Analysis of genetic diversity of lychee (Litchi chinensis Sonn.) and wild forest relatives in the Sapindaceae from Vietnam using microsatellites

We report on 14 microsatellites enriched in CT repeats obtained from a genomic library of lychee (Litchi chinensis Sonn.) cultivar “Hong Huay”. The polymorphisms revealed by these microsatellites were evaluated in a collection of 45 local Vietnamese lychee varieties and 4 Xerospermum noronhianum (Blume) Blume (Sapindaceae) collected from the wild. Samples were collected from local villages and forests in northern Vietnam. Genetic diversity parameters were estimated for the local Vietnamese varieties analyzed. The unweighted pair-group method of clustering using averages divided the lychee cultivars into three main groups: Cluster 1 (Group A) consisting of semi-natural lychees (“extremely early” lychee); Cluster 2 (Group B) consisting of cultivated cultivars (“intermediate” lychee); and Cluster 3 (Group C) representing X. noronhianum accessions. Using STRUCTURE, three subpopulations were also delimited among litchi accessions, including accessions with extremely early- and intermediate/late-maturing traits showing membership coefficients above 0.99 for Cluster 1 and Cluster 2, respectively. Accessions with early- and intermediate-maturing traits were identified as admixture forms with varying levels of membership shared between the two clusters, indicating their hybrid origin during litchi domestication. This is the first report on transferability of SSR markers developed from lychee (L. chinensis) to X. noronhianum. Results demonstrate the usefulness of microsatellites for identification, genetic diversity analysis and germplasm conservation in lychee and related Sapindaceae forest species.