Genetic Diversity and Genome-wide Association Studies of Bush Yam(Dioscorea praehensilis Benth.)

Abstract

ABSTRACT Bush yam (Dioscorea praehensilis Benth.) is a wild yam that provides food and contributes to the livelihoods of people in West Africa. Several socio-cultural, nutritional and agronomic factors impede its production and commercialization. A participatory rural survey conducted in 2019 in 23 communities across Ghana's three main growing regions revealed poor culinary quality (39.9%) and agronomic traits (20.7%) as the leading causes of decreasing productivity and abandonment. A preliminary investigation of genetic diversity among 43 bush accessions previously collected and maintained at School of Agriculture, University of cape Coast, Central Region, Ghana using 11 simple sequence repeats (SSRs) revealed low genetic diversity, suggesting a need for regional germplasm collection. Quantitative traits (15) grouped 162 accessions into best performing accessions for tuber yield and yield-related traits, best in resistance to yam mosaic virus resistance and best for post-harvest tuber quality traits. Using 24 qualitative traits, a high variation among the accessions. Potential sources of genes for yield and quality attributes in 162 accessions of D. praehensilis to improve the predominant yam species, D. rotundata was evaluated. For tuber yield (23.47 t ha-1), yam mosaic virus (YMV) resistance (AUDPC=147.45) and tuber size (2.37), D. praehensilis accessions outperformed the best D. rotundata landraces. Population structure analysis based on hierarchical clustering, admixture and principal component analyses using 4,525 single nucleotide polymorphism (SNP) markers grouped D. praehensilis accessions into five clusters. Genome-wide association study revealed twenty-one SNPs associated with the agronomic and tuber quality traits. The identified SNPs accounted for approximately 16% of the total phenotypic variation. Gene annotation of significant SNPs identified candidate genes with functions related to growth and development of tubers, quality traits and defence mechanisms against yam mosaic virus. This study provides the first insight into the genetic diversity and marker- trait association of bush yam using farmers’ indigenous knowledge, morphological and molecular approaches and genome-wide association studies