花椒cpSSR标记开发及在种间、种内的通用性分析

Development of chloroplast SSR markers of Zanthoxylum bungeanum and their generality for interspecies and intraspecies

叶绿体基因组为母系遗传,保守性高,因此叶绿体基因组中的简单序列重复(SSR)标记可在更高分类水平上进行种质资源鉴定和群体遗传结构分析。利用TRF软件和SSR Hunter软件相结合对花椒Zanthoxylum bungeanum叶绿体基因组中的SSR位点进行筛选。结果显示:花椒叶绿体基因组中共有144个SSR位点,位点间的平均分布距离为1 100.00 bp。基于检测软件设置参数,SSR重复类型主要集中在一、三核苷酸重复,二者占SSR位点总数的91.67%。此外,随机设计合成30对SSR引物对10份花椒种质、5份竹叶花椒Zanthoxylum armatum种质和1份日本花椒Zanthoxylum piperitum种质进行PCR扩增检测,共筛选出10对多态性引物,其中单核苷酸重复位点的多态性高于多核苷酸重复位点。本研究开发的叶绿体SSR标记可有效区分花椒、竹叶花椒和日本花椒,但在花椒种内并未检测出多态性。表明花椒叶绿体基因组的SSR标记可用于花椒属Zanthoxylum不同种间的遗传多样性分析。

Simple sequence repeat(SSR)molecular markers in the chloroplast genome can be used for germplasm resource identification and population genetic structural analysis at a higher classification level due to the chloroplast genome being of maternal inheritance and high conservation.To screen and develop SSR markers which will be useful for genetic diversity analysis,fingerprinting and germplasms resource identification in the chloroplast genome of Zanthoxylum bungeanum,a traditional spice plant in China,TRF software and SSR Hunter were used to screen the mono-,di-,tri-and tetra-nucleotide repeat motifs and 16 germplasms of Zanthoxylum including 10 individuals of Z.bungeanum,5 individuals of Zanthoxylum armatum,and 1 individual of Zanthoxylum piperitum were selected to test polymorphism of these detected loci.As a result,144 SSR loci were identified with an average distribution distance of 1 100.00 bp in the chloroplast genome of Z.bungeanum.Based on parameters set by the detection software,mono-nucleotide and tri-nucleotide repeat motifs were the main repeat types accounting for 91.67%of the total.In addition,30 SSR primer pairs were randomly designed and synthesized with 10 of them showing polymorphism.The polymorphic markers of mono-nucleotide repeat motifs were more than that of polynucleotide repeat motifs in this study.Furthermore,these cpSSR markers could effectively divide Z.bungeanum,Z.armatum,and Z.piperitum,but no polymorphic marker was found in the 10 individuals of Z.bungeanum.Thus,cpSSR markers of Z.bungeanum could be used for genetic diversity analysis among different interspecies of Zanthoxylum.