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Dissecting the Genetic Diversity of USDA Cowpea Germplasm Collection Using Kompetitive Allele Specific PCR-Single
Jesse Potts1,2, Vincent N Michael2, Geoffrey Meru3
1Department of Agricultural Sciences, Tennessee State University, Nashville, TN 37209, USA.
Genes
|March 28, 2024
Summary
Genetic diversity in cowpea (Vigna unguiculata L. Walp) was assessed using Kompetitive Allele Specific PCR (KASP) markers. The study revealed significant variation within populations, aiding cowpea breeding and germplasm management.
Area of Science:
- Agricultural Science
- Genetics
- Plant Breeding
Background:
- Cowpea (Vigna unguiculata L. Walp) is a vital subtropical legume crop, crucial for small-scale farmers in West Africa.
- Production challenges include pests, diseases, weeds, and abiotic stresses, necessitating genetic improvement.
- Exploring diverse genetic resources is key to enhancing cowpea resilience and yield.
Purpose of the Study:
- To evaluate the genetic diversity within 361 cowpea accessions from the USDA core collection.
- To validate and apply Kompetitive Allele Specific PCR (KASP) single nucleotide polymorphism (SNP) markers for genetic analysis.
- To understand population structure and genetic variation for improved cowpea breeding strategies.
Main Methods:
- Genotyping of 361 cowpea accessions using 102 KASP-SNP markers.
- Validation of 72 polymorphic KASP-SNPs across the germplasm panel.
- Population structure analysis, phylogenetic analysis, and Analysis of Molecular Variance (AMOVA).
Main Results:
- An average Polymorphism Information Content (PIC) of 0.29 and mean observed heterozygosity of 0.52 were recorded.
- Phylogenetic analysis identified three distinct populations clustering into two major groups.
- AMOVA indicated that most genetic variation resides within populations rather than among them.
Conclusions:
- Despite a generally narrow genetic base, the studied cowpea accessions show considerable variation across regions, subspecies, and improvement status.
- The KASP genotyping assay is effective for robust and accurate genotyping.
- These findings support the selection and management of cowpea germplasm in breeding programs and genebanks.
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