Identifying Litchi (Litchi chinensis Sonn.) Cultivars and Their Genetic Relationships Using Single Nucleotide Polymorphism (SNP) Markers.
Identifying Litchi (Litchi chinensis Sonn.) Cultivars and Their Genetic Relationships Using Single Nucleotide Polymorphism (SNP) Markers.
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DOI：
10.1371/journal.pone.0135390
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发表时间：
2015
期刊：
影响因子：
3.7
通讯作者：
Xiang X
中科院分区：
文献类型：
--
作者：
Liu W;Xiao Z;Bao X;Yang X;Fang J;Xiang X
荔枝是世界热带、亚热带地区的重要果树。然而，荔枝品种命名普遍混乱，荔枝种质资源之间的遗传关系的详细信息不清楚。利用155个均匀分布在荔枝基因组上的单核苷酸多态性（SNP），对我国96份代表性荔枝种质资源及其亲缘关系进行了分析。90个次要等位基因频率高于0.05且基因分型成功率高的SNP用于进一步分析。一个相对较高的遗传变异水平之间观察荔枝加入，量化的预期杂合性（He = 0.305）。基于SNP的多位点匹配确定了两个同义组，“黑叶”和“乌叶”，以及“成坨”和“白塘里1号”。14个SNPs的子集足以区分所有的非冗余荔枝基因型，这些SNPs被证明是高度稳定的一组选定的品种重复分析。UPGMA聚类分析结果表明，荔枝品种可分为极早熟、早熟、中熟和晚熟4大类，果实成熟期应作为荔枝品种分类的主要依据。结构分析结果表明，荔枝种质分为两个亚群，极早熟和极晚熟种质分别归属于聚类1和聚类2，隶属系数均在0.99以上。早，中熟性状的加入被确定为混合物的形式与不同程度的成员之间共享的两个集群，表明他们的杂交起源荔枝驯化。本研究结果将有助于荔枝种质资源的保存和荔枝育种的遗传改良。
Litchi is an important fruit tree in tropical and subtropical areas of the world. However, there is widespread confusion regarding litchi cultivar nomenclature and detailed information of genetic relationships among litchi germplasm is unclear. In the present study, the potential of single nucleotide polymorphism (SNP) for the identification of 96 representative litchi accessions and their genetic relationships in China was evaluated using 155 SNPs that were evenly spaced across litchi genome. Ninety SNPs with minor allele frequencies above 0.05 and a good genotyping success rate were used for further analysis. A relatively high level of genetic variation was observed among litchi accessions, as quantified by the expected heterozygosity (He = 0.305). The SNP based multilocus matching identified two synonymous groups, ‘Heiye’ and ‘Wuye’, and ‘Chengtuo’ and ‘Baitangli 1’. A subset of 14 SNPs was sufficient to distinguish all the non-redundant litchi genotypes, and these SNPs were proven to be highly stable by repeated analyses of a selected group of cultivars. Unweighted pair-group method of arithmetic averages (UPGMA) cluster analysis divided the litchi accessions analyzed into four main groups, which corresponded to the traits of extremely early-maturing, early-maturing, middle-maturing, and late-maturing, indicating that the fruit maturation period should be considered as the primary criterion for litchi taxonomy. Two subpopulations were detected among litchi accessions by STRUCTURE analysis, and accessions with extremely early- and late-maturing traits showed membership coefficients above 0.99 for Cluster 1 and Cluster 2, respectively. Accessions with early- and middle-maturing traits were identified as admixture forms with varying levels of membership shared between the two clusters, indicating their hybrid origin during litchi domestication. The results of this study will benefit litchi germplasm conservation programs and facilitate maximum genetic gains in litchi breeding programs.