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ORIGINAL RESEARCH article

Front. Plant Sci.
Sec. Plant Breeding
Volume 15 - 2024 | doi: 10.3389/fpls.2024.1461631

Cowpea Genetic Diversity, Population Structure and Genome-Wide Association Studies in Malawi: Insights for Breeding Programs

Provisionally accepted
Michael M Chipeta Michael M Chipeta 1*John Kafwambira John Kafwambira 1Esnart Yohane Esnart Yohane 2
  • 1 Department of Crop and Soil Sciences, Lilongwe University of Agriculture and Natural Resources, Lilongwe, Malawi
  • 2 Department of Agricultural Research Services, Chitedze Research Station, Lilongwe, Malawi

The final, formatted version of the article will be published soon.

    This study on cowpea, a vital crop for smallholder farmers in sub-Saharan Africa, aimed to understand its genetic diversity, population structure and perform genome-wide association studies (GWAS) to identify marker trait associations for yield and related traits for varietal development in Malawi. A total of 306 genotypes were characterized using single nucleotide polymorphism (SNP) markers and morphological traits. The morphological traits showed significant genotype, location and interaction effects. Genotypes MWcp24, MWcp47, MWcp2232 and TVu-3524 yielded the highest values. The grain yield was positively correlated with peduncle length, seeds per pod and pods per plant. Three clusters were revealed based on morphological traits. Minor allele frequency averaged 0.31, observed heterozygosity averaged 0.06, and gene diversity averaged 0.33. The average inbreeding coefficient was 0.82, suggesting inbreeding. Most of the variation (73.1%) was among genotypes within populations. Nine groups and ancestral populations were identified, not entirely overlapping with geographic origins. A total of sixteen significant marker-trait associations (MTAs) were linked to six morphological traits using the Fixed and Random Model Circulating Probability Unification (FarmCPU) algorithm. Validating these identified MTAs, along with the observed genetic diversity, offers valuable opportunities for cowpea improvement through marker-assisted selection, to addresses challenges faced by Malawian farmers. From this work, 30 cowpea lines were identified and included as key founder lines for the cowpea breeding programs in Malawi, Mozambique and Tanzania, targeting the development of more productive cowpea lines for the region

    Keywords: clustering, Cowpea breeding, DarTag single-nucleotide polymorphism, genetic variability, Morphological characterization, Principal Component Analysis

    Received: 08 Jul 2024; Accepted: 19 Dec 2024.

    Copyright: © 2024 Chipeta, Kafwambira and Yohane. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence: Michael M Chipeta, Department of Crop and Soil Sciences, Lilongwe University of Agriculture and Natural Resources, Lilongwe, Malawi

    Disclaimer: All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article or claim that may be made by its manufacturer is not guaranteed or endorsed by the publisher.