日本荚蒾转录组SSR位点分析及多态性SSR标记开发

Analysis of SSR Loci and Development of Polymorphic SSR Markers in Viburnum japonicum Transcriptome

基于极小种群日本荚蒾的转录组测序数据对SSR位点进行检索,分析该物种SSR位点的分布特征,并进一步开发出49个有效的SSR标记,在12份材料中,19个标记显示出多态性,这些标记可以用于后续的遗传学研究。SSR位点分析结果显示,在11244条Unigene上共检测到16059个SSR位点,SSR位点的出现频率为20.72%,平均每3800 bp出现一个SSR位点。在SSR所有重复类型中,以二核苷酸重复位点数量最多,共12065个(75.13%),五核苷酸重复位点数则最少。SSR重复基元类型丰富,共计282种,优势基序分别是AG/CT、AAG/CTT、AAAT/ATTT、AAAAT/ATTTT和AGAGGG/CCCTCT。不同重复位点的长度分布范围较广,介于8~84 bp,其中以12~18 bp为主,共包含9684个SSR位点(60.30%)。SSR标记的多态性分析结果显示,70对SSR引物中,有49对SSR引物扩增出条带,其中19对SSR引物在12份材料中显示出多态性,共扩增出52个等位基因,多态信息含量(PIC)的平均值为0.36。本研究明确了极小种群日本荚蒾SSR位点分布特征,开发出的多态性SSR标记可用于日本荚蒾的遗传多样和居群结构研究,为该珍稀濒危物种制定保护策略。

Based on transcriptome sequencing data of V.japonicum,this study searched SSR loci and analyzed its distribution characteristics.Forty-nine effective SSR markers were further developed.Nineteen of the 12 accessions showed polymorphisms,which could be used in subsequent genetic studies.The results of SSR loci analysis showed that a total of 16059 SSR loci were detected in 11244 Unigenes,and the frequency of occurrence of SSR loci was 20.72%,with an SSR per 3800 bp.In all SSR loci,the dinucleotide repeat type had the largest number of12065 loci,accounting for 75.13%of the total SSR loci.And the lowest number of pentanucleotide repeats.The SSR repeat motif types were abundant with a total of 282 types,and the dominant motifs were AG/CT,AAG/CTT,AAAAT/ATTTT,and AGAGGG/CCCTCT,respectively.Moreover,the length of different motif types varied widely between 8~84 bp,with 12~18 bp predominant,containing a total of 9684 SSR loci(60.30%).The results of polymorphism analysis of SSR markers showed that 49 of 70 SSR primer pairs amplified bands,of which 19SSR primer pairs showed polymorphism in 12 materials,with a total of 52 alleles amplified and a mean polymorphic information content(PIC)of 0.36.This study clarified the distribution characteristics of SSR loci in very small populations of V.japonicum,and the polymorphic SSR markers developed in this study can be used to study the genetic diversity and population structure of V.japonicum and to formulate conservation strategies for this rare and endangered species.