基于高通量GBS-SNP标记分析比较4种石斛的差异和亲缘关系

The Differences and Genetic Relationships of 4 Dendrobium Species based on High Throughput GBS-SNP Markers

本研究以黄石斛(Dendrobium catenatum Lindl.)作为参考基因组,用GBS-SNP标记比较分析4种石斛(霍山石斛,铁皮石斛,细茎石斛,梵净山石斛)的差异和亲缘关系,以期为这4种石斛的研究提供参考。结果表明:4种石斛每个样本产生的clean reads值分别为1390262、1286162、1380009、1170337;每个样本的单核苷酸多态性位点(SNP)数目分别为1507746、893333、1364605和1227006个;Admixture软件分析遗传结构显示:最佳的K值是2时,铁皮石斛聚为一支,其余石斛聚为一支;而当K=3时,铁皮石斛聚为一支,部分霍山石斛与细茎石斛、梵净山石斛聚为一支,另一部分霍山石斛聚为一支;K=4时,分为4支,铁皮石斛聚为一支,细茎石斛与梵净山石斛聚为一支,霍山石斛被分为两支,这结果与邻接NJ树相似;主成分分析(PCoA)显示91个石斛样本被分为三支,铁皮石斛聚为一支,霍山石斛聚为一支,细茎石斛和梵净山石斛聚为一支。根据本研究结果揭示铁皮石斛与其余3种石斛亲缘关系较远,细茎石斛与梵净山石斛亲缘关系较近,霍山石斛可被分为两大支,其中一支霍山石斛与细茎石斛、梵净山石斛亲缘关系较近。本研究证实了GBS产生高通量SNP可应用于不同种石斛或其他不同种植物的亲缘关系鉴定。

The differences and genetic relationships of 4 Dendrobium species(Dendrobium huoshanense,Dendrobium officinale,Dendrobium moniliforme,Dendrobium Fanjingshanense)were analyzed based on high throughput SNP markers obtained by GBS,using Dendrobium catenatum as the reference genome,for providing reference for the study of these 4 Dendrobium species.The results showed that the number of clean reads per each sample in D.huoshanense,D.officinale,D.moniliforme,D.Fanjingshanense were 1390262,1286162,1380009 and 1170337,respectively,and the number of SNPs per each sample were 1507746,893333,1364605 and 1227006,respectively.The genetic structure based on Admixture software revealed that the samples of D.officinale were clustered into one branch,and the remaining Dendrobium samples were clustered into the other branch,when the best K value was 2;when K=3,the samples of D.officinale were grouped into one cluster,some samples of D.huoshanense,all samples of D.moniliforme and D.fanjingshanense were grouped into the second cluster,and some samples of D.huoshanense were grouped into the third cluster;When K=4,it was divided into four branches:the samples of D.officinale were grouped one branch,the samples of D.moniliforme and D.fanjingshanense were grouped one branch,the samples of D.huoshanense were divided into two branches,which was similar to the result of an unrooted neighbor-joining phylogenetic tree(NJ tree).Furthermore,principal coordinates analyses(PCoA)revealed that 91 Dendrobium samples were classed into three cluster.All samples of D.officinale and D.huoshanense were grouped together,respectively,and the samples of D.moniliforme and D.fanjingshanense were grouped together.According to the results of this study,the genetic relation of D.officinale and the other 3 species of Dendrobium are relatively distant,and the genetic relationship of D.moniliforme and D.fanjingshanense were relatively close,72 samples of D.huoshanense in the study were divided into two branches,the genetic relationship in one of which was relatively close to D.moniliforme and D.fanjingshanense.The study verified that the genetic relationships between different Dendrobium species or different species of plants were investigated using SNPs detected by GBS.