基于SNP标记的不同居群文山三七遗传结构分析  

Genetic Structure Analysis of Wenshan Panax notoginseng Based on SNP Markers

作　　者：王灿 黄玉玲 杨清松 彭翠仙 李玲 赵大伟[1] 陶永宏[1] Wang Can;Huang Yuling;Yang Qingsong;Peng Cuixian;Li Ling;Zhao Dawei;Tao Yonghong(Wenshan Academy of Agricultural Sciences,Wenshan 663000,China)

机构地区：[1]云南省文山州农业科学院,云南文山663000

出　　处：《中国野生植物资源》2023年第11期57-63,共7页Chinese Wild Plant Resources

基　　金：云南省中青年学术和技术带头人后备人才项目(202105AC160003);文山州科技领军人才项目(WS-KJLJ0009);道地药材(三七、草果)林下生态高效栽培关键技术集成示范项目(202304BP090026)。

摘　　要：目的:研究三七居群间、居群内及其近缘种植物的遗传背景差异,为三七种质资源的有效利用和生物育种提供依据。方法:以25份文山三七和3份近缘种材料进行简化基因组测序,并进行遗传结构分析。结果:测序共获得115.64 Gb数据,比对率为70.03%~99.45%。此外在杂合率比较中,三七杂合率最高,范围在5.6%~12.9%,平均值为10.02%;而在近缘种中屏边三七是1.3%、姜状三七是6.2%、狭叶竹节参是5.1%,其杂合率低于三七。高质量单核苷酸多态性(SNP)位点1968786个,其中约5.30%(109188)位于外显子区域。SNP功能注释显示2548个(约占2.333%)具有终止子获得功能。进化树及群体遗传结构分析表明屏边三七单独聚为一类,姜状三七和狭叶竹节参聚为一类,文山三七单独聚为一类。结论:文山三七及其近缘种遗传距离较远,尤其是屏边三七与文山三七遗传距离最远,不同地区三七居群间遗传背景差异不显著,遗传分化水平程度较低,这为三七资源收集、鉴定和生物育种等提供新的见解。此外位于外显子区域的109188个SNP具有开发成功能基因标记的潜力,同时SNP产生的2548处终止子获得可能对三七基因功能如生物抗性及皂苷合成等研究具有重要意义。Objective:To study the genetic background of Panax notoginseng among population,within population and closely related plants,and provide a basis for the effective utilization and biological breeding of P.notoginseng germplasm resources.Methods:Genotyping-by-Sequencing and genetic structure analysis were performed on 25 Wenshan P.notoginseng samples and 3 closely related species.Results:The results showed that a total of 115.64 Gb of data were obtained by sequencing,with a comparison rate of 70.03%to 99.45%.In addition,the heterozygosity rate of P.notoginseng was higher,ranging from 5.6%~12.9%,with an average of 10.02%.Among closely related species,the heterozygosity of P.stipu⁃leanatus was 1.3%,P.zingiberensis was 6.2%,and P.japonicas var.angustifolius was 5.1%,which was lower than that of P.notoginseng.There were 1968786 high-quality single nucleotide polymorphisms(SNP)sites,of which about 5.30%(109188)were located in the exonic region.The functional annotation of SNP showed that 2548(approximately 2.333%)had terminator acquisition function.Phylogenetic tree and population genetic structure analysis showed that P.stipuleanatus was clustered into one group,P.zingiberensis and P.japonicas var.angustifolius were clustered into one group,and P.notoginseng was clustered into one group.Conclusion:The genetic distance between P.notoginseng and its related species was far,especially between P.stipuleanatus and P.notoginseng.The genetic background difference between P.notoginseng populations in different regions was not significant,and the genetic differentiation level was low,which would provide new insights for resource collection,identification and biological breeding of P.notoginseng.In addition,109188 SNPs located in the exon region have the potential to develop successful genetic markers,and the acquisition of 2548 terminators generated by SNPs may be of great significance for research on gene functions of P.notoginseng such as biological resistance and saponin synthesis.

关 键 词：三七 单核苷酸多态性 遗传结构 

分 类 号：Q945[生物学—植物学]