基于全长转录组测序的盐生草SSR标记开发及其遗传多样性分析

Development of SSR markers based on full-length transcriptome sequencing and genetic diversity analysis of Halogeton glomeratus

以盐生草全长转录组数据为基础,用MISA在线软件对盐生草转录组水平SSR位点进行搜索,共鉴定到29640个SSR位点,每SSR的发生频率为4.93 kb。SSR种类包含1~6核苷酸重复类型,重复次数主要为4~20次,其中,三核苷酸重复单位最多,占38.25%;四核苷酸重复单位类型最少,仅占3.26%。鉴定到的327种SSR重复类型中,A/T、AG/CT、ATC/GAT、AAG/CTT重复类型出现次数较多。进一步地,对甘肃18个不同生态点盐生草材料进行SSR标记位点的开发及遗传多样性分析。从检测到的29640个SSR标记中选择218对标记进行多态性筛选,共筛选到多态性较高的33对标记,这些标记共检测得到199个等位基因位点,等位基因数(AN)为3~13个,平均为6.03个;基因多样性指数(GD)为0.583~0.869,平均为0.698;基因型数量(GN)为2~13,平均值为5.88;多态性信息含量(PIC)值为0.527~0.856,平均值为0.623。聚类分析结果表明,18个不同生态点盐生草的遗传相似系数(GS)为0.528~0.859,平均值为0.683。在GS为0.68处,可将供试材料划分为四大类。本研究为盐生草种质资源开发及利用提供了参考依据。

In this study,we used MISA online software to search for SSR loci at the transcriptome level of Halogeton glomeratus based on the full-length transcriptome data of H.glomeratus.A total of 29640 SSR loci were identified.The frequency of each SSR locus was 4.93 kb.SSR types included one-to six-nucleotide repeats,with the number of repeats ranging from four to 20,of which the trinucleotide repeats were the highest,at 38.25% of the total.Tetranucleotide repeats were the least common,comprising only 3.26%.A total of 327 SSR repeat types were identified,the frequencies of A/T,AG/CT,ATC/GAT and AAG/CTT repeat types were much higher than others.Further,SSR markers were developed and the genetic diversity of H.glomeratus from 18 different ecological sites in Gansu was analyzed.From the available 29640 SSR markers,218 pairs of markers were identified as candidates for polymorphism screening,and 33 pairs of markers with high polymorphism were screened.A total of 199 alleles were detected for these markers,with the number of alleles varying from three to 13 and an average of 6.03.The gene diversity index(GD) ranged from 0.583 to 0.869 with an average of 0.698;the number of genotypes(GN)ranged from two to 13 with an average of 5.88;the polymorphism information content value varied from 0.527 to 0.856 with an average of 0.623.Cluster analysis indicated that the genetic similarity coefficient(GS)of H.glomeratus ranged from 0.528 to 0.859 with an average of 0.683 for 18 different ecological sites in Gansu.At a GS of 0.68,the tested materials were divided into four categories.This study provides reference data for the development and utilization of H.glomeratus germplasm resources.