珍稀濒危植物卵叶羌活自然群体遗传变异的地理分布研究
|
摘要
目的检测珍稀濒危药用植物卵叶羌活自然群体遗传变异的地理分布式样和结构。方法利用二代简化基因组测序技术开发卵叶羌活的微卫星分子标记(SSR)引物,并对覆盖卵叶羌活整个自然地理分布范围的群体样品进行遗传多态性分析。结果通过基因组de novo组装共获得了780条含SSR位点的基因片段序列;筛选出10对具有较高多态性的SSR标记引物,对卵叶羌活整个自然地理分布区的6个群体共105个样品进行遗传变异分析,发现每条引物的等位基因数(No)在1～6(平均值为3.530);每个群体的平均观测杂合度范围在0.305～0.457,说明卵叶羌活具有中到高度水平的遗传变异。基于Bayesian的群体结构分析表明,卵叶羌活的6个地理群体可以分为2个大的遗传分组,两组之间存在着一定程度的基因交流或遗传渐渗。结论二代高通量简化基因组测序技术极大丰富了珍稀濒危植物卵叶羌活的SSR数据库,其自然群体遗传变异式样可能与该物种较长的进化历史以及不同地理群体之间长距离的花粉扩散有关。
Objective In order to determine the geographic distribution of genetic variation and structure of natural populations in an endangered and rarely medicinal herb Notopterygium forbesii var. oviforme. Methods The primers of polymorphic microsatellite molecular markers of N. forbesii var. oviforme were firstly developed using the next generation reduced-representation sequencing technology. Then, the genetic polymorphisms of the whole geographical distributional population samples of N. forbesii var. oviforme were investigated based on the polymorphic SSRs. Results A total of 780 SSR-containing DNA sequences were obtained by genome De novo assembly. Ten pairs of polymorphic SSR primers were developed and used to analyze the genetic variability of 105 individuals from six natural populations that covered the entire geographical distributions of N. forbesii var. oviforme. The results showed that the number of observed alleles(No) per locus varied between 1 and 6(mean = 3.530). The mean observed heterozygosity(Ho) per population ranged from 0.305 to 0.457. These finds suggested that N. forbesii var. oviforme had the moderate to high level of genetic variability. Bayesian clustering analyses demonstrated that the six natural populations of N. forbesii var. oviforme have formed two clear genetic lineages. The gene flow and/or genetic introgression have occurred between these two groups. Conclusion The next generation reduced-representation sequencing technology largely enriched SSRs database of N. forbesii var. oviforme. The geographic distribution patterns of genetic variations of N. forbesii var. oviforme may be related to the long evolutionary history of species and pollen dispersal of long distance among different natural populations.
Objective In order to determine the geographic distribution of genetic variation and structure of natural populations in an endangered and rarely medicinal herb Notopterygium forbesii var. oviforme. Methods The primers of polymorphic microsatellite molecular markers of N. forbesii var. oviforme were firstly developed using the next generation reduced-representation sequencing technology. Then, the genetic polymorphisms of the whole geographical distributional population samples of N. forbesii var. oviforme were investigated based on the polymorphic SSRs. Results A total of 780 SSR-containing DNA sequences were obtained by genome De novo assembly. Ten pairs of polymorphic SSR primers were developed and used to analyze the genetic variability of 105 individuals from six natural populations that covered the entire geographical distributions of N. forbesii var. oviforme. The results showed that the number of observed alleles(No) per locus varied between 1 and 6(mean = 3.530). The mean observed heterozygosity(Ho) per population ranged from 0.305 to 0.457. These finds suggested that N. forbesii var. oviforme had the moderate to high level of genetic variability. Bayesian clustering analyses demonstrated that the six natural populations of N. forbesii var. oviforme have formed two clear genetic lineages. The gene flow and/or genetic introgression have occurred between these two groups. Conclusion The next generation reduced-representation sequencing technology largely enriched SSRs database of N. forbesii var. oviforme. The geographic distribution patterns of genetic variations of N. forbesii var. oviforme may be related to the long evolutionary history of species and pollen dispersal of long distance among different natural populations.
引文
[1]单人骅,佘孟兰.中国植物志[M].北京:科学出版社,1979.
[2]王幼平,溥发鼎,王萍莉,等.中国特有属--羌活属的系统分类研究[J].云南植物研究,1996,18(4):424-430.
[3]中国科学院《中国植物志》编辑委员会.中国植物志[M].北京:科学出版社,1976.
[4]江纪武.药用植物辞典[M].天津:天津科学技术出版社,2005.
[5]Booy G,Hendriks R J J,Smulders M J M,et al.Genetic diversity and the survival of populations[J].Plant Biol,2000,2(4):379-395.
[6]Hamrick J L,Blanton H M,Hamrick K J.Genetic structure of geographically marginal populations of ponderosa pine[J].Am J Bot,2010,76(11):1559-1568.
[7]Jia Y,Liu M L,Yue M,et al.Comparative transcriptome analysis reveals adaptive evolution of Notopterygium incisum and Notopterygium franchetii,two high-alpine herbal species endemic to China[J].Molecules,2017,22(7):1158-1165.
[8]He Y,Zhao Z,Shi Y Y,et al.Novel microsatellite markers for Notopterygium oviforme(Apiaceae),an endangered endemic herb to China[J].Ann Bot Fennici,2017,54(4/6):423-427.
[9]孙辉,蒋舜媛,周毅,等.药用植物羌活现状及其民族植物学调查[J].世界科技研究与发展,2004,(6):42-44.
[10]Yang J,Yue M,Niu C,et al.Comparative analysis of the complete chloroplast genome of four endangered herbals of Notopterygium[J].Genes,2017,8(4):124.
[11]孙稚颖,陈士林,姚辉,等.基于ITS2序列的羌活及其混伪品的DNA条形码鉴定[J].中草药,2012,43(3):568-571.
[12]杨路存,刘何春,周学丽,等.羌活不同地理种群cpDNA trnT-trnL多态性分析[J].中草药,2015,46(22):3390-3395.
[13]杨路存,周国英,聂学敏.濒危植物宽叶羌活天然居群cp DNA非编码区多态性分析[J].西北植物学报,2013,33(8):1535-1543.
[14]Shahzad K,Jia Y,Chen F L,et al.Effects of mountain uplift and climatic oscillations on phylogeography and species divergence in four endangered Notopterygium herbs[J].Frontiers Plant Sci,2017,8:1929-1934.
[15]Doyle J J,Doyle J L.A rapid DNA isolation procedure for small quantities of fresh leaf tissue[J].Phytochem Bull,1987,19:11-15.
[16]Kofler R,Schl?tterer C,Lelley T.Sci Ro Ko:A new tool for whole genome microsatellite search and investigation[J].Bioinformatics,2007,23(13):1683-1685.
[17]Clarke K R,Gorley R N.PRIMER v7:User Manual/Tutorial,PRIMER-E[D].Plymouth:University of Gdańsk,2015.
[18]Peakall R,Smouse P E.GenAlEx 6.5:Genetic analysis in excel.Population genetic software for teaching and research-an update[J].Bioinformatics,2012,28(19):2537-2539.
[19]Evanno G,Regnaut S,Goudet J.Detecting the number of clusters of individuals using the software STRUCTURE:A simulation study[J].Mol Ecol,2005,14(8):2611-2620.
[20]Earl D A.Structure harvester:A website and program for visualizing STRUCTURE output and implementing the Evanno method[J].Conser Genet Resour,2012,4(2):359-361.
[21]Rosenberg N A.Distruct:A program for the graphical display of population structure[J].Mol Ecol Resour,2004,4(1):137-138.
[22]徐敏,吴生,刘小霞,等.秦岭地区华中五味子SSR遗传多样性分析[J].中药材,2013,36(8):1215-1218.
[23]赵冰,徐曼,司国臣,等.秦岭秀雅杜鹃野生种群遗传多样性和遗传分化的AFLP分析[J].应用生态学报,2012,23(11):2983-2990.
[2]王幼平,溥发鼎,王萍莉,等.中国特有属--羌活属的系统分类研究[J].云南植物研究,1996,18(4):424-430.
[3]中国科学院《中国植物志》编辑委员会.中国植物志[M].北京:科学出版社,1976.
[4]江纪武.药用植物辞典[M].天津:天津科学技术出版社,2005.
[5]Booy G,Hendriks R J J,Smulders M J M,et al.Genetic diversity and the survival of populations[J].Plant Biol,2000,2(4):379-395.
[6]Hamrick J L,Blanton H M,Hamrick K J.Genetic structure of geographically marginal populations of ponderosa pine[J].Am J Bot,2010,76(11):1559-1568.
[7]Jia Y,Liu M L,Yue M,et al.Comparative transcriptome analysis reveals adaptive evolution of Notopterygium incisum and Notopterygium franchetii,two high-alpine herbal species endemic to China[J].Molecules,2017,22(7):1158-1165.
[8]He Y,Zhao Z,Shi Y Y,et al.Novel microsatellite markers for Notopterygium oviforme(Apiaceae),an endangered endemic herb to China[J].Ann Bot Fennici,2017,54(4/6):423-427.
[9]孙辉,蒋舜媛,周毅,等.药用植物羌活现状及其民族植物学调查[J].世界科技研究与发展,2004,(6):42-44.
[10]Yang J,Yue M,Niu C,et al.Comparative analysis of the complete chloroplast genome of four endangered herbals of Notopterygium[J].Genes,2017,8(4):124.
[11]孙稚颖,陈士林,姚辉,等.基于ITS2序列的羌活及其混伪品的DNA条形码鉴定[J].中草药,2012,43(3):568-571.
[12]杨路存,刘何春,周学丽,等.羌活不同地理种群cpDNA trnT-trnL多态性分析[J].中草药,2015,46(22):3390-3395.
[13]杨路存,周国英,聂学敏.濒危植物宽叶羌活天然居群cp DNA非编码区多态性分析[J].西北植物学报,2013,33(8):1535-1543.
[14]Shahzad K,Jia Y,Chen F L,et al.Effects of mountain uplift and climatic oscillations on phylogeography and species divergence in four endangered Notopterygium herbs[J].Frontiers Plant Sci,2017,8:1929-1934.
[15]Doyle J J,Doyle J L.A rapid DNA isolation procedure for small quantities of fresh leaf tissue[J].Phytochem Bull,1987,19:11-15.
[16]Kofler R,Schl?tterer C,Lelley T.Sci Ro Ko:A new tool for whole genome microsatellite search and investigation[J].Bioinformatics,2007,23(13):1683-1685.
[17]Clarke K R,Gorley R N.PRIMER v7:User Manual/Tutorial,PRIMER-E[D].Plymouth:University of Gdańsk,2015.
[18]Peakall R,Smouse P E.GenAlEx 6.5:Genetic analysis in excel.Population genetic software for teaching and research-an update[J].Bioinformatics,2012,28(19):2537-2539.
[19]Evanno G,Regnaut S,Goudet J.Detecting the number of clusters of individuals using the software STRUCTURE:A simulation study[J].Mol Ecol,2005,14(8):2611-2620.
[20]Earl D A.Structure harvester:A website and program for visualizing STRUCTURE output and implementing the Evanno method[J].Conser Genet Resour,2012,4(2):359-361.
[21]Rosenberg N A.Distruct:A program for the graphical display of population structure[J].Mol Ecol Resour,2004,4(1):137-138.
[22]徐敏,吴生,刘小霞,等.秦岭地区华中五味子SSR遗传多样性分析[J].中药材,2013,36(8):1215-1218.
[23]赵冰,徐曼,司国臣,等.秦岭秀雅杜鹃野生种群遗传多样性和遗传分化的AFLP分析[J].应用生态学报,2012,23(11):2983-2990.