Background Yam (Dioscorea spp.) is multiple species with various ploidy levels and is considered as a cash crop in many producing areas. Phenotypic selection in yam improvement is a lengthy procedure. However, marker-assisted selection has proven to reduce the breeding cycle with enhanced selection efficiency. Methodology In this study, a panel of 182 yam accessions distributed across six yam species were assessed for diversity and marker-traits association study using SNP markers generated from Diversity Array Technology platform. Association analysis was performed using mixed linear model (K + Q) implemented in GAPIT followed by gene annotation. Results Accessions performance were significantly different (p < 0.001) across all the traits with high broad-sense heritability (H2). Phenotypic and genotypic correlations showed positive relationships between yield and vigor but negative for yield and yam mosaic disease. Population structure revealed k = 6 as optimal clusters-based species. A total of 15 SNP markers distributed across nine chromosomes loci were associated with yield, vigor, mosaic, and anthracnose disease resistance. Gene annotation for the significant SNP loci identified some putative genes associated with primary metabolism, pest, and disease resistance for resistance to anthracnose, maintenance of NADPH in biosynthetic reaction especially those involving nitro-oxidative stress for resistance to mosaic virus, and seed development, photosynthesis, nutrition use efficiency, stress tolerance, vegetative and reproductive development for tuber yield. Conclusion This study provides valuable insights into the genetic control of plant vigor, anthracnose, mosaic virus resistance, and tuber yield in yam and thus, opens an avenue for developing additional genomic resources for markers-assisted selection focusing on multiple yam species.

https://doi.org/10.1186/s12870-023-04350-4

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Paterne AGREhttps://orcid.org/0000-0003-1231-2530

Adeyinka Adewumihttps://orcid.org/0000-0002-5981-1882

https://doi.org/10.1186/s12870-023-04350-4

Biotech and Plant Breeding

Agronomy; Food Security; Genetic Improvement; Plant Breeding; Plant Genetic Resources; Plant Production; Yam

Yams; Democratic Republic of the Congo; Genome-Wide Association Studies; Linear Models; Population Structure; Genes; Quantitative Trait Loci

Africa; Central Africa

Democratic Republic of the Congo

Headquarters and Western Africa Hub

BMC Plant Biology