Background White Guinea yam (Dioscorea rotundata) is primarily a dioecious species with distinct male and female plants. Its breeding is constrained by sexual reproduction abnormalities, resulting in low success rates in cross-pollination. An accurate method for early detection of this plant’s sex and compatible fertile parents at the seedling stage would improve levels of cross-pollination success in breeding. We used the genome-wide association studies (GWAS) to dissect the molecular basis of plant sex and cross-compatibility-related traits in a panel of 112 parental clones used in D. rotundata crossing blocks from 2010 to 2020. Results Population structure and phylogeny analyses using 8326 single nucleotide polymorphism (SNP) markers grouped the 112 white yam clones into three subpopulations. Using Multi-locus random-SNP-effect Mixed Linear Model, we identified three, one, and three SNP markers that were significantly associated with the average crossability rate (ACR), the percentage of high crossability (PHC), and the plant sex, respectively. In addition, five genes considered to be directly linked to sexual reproduction or regulating the balance of sex hormones were annotated from chromosomal regions controlling the assessed traits. This study confirmed the female heterogametic sex determination (ZZ/ZW) system proposed for D. rotundata. Conclusions This study provides valuable insights on the genomic control of sex identity and cross-pollination success in D. rotundata. It, therefore, opens an avenue for developing molecular markers for predicting plant sex and cross-pollination success at the early growth stage before field sex expression in this crop.

https://dx.doi.org/10.1186/s12870-022-03673-y

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Asrat Asfawhttps://orcid.org/0000-0002-4859-0631

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

Robert Asieduhttps://orcid.org/0000-0001-8943-2376

https://dx.doi.org/10.1186/s12870-022-03673-y

Biotech and Plant Breeding

Aflatoxin; Agronomy; Crop Systems; Genetic Improvement; Plant Breeding; Plant Genetic Resources; Yam

Genes; Cross-pollination; Population Structure; Sex Determination; Plant Breeding; Dioscorea Rotundata

Africa; West Africa

Nigeria

Headquarters and Western Africa Hub

BMC Plant Biology