基于SSR技术的古银杏群体遗传结构分析
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摘要
银杏(Ginkgo biloba L.)作为裸子植物银杏纲中现存的唯一树种,素有"活化石"之称,同时又集叶、果、材、观赏用于一身,具有较高的经济和科研价值。为探究分布在我国5个省市7个地区的银杏古树的遗传多样性水平和群体遗传结构,本研究利用21个多态性SSR标记对7个古树群体共计214个古树样本进行了研究,共扩增出137个等位基因。结果表明,银杏表现出较高的遗传多样性水平(He=0.764),其中,湖北省境内的安陆(AL)、京山(JS)和随州(SZ)银杏古树群体的遗传多样性水平高于其他地区。银杏的变异主要存在于群体内,群体间的分化系数为9.4%(Fst=0.094),这可能与群体间较多的基因流有关(Nm=2.405)。通过对7个银杏古树群体的STRUCTURE、PCA和系统进化分析,结果均显示7个群体可明显区分为3类,其中,诸暨(ZJ)群体与其他群体表现出了明显的遗传分化。21个SSR位点在群体中均显著偏离Hardy-Weinberg平衡,人为干扰导致雌雄比例失衡可能是其重要原因。古银杏资源丰富的遗传多样性为今后利用提供了物质基础,应充分给予保护,尤其应重视雄银杏古树的保护。
Ginkgo biloba L.,a unique species in Ginkgopside and known as the "living fossil",has high value on economic and scientific research due to its wide usage with fruit,leaf,wood and ornament. In this study,21 polymorphic SSR primers were used to analyze the genetic diversity and population genetic structure of G. biloba distributed in seven regions of China,with 137 alleles being detected in 214 individuals from seven ancient G. biloba populations. We observed high levels of genetic diversity( He= 0.764) in the G. biloba populations,and the populations with highest level of genetic diversity came from Anlu( AL),Jingshan( JS) and Suizhou( SZ).The genetic differentiation coefficient( Fst= 0.094) indicated that the most of the genetic variation were within population because of the high gene flow among populations( Nm= 2.405). The seven populations were clustered into three major groups by STRUCTURE,PCA and phylogenetic analysis,with the population from Zhuji( ZJ) being significantly different from the others. The genotype frequencies of 21 SSR loci significantly deviated from the Hardy-Weinberg equilibrium within all populations. The imbalance of sex ratio caused by human interference might be the main reason. The abundant resources of ancient G. biloba in genetic diversity provided material basis for its use,and should be given priority in protection,especially for the male individuals of ancient G. biloba.
Ginkgo biloba L.,a unique species in Ginkgopside and known as the "living fossil",has high value on economic and scientific research due to its wide usage with fruit,leaf,wood and ornament. In this study,21 polymorphic SSR primers were used to analyze the genetic diversity and population genetic structure of G. biloba distributed in seven regions of China,with 137 alleles being detected in 214 individuals from seven ancient G. biloba populations. We observed high levels of genetic diversity( He= 0.764) in the G. biloba populations,and the populations with highest level of genetic diversity came from Anlu( AL),Jingshan( JS) and Suizhou( SZ).The genetic differentiation coefficient( Fst= 0.094) indicated that the most of the genetic variation were within population because of the high gene flow among populations( Nm= 2.405). The seven populations were clustered into three major groups by STRUCTURE,PCA and phylogenetic analysis,with the population from Zhuji( ZJ) being significantly different from the others. The genotype frequencies of 21 SSR loci significantly deviated from the Hardy-Weinberg equilibrium within all populations. The imbalance of sex ratio caused by human interference might be the main reason. The abundant resources of ancient G. biloba in genetic diversity provided material basis for its use,and should be given priority in protection,especially for the male individuals of ancient G. biloba.
引文
曹福亮. 2007.中国银杏志.北京:中国林业出版社.
曹福亮,花喆斌,汪贵斌,等.2008.野生银杏资源群体遗传多样性的RAPD分析.浙江林学院学报,25(1):22-27.
葛永奇,邱英雄,丁炳扬,等.2003.孑遗植物银杏群体遗传多样性的ISSR分析.生物多样性,11(4):276-287.
龚维.2007.孑遗植物银杏的分子亲缘地理学研究(博士学位论文).杭州:浙江大学.
郭新安.2006.湖北省三大区域群体银杏古树遗传多样性的ISSR分析(硕士学位论文).武汉:华中农业大学.
李建文,刘正宇,谭杨梅,等.1999.金佛山银杏的调查研究.林业科学研究,12(2):90-94.
骆鹏,曹玉婷,莫家兴,等.2017.柳杉无性系指纹图谱的构建及遗传多样性分析.南京林业大学学报:自然科学版,41(4):191-196.
沈永宝,施季森.2001.银杏、板栗不同组织DNA的提取.南京林业大学学报:自然科学版,25(6):80-82.
王利,陈述,董金伟,等.2010.古银杏种质亲缘关系及遗传多样性的ISSR分析.经济林研究,28(3):20-24.
王星星,周琦,陶园园,等.2017.48个果用银杏品种SSR指纹图谱构建与遗传多样性分析.分子植物育种,15(5):1963-1970.
王萱,刘晓静,邢世岩,等.2016.中国部分古银杏资源遗传多样性的AFLP分析及核心种质的构建.园艺学报,43(2):249-260.
王紫阳,成彦丽,殷云龙,等.2015.中山杉EST-SSR引物通用性及基因分型检测.分子植物育种,13(7):1631-1638.
吴岐奎,邢世岩,范圣明,等.2014.基于AFLP的垂乳银杏种质遗传多样性分析.西南林业大学学报,34(3):7-11.
向应海,鲁新成,向碧霞.1997.贵州省务川县银杏古森林残存群落考证初报.贵州科学,15(4):239-244.
许玉兰,蔡年辉,陈诗,等.2016.云南松天然群体遗传变异与生态因子的相关性.生态学杂志,35(7):1767-1775.
闫小玲.2010.基于cpD NA单倍型和SSR分析的银杏群体遗传结构和谱系地理学研究(博士学位论文).杭州:浙江大学.
张金池,贺娜,靳蓉,等.2016.不同地理漆树种源的遗传多样性AFLP分析.中国生漆,35(2):45-52.
张玲,焦培培,李志军.2012.中国新疆灰叶胡杨群体遗传多样性的SSR分析.生态学杂志,31(11):2755-2761.
左雄中.2005.湖北省银杏树资源研究(硕士学位论文).武汉:华中农业大学.
Boys J,Cherry M,Dayanandan S.2005.Microsatellite analysis reveals genetically distinct populations of red pine(Pinus resinosa,Pinaceae).American Journal of Botany,92:833-841.
Evanno G,Regnaut S,Goudet J.2005.Detecting the number of clusters of individuals using the software STRUCTURE:Asimulation study.Molecular Ecology,14:2611-2620.
Falush D,Stephens M,Pritchard JK.2003.Inference of population structure using multilocus genotype data:Linked loci and correlated allele frequencies.Genetics,164:1567-1587.
Fan XX,Shen L,Zhang X,et al.2004.Assessing genetic diversity of Ginkgo biloba L.(Ginkgoaceae)populations from China by RAPD markers.Biochemical Genetics,42:269-278.
Gong W,Zeng Z,Chen YY,et al.2008a.Glacial refugia of Ginkgo biloba and human impact on its genetic diversity:Evidence from chloroplast DNA.Journal of Integrative Plant Biology,50:368-374.
Hintsteiner WJ,Van Loo M,Neophytou C,et al.2018.The geographic origin of old Douglas-fir stands growing in Central Europe.European Journal of Forest Research,137:447-461.
Kuddus RH,Kuddus NN,Dvorchik I.2002.DNA polymorphism in the living fossil Ginkgo biloba from the eastern United States.Genome,45:8-12.
Liu C,Qi X,Song L,et al.2018.Species identification,genetic diversity and population structure of sweet cherry commercial cultivars assessed by SSRs and the gametophytic self-incompatibility locus.Scientia Horticulturae,237:28-35.
Nybom H.2004.Comparison of different nuclear DNA markers for estimating intraspecific genetic diversity in plants.Molecular Ecology,13:1143-1156.
Pritchard JK,Stephens M,Rosenberg NA,et al.2000.Association mapping in structured populations.The American Journal of Human Genetics,67:170-181.
Pritchard JK,Stephens M,Donnelly P.2000.Inference of population structure using multilocus genotype data.Genetics,155:945-959.
Wang L,Xing SY,Yang KQ,et al.2006.Genetic relationships of ornamental cultivars of Ginkgo biloba analyzed by AFLPtechniques.Acta Genetica Sinica,33:1020-1026.
Wang ZS,Sun HQ,Wang HW,et al.2010.Isolation and characterization of 50 nuclear microsatellite markers for Cathaya argyrophylla,a Chinese endemic conifer.American Journal of Botany,97:e117-e120.
Yang H,Zhang R,Jin G,et al.2016.Assessing the genetic diversity and genealogical reconstruction of cypress(Cupressus funebris Endl.)breeding parents using SSR markers.Forests,7:160.
Zhou Q,Wang XX,Xu M,et al.2016.Development and characterization of novel microsatellite markers for Ginkgo biloba using 454 pyrosequencing.Genetics and Molecular Research,15,doi:10.4238/gmr.15017385.
曹福亮,花喆斌,汪贵斌,等.2008.野生银杏资源群体遗传多样性的RAPD分析.浙江林学院学报,25(1):22-27.
葛永奇,邱英雄,丁炳扬,等.2003.孑遗植物银杏群体遗传多样性的ISSR分析.生物多样性,11(4):276-287.
龚维.2007.孑遗植物银杏的分子亲缘地理学研究(博士学位论文).杭州:浙江大学.
郭新安.2006.湖北省三大区域群体银杏古树遗传多样性的ISSR分析(硕士学位论文).武汉:华中农业大学.
李建文,刘正宇,谭杨梅,等.1999.金佛山银杏的调查研究.林业科学研究,12(2):90-94.
骆鹏,曹玉婷,莫家兴,等.2017.柳杉无性系指纹图谱的构建及遗传多样性分析.南京林业大学学报:自然科学版,41(4):191-196.
沈永宝,施季森.2001.银杏、板栗不同组织DNA的提取.南京林业大学学报:自然科学版,25(6):80-82.
王利,陈述,董金伟,等.2010.古银杏种质亲缘关系及遗传多样性的ISSR分析.经济林研究,28(3):20-24.
王星星,周琦,陶园园,等.2017.48个果用银杏品种SSR指纹图谱构建与遗传多样性分析.分子植物育种,15(5):1963-1970.
王萱,刘晓静,邢世岩,等.2016.中国部分古银杏资源遗传多样性的AFLP分析及核心种质的构建.园艺学报,43(2):249-260.
王紫阳,成彦丽,殷云龙,等.2015.中山杉EST-SSR引物通用性及基因分型检测.分子植物育种,13(7):1631-1638.
吴岐奎,邢世岩,范圣明,等.2014.基于AFLP的垂乳银杏种质遗传多样性分析.西南林业大学学报,34(3):7-11.
向应海,鲁新成,向碧霞.1997.贵州省务川县银杏古森林残存群落考证初报.贵州科学,15(4):239-244.
许玉兰,蔡年辉,陈诗,等.2016.云南松天然群体遗传变异与生态因子的相关性.生态学杂志,35(7):1767-1775.
闫小玲.2010.基于cpD NA单倍型和SSR分析的银杏群体遗传结构和谱系地理学研究(博士学位论文).杭州:浙江大学.
张金池,贺娜,靳蓉,等.2016.不同地理漆树种源的遗传多样性AFLP分析.中国生漆,35(2):45-52.
张玲,焦培培,李志军.2012.中国新疆灰叶胡杨群体遗传多样性的SSR分析.生态学杂志,31(11):2755-2761.
左雄中.2005.湖北省银杏树资源研究(硕士学位论文).武汉:华中农业大学.
Boys J,Cherry M,Dayanandan S.2005.Microsatellite analysis reveals genetically distinct populations of red pine(Pinus resinosa,Pinaceae).American Journal of Botany,92:833-841.
Evanno G,Regnaut S,Goudet J.2005.Detecting the number of clusters of individuals using the software STRUCTURE:Asimulation study.Molecular Ecology,14:2611-2620.
Falush D,Stephens M,Pritchard JK.2003.Inference of population structure using multilocus genotype data:Linked loci and correlated allele frequencies.Genetics,164:1567-1587.
Fan XX,Shen L,Zhang X,et al.2004.Assessing genetic diversity of Ginkgo biloba L.(Ginkgoaceae)populations from China by RAPD markers.Biochemical Genetics,42:269-278.
Gong W,Zeng Z,Chen YY,et al.2008a.Glacial refugia of Ginkgo biloba and human impact on its genetic diversity:Evidence from chloroplast DNA.Journal of Integrative Plant Biology,50:368-374.
Hintsteiner WJ,Van Loo M,Neophytou C,et al.2018.The geographic origin of old Douglas-fir stands growing in Central Europe.European Journal of Forest Research,137:447-461.
Kuddus RH,Kuddus NN,Dvorchik I.2002.DNA polymorphism in the living fossil Ginkgo biloba from the eastern United States.Genome,45:8-12.
Liu C,Qi X,Song L,et al.2018.Species identification,genetic diversity and population structure of sweet cherry commercial cultivars assessed by SSRs and the gametophytic self-incompatibility locus.Scientia Horticulturae,237:28-35.
Nybom H.2004.Comparison of different nuclear DNA markers for estimating intraspecific genetic diversity in plants.Molecular Ecology,13:1143-1156.
Pritchard JK,Stephens M,Rosenberg NA,et al.2000.Association mapping in structured populations.The American Journal of Human Genetics,67:170-181.
Pritchard JK,Stephens M,Donnelly P.2000.Inference of population structure using multilocus genotype data.Genetics,155:945-959.
Wang L,Xing SY,Yang KQ,et al.2006.Genetic relationships of ornamental cultivars of Ginkgo biloba analyzed by AFLPtechniques.Acta Genetica Sinica,33:1020-1026.
Wang ZS,Sun HQ,Wang HW,et al.2010.Isolation and characterization of 50 nuclear microsatellite markers for Cathaya argyrophylla,a Chinese endemic conifer.American Journal of Botany,97:e117-e120.
Yang H,Zhang R,Jin G,et al.2016.Assessing the genetic diversity and genealogical reconstruction of cypress(Cupressus funebris Endl.)breeding parents using SSR markers.Forests,7:160.
Zhou Q,Wang XX,Xu M,et al.2016.Development and characterization of novel microsatellite markers for Ginkgo biloba using 454 pyrosequencing.Genetics and Molecular Research,15,doi:10.4238/gmr.15017385.