基于RAD-seq的苦草属(Vallisneria)SSR标记开发

Development of Polymorphic SSR Markers in Vallisneria Based on RAD-seq

苦草(Vallisneria)隶属于水鳖科(Hydrocharitaceae),是水域生态修复的先锋物种。为了对苦草属植物进行比较全面的SSR信息分析,本研究基于RAD-seq (restriction-site associated DNA sequencing)简化基因组测序技术获得了苦草的简化基因组序列信息,并开发了SSR分子标记与引物设计。在所得序列中共检测到366个SSR位点,成功设计出引物的有355个,其中二碱基重复基序数量最多,占总数的59.56%,通过筛选和验证,最终确定了23对具有多态性的SSR引物。Genepop软件分析结果显示,这23个位点的等位基因数均值为3.26,多态性高且不连锁(P<0.05);4个位点在多数群体中偏离哈迪温伯格平衡(P<0.01)且纯合子与杂合子比例相当(观测杂合度均值0.460),近交系数高(Fis均值0.880),可能是因为单个群体采样集中,且由于苦草属植物同时具备无性、有性两种繁殖方式中的无性繁殖所致。

Vallisneria belongs to Hydrocharitaceae, which is a pioneer species of ecological restoration in waters.In order to carry out a more comprehensive SSR analysis of Vallisneria, we used the restriction-site associated DNA sequencing(RAD-seq) technology to analyze Simple Sequence Repeats(SSR) information of Vallisneria,SSR markers and primer of Vallisneria were developed based on RAD-seq data. A total of 366 SSR loci were detected in the obtained sequences. Primers of 355 loci were designed successfully, and the two base repeat type SSR loci were the largest(59.56%). Finally, we confirmed 23 pairs of polymorphic SSR primers after the screening and validation. The analysis results by Genepop software showed that the mean number of alleles of the 23 loci is 3.26, and these loci do not link to each other(P<0.05). Four loci deviate from HWE(P<0.01) and the number of heterozygous roughly the same as that of homozygotes(observed heterozygosity mean of 0.460), inbreeding coefficient is high(mean of 0.880). Which could be caused by take sample too closely in the same sampling, and Vallisneria have a combination of generative propagation and clone.