三七基因组SSR位点分析和多态性引物开发

Analysis of SSR Loci Information in Panax notoginseng Genomes and Polymorphic Primers Development

本研究通过分析三七(Panax notoginseng)基因组中简单重复序列(simple sequence repeats,SSRs)位点信息,对基因组中SSR位点的分布特征进行描述,并开发多态性引物,为评价三七遗传多样性和群体结构提供理论依据。利用MISA软件对重新组装的三七基因组进行SSR位点搜索,primer3设计引物。用随机合成的200对引物,在16个三七单株中进行PCR扩增,来筛选具有多态性的引物。在去除冗余序列后组装得到2.39 Gb大小的三七基因组中总共识别到314 060个SSR位点,SSR分布频率为0.13/kb,其中占主导地位的是二核苷酸重复基序,占所有重复基序类型的68.55%,其次是三核苷酸56 250(17.91%)和单核苷酸22 475(7.16%)。在二核苷酸为主的重复类型中,出现频率最高的是AT/AT重复基序占所有二核苷酸重复的63.66%,最低的是CG/CG重复基序占0.15%。同时,在单核苷酸重复中出现频率最高的也是A/T重复类型(79.01%)。经过多态性筛选最终得到41对多态性较好的引物,PIC值范围为0.11~0.78,平均值为0.46。本研究获得的大量SSR位点信息为三七全基因组SSR标记的开发,三七分子标记辅助育种以及遗传多样性分析提供方便。

The analysis of simple sequence repeat（simple sequence repeats; SSRs） site information in the genome of P. notoginseng was used to describe the distribution characteristics of genome SSR loci, and to develop polymorphic primers to evaluate the genetic diversity and population structure of P notoginseng. MISA software was used to search for the SSR loci of the assembled genome of P. notoginseng. Primers were designed by Primer3, and 200 pairs of primers randomly synthesized were used to amplify PCR in 16 P. notoginseng plants to screen primers with polymorphism. Totally, 314, 060 SSR loci were identified, with an average distance of 0.13 kb between each loci. A large proportion of the SSRs included di-, tri-and mono-repeat motifs, which accounted for 68.55%, 17.91% and 7.16% of all repeats, respectively. Dinucleotide is the main type of repeated categories, the highest frequency of occurrence was AT/AT which accounted for 63.66% in total di-repeats, whereas the lowest frequency of occurrence was CG/CG（0.15%）. A/T was the most common in mononucleotide repeat（79.01%）. After polymorphic screening, we obtained 41 primers with preferable polymorphic primers. The PIC value was 0.11~0.78, with an average of 0.46. Plenty of the SSR locus information and SSR markers were provided in this research, not only provide valuable resources for the development of SSR markers in P. notoginseng, but also provide convenience for P. notoginseng marker-assisted breeding and genetic diversity analysis.