SNP-based diversity, introgression pattern and early phenotypic segregation in a yam pre-breeding population

Abstract

Yams ( Dioscorea spp.) remain an important staple food crop for millions of people in Sub-Saharan Africa. Pre-breeding is a key strategy for broadening the genetic base of cultivated yams, particularly for traits related to biotic stress, yield and environmental adaptation. However, the efficiency of transferring useful alleles from wild species into cultivated backgrounds and their relationship with early phenotypic expression remains poorly understood. This study investigated introgression patterns and early phenotypic expression in interspecific hybrids derived from wild yams ( Dioscorea abyssinica × D. praehensilis ) and cultivated D. rotundata using SNP marker analysis and seedling-stage phenotypic characterisation. A total of 163 progenies and two parental genotypes were evaluated using 1358 SNP markers across 20 chromosomes alongside six vegetative traits. Early phenotypic assessment revealed substantial segregation across all traits, with seedling vigour showing the highest variability (CV = 78.3%). SNP analysis confirmed genetic diversity and hybrid origin, with expected heterozygosity of 0.17 and 40.6% polymorphic loci, while population structure revealed two major genetic clusters corresponding to wild and cultivated ancestry. Introgression analysis showed an average wild (35%) and cultivated (65%) ancestries, with no SNP locus reaching complete fixation for either wild or cultivated alleles across the progeny population. Chromosomal analysis indicated heterogeneous introgression, with wild allele proportions ranging from 22% (chromosome 20) to 43% (Chromosome 12). However, Mantel analysis revealed no significant correlation between genetic and phenotypic distances ( r = 0.004, p = 0.931), suggesting possible influence of specific genomic regions rather than overall ancestry. These findings demonstrate that early-generation introgression populations retain substantial genetic diversity and wild genomic contributions, providing a valuable foundation for targeted selection and future marker-assisted yam breeding programmes.