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ARS Home » Southeast Area » Griffin, Georgia » Plant Genetic Resources Conservation Unit » Research » Publications at this Location » Publication #415287

Research Project: An Integrated Approach for Plant Genetic Resources Conservation, Characterization, Evaluation, Documentation, and Distribution

Location: Plant Genetic Resources Conservation Unit

Title: Genetic Diversity and Genome-Wide Association in Cowpeas (Vigna unguiculata L.Walp)

item WU, XINGBO - Tennessee State University
item VINCENT, MICHAEL - University Of Florida
item LOPEZ-HERNANDEZ, FELIPE - Colombian Corporation Of Agriculture And Livestock- Agrosavia
item CORTES, ANDRES - Colombian Corporation Of Agriculture And Livestock- Agrosavia
item Morris, John - Brad
item Wang, Ming
item Tallury, Shyamalrau - Shyam
item MILLER II, MAX - Tennessee State University
item BLAIR, MATTHEW - Tennessee State University

Submitted to: Agronomy
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/25/2024
Publication Date: 5/2/2024
Citation: Wu, X., Vincent, M.N., Lopez-Hernandez, F., Cortes, A.J., Morris, J.B., Wang, M.L., Tallury, S.P., Miller II, M.C., Blair, M.W. 2024. Genetic Diversity and Genome-Wide Association in Cowpeas (Vigna unguiculata L.Walp). Agronomy. 14(5):961.

Interpretive Summary: Cowpea is an important crop worldwide and more information about some important traits in cowpea is needed. Genes responsible for flower color, root nutrients, and environmental stresses were found. This information is useful because it helps other scientist's develop new cowpea varieties.

Technical Abstract: Cowpea is one of the most popular dry-land legumes cultivated for food and forage in arid and semi-arid areas. Genetic diversity for global germplasm can be organized into core collections providing optimum resources to serve breeding requirements. Here, we present diversity analysis and genome-wide association study (GWAS) results for part of the cowpea core collection of the United States Department of Agriculture (USDA) along with breeding line controls. Included in the analysis were a total of 373 accessions analyzed with 6880 Single Nucleotide Polymorphism (SNP) markers from Genotyping by Sequencing (GBS). Population structure differentiated accessions into two groups irrespective of geographical origin and formed three clusters based on taxa upon phylogenetic analysis. A total of 56 SNPs were significantly associated to nine traits including pod length (25 Quantitative Trait Nucleotides, QTNs), seed anti-oxidant content (7 QTNs), dry pod color (7 QTNs), plant maturity (5 QTNs), flower color (5 QTNs), seed weight (4 QTNs), tolerance to low phosphate (1 QTN), growth habit (1 QTN), and response to rock phosphate (1 QTN) using Bayesianinformation, Linkage-disequilibrium Iteratively Nested Keyway (BLINK), and Fixed and random model Circulating Probability Unification (FarmCPU) association models. Key genes related to all significant SNPs were identified based on annotations of the cowpea reference genome, including a flavonoid gene controlling flower color (Vigun08g040200.1), a root nodulation regulator for tolerance to low phosphate (Vigun11g168000.1), and numerous genes involved in signaling, biosynthesis, metabolite transport, and abiotic stress. Our results highlight the importance of maintaining public phenotyping databases at USDA and strengthening collaborations for data collection in cowpea to maximize research impacts.