Assessment of genetic diversity and population structure of mango (Mangifera spp.) germplasms using GBS - based SNP markers

Abstract

Mango (Mangifera indica L.) is an economically significant fruit tree in Vietnam. This study aims to evaluate the genetic diversity of 15 mango accessions collected nationwide using single nucleotide polymorphism (SNP) markers. The GBS (Genotyping by sequencing) technique was applied to explore and screen 1,860 high - quality SNP markers, which were then utilized in population structure analysis (using the STRUCTURE v.4.3 software) and genetic clustering (using the PowerMarker v.3.25 software) as well as determining genetic indices among collected mango samples. The results showed that the studied mango accessions harbor a relatively high level of genetic diversity, as demonstrated by the genetic diversity index (GD) and the polymorphic information coefficient (PIC) determined based on the SNP markers. In addition to the subgroup of the out-group, interspecific Thanh Tra accessions, two subgroups of the mango accessions were identified - one consisting of southern - originated accessions with a homogeneous genetic background and one of the remaining accessions having an admixture genetic background. This result reflected the history of closed breeding and selection among mango varieties in the southern region. It might contribute to an essential genetic foundation for research in the conservation and exploitation of mango genetic resources in Vietnam.