Abstract

Dioscorea bulbifera L. is a widely distributed plant in the humid and sub-humid tropics. The taxonomic treatment of this species is ambiguous due to its extreme polymorphic morphological characters. Therefore, it is imperative to assess the species distribution, and the inter and intraspecific variability relationships in D. bulbifera. In this study, the genetic diversity and species distribution of 41 accessions of D. bulbifera in Uganda were investigated. Diversity among the 41 accessions was assessed using distribution of accessions, morphological descriptors and SNP markers. To investigate the relationship between individuals and populations, a heat map, phylogenetic tree, and principal components analysis were used. A total of 221455432 paired-end raw reads were generated out of which 162662 SNP loci were called with 150 bp reads (2×150) to a targeted depth of 112 million reads. Analysis of SNP data has proved a heterogenous population of D. bulbifera with an exception of Abur accessions that stand out as homogenous populations. This study has revealed that the utilization of advanced sequencing techniques such as GBS in combination with statistical analysis is a robust method for evaluating genetic diversity in a complex crop such as aerial yam.

Key words: Aerial yam (Dioscorea bulbifera Linn), genetic diversity, SNP markers, Uganda.

Abbreviation

AEZ, Agroecological zone; IPGRI, International Plant Genetic Resources Institute; IUCN, international union for conservation of nature; GBS, genotyping-by-Sequencing; MAF, minor allele frequency; MDS, multi-dimensional scaling analysis; PCA, principal component analysis; SNP, single nucleotide polymorphism. SPRI, solid phase reverse immobilization; UNEAK, Universal Network Enabled Analysis Kit; VCF, variant call format.