黄芩基因组SSR分子标记的开发及遗传多样性分析

Development of microsatellites and genetic diversity analysis of Scutellaria baicalensis Georgi using genomic-SSR markers

本文通过生物信息学方法对黄芩基因组序列进行搜索,共得到12 775条SSR(simple sequence repeat)序列。黄芩基因组SSR重复主要以二核苷酸(68.32%)为主,其次为三核苷酸(18.63%);主要重复基序类型为CT/GA、TTC/GAA。通过SSR-PCR扩增,共筛选出9对扩增产物稳定性好,多态性及清晰度高的引物用于10个不同产地共50份黄芩材料的遗传多样性分析。结果显示,9对引物共检测出68个等位基因,平均每个SSR位点等位基因数是7个,有效等位基因数为3。He(expected heterozygosities)值为0.6,远远高于双子叶植物平均水平;PIC(polymorphism information content)平均值为0.72,大于0.5;Shannon’s信息指数为1.32,证明所收集的黄芩种质资源具有较高的遗传多样性。种间遗传分化系数(Gst)为0.131,即13.1%的遗传变异存在于居群间,86.9%的遗传变异存在于居群内。聚类分析结果表明,10个不同产地黄芩可分成两大类,但其与地理分布无显著关系。

A total of 12 775 SSRs were identified from Scutellaria baicalensis Georgi genomic database, accounting for 2.56% of the total genomic sequences. The result showed that S. baicalensis SSRs were based on 68.32% dinucleotide and 18.63% trinucleotide repeats; CT/GA and TTC/GAA were predominant in the dinucleotide motifs and the trinucleotide motifs respectively. Nine primers were selected to produce highly reproducible SSR bands and were used in studying the genetic diversity of S. baicalensis, 50 individuals from ten populations. 68 SSR polymorphic loci were detected, these loci were polymorphic and displayed 4 to 12 alleles per locus with a mean number of 7; the effect number of alleles was 3. Expected heterozygosities were 0.6 and were far more greater than the average in dicotyledonous plants. PIC（polymorphism information content） was 0.72, Shannon＇s information index was 1.32, these all proved that S. baicalensis had a high genetic diversity in general. Genetic differentiation among population Gst was 0.131, genetic variation among population accounted for 13.1% and genetic variation within population accounted for 86.9%. The cluster analysis showed that 10 populations S. Baicalensis were classified into 2 groups, but it was not associated with geographical distribution.