular marker-assisted selection (MAS) will expedite cowpea breeding procedures, but it is limited by the lack of information on markers associated with the aphid resistance. The objective of this study was to identify single nucleotide polymorphism (SNP) markers associated with aphid resistance in cowpea and to conduct genetic diversity analysis for aphid resistant resources. In this study, 338 cowpea accessions from the USDA cowpea core collection, originally collected from 40 countries, were evaluated for their aphid resistance and 1,047 SNP markers identified from DNA sequencing were used to analyze their association with aphid resistance. The 338 cowpea varieties were grouped into three clusters according to their genetic structures. The association study revealed that two SNP markers, C35011941_894 and Scaffold30061_3363, were strongly associated with aphid resistance by using three different methods of analysis. The results will provide useful information for selecting aphid resistance in cowpea breeding.

Technical Abstract: Cowpea aphid (CPA; Aphis craccivora) is a destructive insect pest of cowpea, as well as other legume crops including alfalfa, beans, chickpea, lentils, lupins and peanuts. The utilization of aphid resistance in cowpea breeding is one of the most efficient and environmental friendly methods to control aphids. Using marker-assisted selection (MAS) will expedite cowpea breeding procedures, but it is limited by the lack of information on marker associations of the aphid resistance. The objective of this study was to identify single nucleotide polymorphism (SNP) markers associated with aphid resistance in cowpea and to conduct genetic diversity analysis for aphid resistant resources. In this study, 338 cowpea accessions from the cowpea core collection in USDA-GRIN, originally collected from 40 countries, were evaluated for their aphid resistance and 1,047 SNPs identified from genotyping by sequencing (GBS) were used as the genotypic data. Single marker regression (SMR), general linear model (GLM), and mixed linear model (MLM) in TASSEL were used for association analysis between the SNPs and the phenotypic data. Three clusters for the association panel of the 338 cowpea accessions were inferred by STRUCTURE analysis, in good agreement with the phylogenetic tree drawn by MEGA 6 based on the maximum likelihood model with the neighbor joining method. A genome-wide association study revealed that two SNP markers, C35011941_894 and Scaffold30061_3363, were strongly associated with aphid resistance across three models with the log of odds (LOD) value greater than 2.5. The results will provide useful information for selecting aphid resistance in cowpea molecular breeding.