Background Genome-wide association studies (GWAS) are important for the acceleration of crop improvement through knowledge of marker-trait association (MTA). This report used DArT SNP markers to successfully perform GWAS on agro-morphological traits using 270 bambara groundnut [Vigna subterranea (L.) Verdc.] landraces sourced from diverse origins. The study aimed to identify marker traits association for nine agronomic traits using GWAS and their candidate genes. The experiment was conducted at two different locations laid out in alpha lattice design. The cowpea [Vigna unguiculata (L.) Walp.] reference genome (i.e. legume genome most closely related to bambara groundnut) assisted in the identification of candidate genes. Results The analyses showed that linkage disequilibrium was found to decay rapidly with an average genetic distance of 148 kb. The broadsense heritability was relatively high and ranged from 48.39% (terminal leaf length) to 79.39% (number of pods per plant). The GWAS identified a total of 27 significant marker-trait associations (MTAs) for the nine studied traits explaining 5.27% to 24.86% of phenotypic variations. Among studied traits, the highest number of MTAs was obtained from seed coat colour (6) followed by days to flowering (5), while the least is days to maturity (1), explaining 5.76% to 11.03%, 14.5% to 19.49%, and 11.66% phenotypic variations, respectively. Also, a total of 17 candidate genes were identified, varying in number for different traits; seed coat colour (6), days to flowering (3), terminal leaf length (2), terminal leaf width (2), number of seed per pod (2), pod width (1) and days to maturity (1). Conclusion These results revealed the prospect of GWAS in identification of SNP variations associated with agronomic traits in bambara groundnut. Also, its present new opportunity to explore GWAS and marker assisted strategies in breeding of bambara groundnut for acceleration of the crop improvement.

We appreciate the effort of Integrated Genotyping Service and Support (IGSS) of the Biosciences Eastern and Central Africa (BecA) Hub, Nairobi for subsidizing the genotyping services and International Institute of Agriculture (IITA), Ibadan Nigeria for providing most of the accessions used for this study.

https://doi.org/10.1186/s12864-023-09684-9

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Abush Tesfayehttps://orcid.org/0000-0002-9245-360X

https://doi.org/10.1186/s12864-023-09684-9

Biotech and Plant Breeding

Agronomy; Food Security; Genetic Improvement; Grain Legumes; Plant Breeding; Plant Genetic Resources; Plant Production

Bambara Groundnuts; Genes; Single Nucleotide Polymorphism; Linkage Disequilibrium; Quantitative Trait Loci; Genome-Wide Association Studies

Africa; West Africa

Nigeria

Headquarters and Western Africa Hub

BMC Genomics