Genetic diversity and population structure ofLuffa acutangulaaccessions in a Thailand collection using SNP markers

Abstract

This study explored a germplasm consisting of 112 Luffa acutangula (ridge gourd) accessions originating from Thailand, Vietnam, China, Philippines, Indonesia, USA, Bangladesh and Laos for an analysis of the population structure and underlying genetic diversity using 2,834 DArTseq based SNPs. STRUCTURE analysis (ΔK at K=6) allowed us to group the accessions into six populations that corresponded well with the unrooted phylogenetic tree and Principle coordinate analyses. The phylogenetic tree differentiated the accessions into groups according to their passport geographic origin. STRUCTURE also revealed collection locations of the accessions for each cluster, demonstrating that genotypes of the ridge gourds were admixed at places nearby their regions of origin. AMOVA based on STRUCTURE clustering showed a higher variation within a population (87.17%) than AMOVA groups based on country of origin (84.94%). We also observed significant results in which a higher degree of genetic differentiation between populations according to the Phi statistics based on STRUCTURE clustering (0.128) rather than by country of germplasm collection (0.079). The clusters generated by STRUCTURE assigned characteristic fruit shape and length to each cluster grouping. The ample genetic diversity found in the L. acutangula germplasm can be utilized in ridge gourd breeding programs to help meet the demands of consumers (reduced bitterness) and aid farmers through breeding lines resistant to plant viruses.