基于SNP分子标记的221份荔枝品种(品系)的遗传多样性分析及核心种质库构建

Genetic diversity analysis and core collection construction of 221 cultivars(strains)of Litchi chinensis based on SNP molecular markers

以221份荔枝(Litchi chinensis Sonn.)品种(品系)为研究样本,采用SNP分子标记对供试样本的遗传多样性和遗传结构进行分析,在此基础上构建荔枝核心种质库并进行验证和评价。结果表明:19对SNP引物的观测等位基因数均为2,有效等位基因数为1.1~2.0,Shannon s信息指数为0.236~0.692,观测杂合度为0.081~0.561,期望杂合度为0.119~0.499,多态性信息含量为0.112~0.374;根据果实成熟期,供试样本分为晚熟、中熟、早熟和特早熟4个品种(品系)群体,其中,早熟品种(品系)群体的遗传多样性最高,晚熟品种(品系)群体的遗传多样性最低。供试样本个体间的遗传变异贡献率为85%,群体间和群体内的遗传变异贡献率分别为10%和5%;不同群体间的果实成熟时间相差越大,其遗传分化系数和遗传距离越大,其中,晚熟品种(品系)群体与中熟、早熟和特早熟品种(品系)群体间的遗传距离依次增大,遗传距离分别为0.014、0.091和0.352。遗传结构分析和聚类分析结果基本一致,通过遗传结构分析,供试样本被分为2组,a组包含181份样本,主要为中熟和晚熟品种(品系)以及极少量的早熟品种(品系);b组包含40份样本,包括所有特早熟品种(品系)、大部分早熟品种(品系)、少部分中熟品种(品系)及极少部分晚熟品种(品系);a组和b组的绝大部分样本分别对应聚类分析的Ⅲ组及Ⅰ组和Ⅱ组。综合分析结果表明:供试荔枝品种(品系)的遗传多样性水平较高,且遗传变异主要发生在个体间;群体间的遗传分化系数和遗传距离均与果实成熟期相关。按照不同取样比例构建核心种质库,以20%取样比例构建的核心种质库〔包含44份品种(品系)〕的观测等位基因数、有效等位基因数、Shannon s信息指数、观测杂合度、期望杂合度的保留率最高,分别为100%、100%、106%、103%和107%;经检验,构建的核心种质库能充分体现原有品种(品系)的遗传多样性,较全面地保留供试荔枝品种(品系)的相关信息。

Taking 221 cultivars(strains)of Litchi chinensis Sonn.as research samples,the genetic diversity and genetic structure of the test samples were analyzed by using SNP molecular marker,on the basis,core collections of L.chinensis were constructed and then verified and evaluated.The results show that the numbers of observed alleles oF_(1)9 pairs of SNP primers are all 2,the numbers of effective alleles are 1.1-2.0,the Shannon s information indexes are 0.236-0.692,the observed heterozygosity are 0.081-0.561,the expected heterozygosity are 0.119-0.499,and the polymorphic information contents are 0.112-0.374;the test samples can be divided into four cultivar(strain)populations namely late-maturing,mid-maturing,early-maturing,and extremely early-maturing according to fruit maturing stage,in which,the genetic diversity of early-maturing cultivar(strain)population is the highest,while that of late-maturing cultivar(strain)population is the lowest.The contribution rate of genetic variation among individuals of the test samples is 85%,and those among populations and within population are 10%and 5%,respectively;the greater the difference in fruit ripening time among different populations,the greater the genetic differentiation coefficient and genetic distance,in which,the genetic distances of late-maturing cultivar(strain)population with mid-maturing,early-maturing,and extremely early-maturing cultivars(strains)increase successively,and the genetic distances are 0.014,0.091,and 0.352,respectively.The results of genetic structure analysis and cluster analysis are basically consistent,and the test samples can be divided into two groups via genetic structure analysis.Group a contains 181 samples,which are mainly mid-maturing and late-maturing cultivars(strains)as well as a very few early-maturing cultivars(strains);group b contains 40 samples,including all extremely early-maturing cultivars(strains),most early-maturing cultivars(strains),a few mid-maturing cultivars(strains),and a very few late-maturing cultivars(strains);most samples in group a and group b correspond to groupⅢand groupⅠandⅡof cluster analysis,respectively.The comprehensive analysis results show that the genetic diversity level of test cultivars(strains)of L.chinensis is relatively high,and the genetic variation mainly occurs among individuals;the genetic differentiation coefficient and genetic distance among populations are both correlated with fruit maturing stage.The core collections are constructed according to different sampling ratios,and the retention rates of number of observed alleles,number of effective alleles,Shannon s information index,observed heterozygosity,and expected heterozygosity of the core collection constructed with the sampling ratio of 20%are the highest,which are 100%,100%,106%,103%,and 107%,respectively;after testing,the core collections can fully reflect the genetic diversity of original cultivars(strains),and retain relevant information of test cultivars(strains)of L.chinensis.