Identifying Litchi (Litchi chinensis Sonn.) Cultivars and Their Genetic Relationships Using Single Nucleotide Polymorphism (SNP) Markers

• DOI: 10.1371/journal.pone.0135390
• Publication Date: 2015-08-11T17:53:54Z
• Authors: Wei Liu; Zhidan Xiao; Xiuli Bao; Xiaoyan Yang; Jing Fang; Xu Xiang
• Keywords: Germ plasm; UPGMA; Genetic relationship; Minor allele frequency

Litchi is an important fruit tree in tropical and subtropical areas of the world. However, there widespread confusion regarding litchi cultivar nomenclature detailed information genetic relationships among germplasm unclear. In present study, potential single nucleotide polymorphism (SNP) for identification 96 representative accessions their China was evaluated using 155 SNPs that were evenly spaced across genome. Ninety with minor allele frequencies above 0.05 a good genotyping success rate used further analysis. A relatively high level variation observed accessions, as quantified by expected heterozygosity (He = 0.305). The SNP based multilocus matching identified two synonymous groups, 'Heiye' 'Wuye', 'Chengtuo' 'Baitangli 1'. subset 14 sufficient to distinguish all non-redundant genotypes, these proven be highly stable repeated analyses selected group cultivars. Unweighted pair-group method arithmetic averages (UPGMA) cluster analysis divided analyzed into four main which corresponded traits extremely early-maturing, middle-maturing, late-maturing, indicating maturation period should considered primary criterion taxonomy. Two subpopulations detected STRUCTURE analysis, early- late-maturing showed membership coefficients 0.99 Cluster 1 2, respectively. Accessions middle-maturing admixture forms varying levels shared between clusters, hybrid origin during domestication. results this study will benefit conservation programs facilitate maximum gains breeding programs.