Assessment of Genetic Diversity and Discovery of Molecular Markers in Durian (Durio zibethinus L.) in China

Abstract

Durian (Durio zibethinus L.) is a crop of economic and health importance globally. Efforts are being made to revamp China’s only successful commercial-scale durian plantations in Hainan; however, their genetic base is unknown. Therefore, the present study was undertaken to assess the genetic base and population structure of 32 genotypes in durian plantation sites in Hainan, China, and develop simple sequence repeat (SSR) markers by whole genome sequencing through restriction site-associated DNA sequencing technology to facilitate germplasm conservation and breeding. The results from identity by state (IBS), phylogenetic tree, population structure, and principal component analysis grouped the 32 genotypes into two clusters/sub-populations. Based on IBS, genotypes in Cluster I are largely duplicated genotypes; however, results from the model-based population structure demonstrated that most of the genotypes in Sub-population II shared a common genetic background with those in Sub-population I/Cluster I. The results revealed that the core durian collection in the plantation sites in Hainan include D24, D101, MSW, JH, D163, HFH, and NLX-5. In addition, we developed a total of 79,178 SSR markers with varied lengths and amplicon sizes. The genetic diversity and population structure reported in this study will be useful for durian conservation and utilization. In addition, the discovered and developed SSR markers will lay the foundation for molecular breeding via marker-assisted selection, quantitative trait loci mapping, and candidate gene discovery and validation.

Assessing Genetic Variation among Strychnos spinosa Lam. Morphotypes Using Simple Sequence Repeat Markers

“…The affinities produced by population structure (Figure 2) generally agreed with the genetic distance (Supplementary Materials) of closely related morphotypes GSR-GRO and GRP-GEO in sub-population K3.2, and closely related morphotypes GRR-GEF and GvRR-dGEO in subpopulation K3.3. In crop breeding, knowing the population structure benefits the selection of parents with genetic divergence [39]. Knowledge of the population structure can also aid in identifying regions of the genome that are under selection, which can provide insight into the adaptation of the crop to its environment [40], which is essential for plant conservation.…”