基于基因分型测序(GBS)技术的堇叶紫金牛遗传结构分析

Genetic structure analysis of Ardisia violacea based on genotyping by sequencing(GBS)technology

采用基因分型测序(GBS)技术对堇叶紫金牛[Ardisia violacea(T.Suzuki)W.Z.Fang et K.Yao]13个野生居群77份样本进行单核苷酸多态性(SNP)位点挖掘,在此基础上,对13个居群77份样本的遗传多样性、系统发育树、亲缘关系等进行分析。结果表明:共获得有效SNP位点246307个,每份样本检测到SNP位点1154~3789个。13个居群的观测杂合度为0.1569~0.4289,多态信息含量为0.0785~0.3244,核苷酸多样性指数为0.0002~0.0007,Tajima’s D值为0.2247~1.0936,Shannon’s多样性指数为0.2175~0.6649,表明堇叶紫金牛整体遗传多样性水平偏低。系统发育树、主成分分析和遗传结构分析结果显示77份样本可划分为6组。亲缘关系分析结果显示:居群内个体间的亲缘关系整体较近;居群间的亲缘关系与地理距离有一定的相关性。遗传分化和基因流分析结果显示:大部分居群间存在较高的遗传分化,各居群间存在一定程度的基因交流。综上所述,堇叶紫金牛13个居群的整体遗传多样性偏低,但居群间的遗传分化程度较高,这与居群间的地理距离较远、基因交流较少有关。建议优先保护安徽省黄山市祁门县牯牛降、浙江省舟山市定海区蔡家岙和浙江省宁波市象山县屠家园村3个遗传多样性较高的居群,并开展相关繁育工作以维持和扩大居群数量。

Mining of single nucleotide polymorphism(SNP)sites was conducted for 77 samples from 13 wild populations of Ardisia violacea(T.Suzuki)W.Z.Fang et K.Yao by using genotyping by sequencing(GBS)technology,on the basis,genetic diversity,phylogenetic tree,genetic relationship,etc.of 77 samples from 13 natural populations were analyzed.The results show that a total of 246307 effective SNP sites are obtained,and 1154-3789 SNP sites are detected in each sample.The observed heterozygosities of 13 populations are 0.1569-0.4289,the polymorphic information contents are 0.0785-0.3244,the nucleotide diversity indexes are 0.0002-0.0007,the Tajima s D values are 0.2247-1.0936,and the Shannon s diversity indexes are 0.2175-0.6649,indicating that the overall genetic diversity level of A.violacea is relatively low.The phylogenetic tree,principal component analysis,and genetic structure analysis results show that 77 samples can be divided into 6 groups.The genetic relationship analysis result shows that the genetic relationships among individuals of interpopulation are relatively close in general;there are some correlations between genetic relationship and geographical distance of intrapopulation.The genetic differentiation and gene flow analysis results show that there are relatively high genetic differentiations among most populations,and there are gene exchanges among populations to some extent.In conclusion,the overall genetic diversity of 13 populations of A.violacea is relatively low,but the genetic differentiation degree of intrapopulation is relatively high,which is related with far geographical distance and lack of gene exchange between populations.It is suggested to give priority to conservation of three populations with high genetic diversity,namely Guniujiang,Qimen County,Huangshan City,Anhui Province,Caijia ao,Dinghai District,Zhoushan City,Zhejiang Province,and Tujiayuan Village,Xiangshan County,Ningbo City,Zhejiang Province,and carry out relevant breeding work to maintain and expand the population number.