基于SSR标记探讨三种金花茶植物的遗传多样性和遗传结构
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摘要
薄叶金花茶、小花金花茶和小瓣金花茶是三种濒危金花茶植物,为了解珍稀濒危植物遗传多样性和遗传结构,该研究利用微卫星标记对他们的7个种群共184个个体进行了遗传多样性和遗传结构分析。结果表明:11个位点共检测到等位基因92个。在物种水平上,小瓣金花茶平均等位基因数(N_A)为3.9、有效等位基因数(N_E)为2.328、观测杂合度(H_o)为0.520、期望杂合度(H_e)为0.501,高于薄叶金花茶和小花金花茶。在种群水平上,有效等位基因数(N_E)在1.788～2.466之间,期望杂合度(H_e)在0.379～0.543之间;种群间遗传分化系数(FST)在0.143 7～0.453 3之间,种群间基因流(N_m)在0.301 5～1.488 9之间。AMOVA分子变异分析显示65.72%的变异存在于种群内。三种金花茶具有较低水平的遗传多样性和高水平的种群间遗传分化。STRUCTURE和PCoA种群遗传结构分析结果将取样种群分为2组,即薄叶金花茶和小花金花茶大部分个体分为一组,小瓣金花茶大部分个体分为一组。现存所有种群应根据实际情况尽快采取就地保护或迁地保护措施。
Camellia chrysanthoides,C. micrantha and C. parvipetala are three endangered Camellia species. In order to understand genetic diversity and genetic structure of endangered species,SSR marker was used to evaluate genetic diversity and genetic structure of 184 individuals from seven populations of these three endangered Camellia species. We obtained 92 alleles from eleven microsatellite markers. On the level of species,the mean number of alleles( 3.9),the effective number of alleles( 2.328),observed heterozygosity( 0.520) and expected heterozygosity( 0.501) of C. parvipetala were higher than C. chrysanthoides and C. micrantha. On the population level,the effective number of alleles ranged from 1.788 to 2.466 and the expected heterozygosity ranged from 0.379 to 0.543. The FSTvalues between each pair of populations ranged from 0.143 7 to 0.453 3,the Nm values ranged from 0.301 5 to 1.488 9. AMOVA suggested that the variation was 65.72% within populations. Low level of genetic diversity and high levels of genetic differentiation were detected for these three Camellia species. The STRUCTURE and PCoA analysis showed that seven populations were clustered into two groups. One group comprised five populations from C. chrysanthoides and C. micrantha,and the other consisted of two populations from C. parvipetala. In situ and ex situ actions should be urgently implemented as soon as possible.
Camellia chrysanthoides,C. micrantha and C. parvipetala are three endangered Camellia species. In order to understand genetic diversity and genetic structure of endangered species,SSR marker was used to evaluate genetic diversity and genetic structure of 184 individuals from seven populations of these three endangered Camellia species. We obtained 92 alleles from eleven microsatellite markers. On the level of species,the mean number of alleles( 3.9),the effective number of alleles( 2.328),observed heterozygosity( 0.520) and expected heterozygosity( 0.501) of C. parvipetala were higher than C. chrysanthoides and C. micrantha. On the population level,the effective number of alleles ranged from 1.788 to 2.466 and the expected heterozygosity ranged from 0.379 to 0.543. The FSTvalues between each pair of populations ranged from 0.143 7 to 0.453 3,the Nm values ranged from 0.301 5 to 1.488 9. AMOVA suggested that the variation was 65.72% within populations. Low level of genetic diversity and high levels of genetic differentiation were detected for these three Camellia species. The STRUCTURE and PCoA analysis showed that seven populations were clustered into two groups. One group comprised five populations from C. chrysanthoides and C. micrantha,and the other consisted of two populations from C. parvipetala. In situ and ex situ actions should be urgently implemented as soon as possible.
引文
CHANG HT,1979.Chrysantha,a section of golden camellias from Cathaysian flora[J].Acta Sci Nat Univ Sunyatseni,18(3):69-74.[张宏达,1979.华夏植物区系的金花茶组[J].中山大学学报(自然科学版),18(3):69-74.]
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CHEN XY,2000.Effects of habitat fragmentation on genetic structure of plant populations and implications for the biodiversity conservation[J].Acta Ecol Sin,20(5):884-892.[陈小勇,2000.生境片断化对植物种群遗传结构的影响及植物遗传多样性保护[J].生态学报,20(5):884-892.]
CIRES E,SAMAIN MS,GOETGHEBEUR P,et al.,2011.Genetic structure in peripheral Western European populations of the endangered species Cochlearia pyrenaica(Brassicaceae)[J].Plant Syst Evol,297(1-2):75-85.
DENG YY,YU XL,LUO YB,2010.The role of native bees on the reproductive success of Camellia oleifera in Hunan Province,Central South China[J].Acta Ecol Sin,30(16):4427-4436.[邓园艺,喻勋林,罗毅波,2010.传粉昆虫对我国中南地区油茶结实和结籽的作用[J].生态学报,30(16):4427-4436.]
DOYLE JJ,1987.A rapid DNA isolation procedure for small quantities of fresh leaf tissue[J].Phytochem Bull,19(1):11-15.
EARL DA,VONHOLDT BM,2012.STRUCTURE HARVEST-ER:A website and program for visualizing STRUCTUREoutput and implementing the Evanno method[J].Conserv Genet Resour,4(2):359-361.
EXCOFFIER L,LAVAL G,SCHNEIDER S,2005.Arlequin(version 3.0):An integrated software package for population genetics data analysis[J].Evol Bioinform Online,1:47-50.
EXCOFFIER L,SMOUSE PE,QUATTRO JM,1992.Analysis of molecular variance inferred from metric distances among DNA haplotypes:Application to human mitochondrial DNArestriction data[J].Genetics,131(2):479-491.
FRANKHAM R,BALLOU JD,BRISCOE DA,2002.Introduction to conservation genetics[M].Cambridge:Cambridge University Press:182-183
GAO QB,LI Y,GENGJI ZM,et al.,2017.Population genetic differentiation and taxonomy of three closely related species of Saxifraga(Saxifragaceae)from southern Tibet and the hengduan mountains[J].Front Plant Sci,8:1325.
GYORGY Z,VOUILLAMOZ JF,LAD NYI M,et al.,2014.Genetic survey of Rhodiola rosea L.populations from the Swiss Alps based on SSR markers[J].Biochem Syst Ecol,54(54):137-143.
HAMRICK JL,GODT MW,1996.Effects oflife history traits on genetic diversity in plant species[J].Philos T R Soc B,351(1345):1291-1298.
HE YL,HE Y,GONG LL,et al.,2017.Population genetic structure and interspecific differentiation between Acer davidii Franchi.and A.morrisonense Hayata(Aceraceae)based on SSR markers[J].Biochem Syst Ecol,71:42-49.
LI XL,LI SC,CHU HJ,et al.,2013.Genetic diversity and population structure of the endangered alpine quillwort Isoetes hypsophila(Isoetaceae)revealed by SSR analysis[J].Biochem Syst Ecol,47(4):11-20.
LIANG SY,1995.Comparison of karyotypes of sect.Chrysantha Chang[J].Guangxi For Sci,24(3):142-144.[梁盛业,1995.金花茶组植物核型比较[J].广西林业科学,24(3):142-144.]
LIUFU YQ,PENG GQ,LU YB,et al.,2014.Development and characterization of 38 microsatellite markers for Camellia flavida based on transcriptome sequencing[J].Conserv Genet Resour,6(4):1007-1010.
LIU Y,YANG S,JI P,et al.,2012.Phylogeography of Camellia taliensis(Theaceae)inferred from chloroplast and nuclear DNA:Insights into evolutionary history and conservation[J].BMC Evol Biol,12(1):92.
LU YB,2015.The population genetic structure of Camellia flavida Chang[D].Guilin:Guangxi Normal University:22-23.[卢永彬,2015.淡黄金花茶种群遗传结构研究[D].桂林:广西师范大学:22-23.]
LU YB,LIUFU YQ,PENG GQ,et al.,2014.Development of21 microsatellite primers for Camellia pingguoensis(Theaceae)using 454 sequencing[J].Conserv Genet Resour,6(3):791-793.
MA Q,DU YJ,CHEN N,et al.,2015.Phylogeography of Davidia involucrata(Davidiaceae)Inferred from cp DNA Haplotypes and n SSR Data[J].Syst Bot,40(3):796-810.
MENG FJ,LIU L,PENG M,et al.,2015.Genetic diversity and population structure analysis in wild strawberry(Fragaria nubicola L.)from Motuo in Tibet Plateau based on simple sequence repeats(SSRs)[J].Biochem Syst Ecol,63(2):113-118.
MING TL,BARTHOLOMEW B,2007.Theaceae[M]//Flora Reipublicae Popularis Sinicae[M].Beijing:Science Press:368-372.
NYBOM H,2004.Comparison of different nuclear DNA markers for estimating intraspecific genetic diversity in plants[J].Mol Ecol,13(5):1143-1155.
PEAKALL R,SMOUSE PE,2012.Gen AlEx 6.5:Genetic analysis in Excel.Population genetic software for teaching and research-an update[J].Bioinformatics,28(28):2537-2539.
PENG GQ,TANG SQ,2017.Fine-scale spatial genetic structure and gene flow of Camellia flavida,a shadetolerant shrub in karst[J].Acta Ecol Sin,37(21):7313-7323.[彭国清,唐绍清,2017.喀斯特耐阴灌木淡黄金花茶的精细空间遗传结构与基因流[J].生态学报,37(21):7313-7323.]
PRITCHARD JK,STEPHENS M,DONNELLY P,2000.Inference of population structure using multilocus genotype data[J].Genetics,155(2):945-959.
QIN HN,YANG Y,DONG SY,et al.,2017.Threatened species list of China’s higher plants[J].Biodivers Sci,25(7):696-744.[覃海宁,杨永,董仕勇,等,2017.中国高等植物受威胁物种名录[J].生物多样性,25(7):696-744.]
RICE WR,1989.Analyzing tables of statistical tests[J].Evolution,43(1):223-225.
ROUSSET F,2008.Genepop'007:A complete re-implementation of the genepop software for Windows and Linux[J].Mol Ecol Resour,8(1):103-106.
RYALL CL,1998.Principles of conservation biology[J].Environmentalist,19(2):171.
SEGARRA-MORAGUES JG,PALOP-ESTEBAN M,GONZLEZ-CANDELAS F,et al.,2005.On the verge of extinction:Genetics of the critically endangered Iberian plant species,Borderea chouardii(Dioscoreaceae)and implications for conservation management[J].Mol Ecol,14(4):969-982.
SPIELMAN D,BROOK BW,FRANKHAM R,2004.Most species are not driven to extinction before genetic factors impact them[J].Proc Natl Acad Sci USA,101(42):15261-15264.
SU Z,RICHARDSON BA,ZHUO L,et al.,2017.Genetic diversity and structure of an endangered desert shrub and the implications for conservation[J].Aob Plants,9(3):plx016.
UENO S,TOMARU N,YOSHIMARU H,et al.,2000.Genetic structure of Camellia japonica L.in an old-growth evergreen forest,Tsushima,Japan[J].Mol Ecol,9(6):647-656.
WEI SJ,LU YB,YE QQ,et al.,2017.Populationgenetic structure and phylogeography of Camellia flavida(Theaceae)based on chloroplast and nuclear DNA sequences[J].Front Plant Sci,8:718.
WRIGHT S,1968.Evolution and the genetics of populations[M].Chicago:University of Chicago Press:1191-1192.
WRIGHT S,1931.Evolution in Mendelian populations[J].Genetics,16(2):97-159.
YANG HS,LI XP,LIU DJ,et al.,2016.Genetic diversity and population structure of the endangered medicinal plant Phellodendron amurense in China revealed by SSR markers[J].Biochem Syst Ecol,66:286-292.
YAO MZ,MA CL,QIAO TT,et al.,2012.Diversity distribution and population structure of tea germplasms in China revealed by EST-SSR markers[J].Tree Genet Genom,8(1):205-220.
YE QQ,XUE YG,2013.Classification of Camellia chrysanthoides,C.micrantha,C.parvipetala and C.xiashiensis[M]//LIANG SC,MA JM.Guangxi Dongzhiwu Shengtaixue Yanjiu.Beijing:China Forestry Press:23-27.[叶泉清,薛跃规,2013.薄叶金花茶、小花金花茶、小瓣金花茶、夏石金花茶分类的探讨[M]//梁士楚,马姜明.广西动植物生态学研究.北京:中国林业出版社:23-27.]
ZHAO DW,YANG JB,YANG SX,et al.,2014.Genetic diversity and domestication origin of tea plant Camellia taliensis(Theaceae)as revealed by microsatellite markers[J].BMCPlant Biol,14(1):14.
ZHAO Y,TANG M,BI YF,2017.Nuclear genetic diversity and population structure of a vulnerable and endemic orchid(Cymbidium tortisepalum)in Northwestern Yunnan,China[J].Sci Hortic-amsterdam,219:22-30.
CHANG HT,REN SX,1998.Theaceae[M]//Flora Reipublicae Popularis Sinicae.Beijing:Science Press:101-112.[张宏达,任善湘,1998.中国植物志:第四十九卷第三分册[M].北京:科学出版社:101-112.]
CHEN XY,2000.Effects of habitat fragmentation on genetic structure of plant populations and implications for the biodiversity conservation[J].Acta Ecol Sin,20(5):884-892.[陈小勇,2000.生境片断化对植物种群遗传结构的影响及植物遗传多样性保护[J].生态学报,20(5):884-892.]
CIRES E,SAMAIN MS,GOETGHEBEUR P,et al.,2011.Genetic structure in peripheral Western European populations of the endangered species Cochlearia pyrenaica(Brassicaceae)[J].Plant Syst Evol,297(1-2):75-85.
DENG YY,YU XL,LUO YB,2010.The role of native bees on the reproductive success of Camellia oleifera in Hunan Province,Central South China[J].Acta Ecol Sin,30(16):4427-4436.[邓园艺,喻勋林,罗毅波,2010.传粉昆虫对我国中南地区油茶结实和结籽的作用[J].生态学报,30(16):4427-4436.]
DOYLE JJ,1987.A rapid DNA isolation procedure for small quantities of fresh leaf tissue[J].Phytochem Bull,19(1):11-15.
EARL DA,VONHOLDT BM,2012.STRUCTURE HARVEST-ER:A website and program for visualizing STRUCTUREoutput and implementing the Evanno method[J].Conserv Genet Resour,4(2):359-361.
EXCOFFIER L,LAVAL G,SCHNEIDER S,2005.Arlequin(version 3.0):An integrated software package for population genetics data analysis[J].Evol Bioinform Online,1:47-50.
EXCOFFIER L,SMOUSE PE,QUATTRO JM,1992.Analysis of molecular variance inferred from metric distances among DNA haplotypes:Application to human mitochondrial DNArestriction data[J].Genetics,131(2):479-491.
FRANKHAM R,BALLOU JD,BRISCOE DA,2002.Introduction to conservation genetics[M].Cambridge:Cambridge University Press:182-183
GAO QB,LI Y,GENGJI ZM,et al.,2017.Population genetic differentiation and taxonomy of three closely related species of Saxifraga(Saxifragaceae)from southern Tibet and the hengduan mountains[J].Front Plant Sci,8:1325.
GYORGY Z,VOUILLAMOZ JF,LAD NYI M,et al.,2014.Genetic survey of Rhodiola rosea L.populations from the Swiss Alps based on SSR markers[J].Biochem Syst Ecol,54(54):137-143.
HAMRICK JL,GODT MW,1996.Effects oflife history traits on genetic diversity in plant species[J].Philos T R Soc B,351(1345):1291-1298.
HE YL,HE Y,GONG LL,et al.,2017.Population genetic structure and interspecific differentiation between Acer davidii Franchi.and A.morrisonense Hayata(Aceraceae)based on SSR markers[J].Biochem Syst Ecol,71:42-49.
LI XL,LI SC,CHU HJ,et al.,2013.Genetic diversity and population structure of the endangered alpine quillwort Isoetes hypsophila(Isoetaceae)revealed by SSR analysis[J].Biochem Syst Ecol,47(4):11-20.
LIANG SY,1995.Comparison of karyotypes of sect.Chrysantha Chang[J].Guangxi For Sci,24(3):142-144.[梁盛业,1995.金花茶组植物核型比较[J].广西林业科学,24(3):142-144.]
LIUFU YQ,PENG GQ,LU YB,et al.,2014.Development and characterization of 38 microsatellite markers for Camellia flavida based on transcriptome sequencing[J].Conserv Genet Resour,6(4):1007-1010.
LIU Y,YANG S,JI P,et al.,2012.Phylogeography of Camellia taliensis(Theaceae)inferred from chloroplast and nuclear DNA:Insights into evolutionary history and conservation[J].BMC Evol Biol,12(1):92.
LU YB,2015.The population genetic structure of Camellia flavida Chang[D].Guilin:Guangxi Normal University:22-23.[卢永彬,2015.淡黄金花茶种群遗传结构研究[D].桂林:广西师范大学:22-23.]
LU YB,LIUFU YQ,PENG GQ,et al.,2014.Development of21 microsatellite primers for Camellia pingguoensis(Theaceae)using 454 sequencing[J].Conserv Genet Resour,6(3):791-793.
MA Q,DU YJ,CHEN N,et al.,2015.Phylogeography of Davidia involucrata(Davidiaceae)Inferred from cp DNA Haplotypes and n SSR Data[J].Syst Bot,40(3):796-810.
MENG FJ,LIU L,PENG M,et al.,2015.Genetic diversity and population structure analysis in wild strawberry(Fragaria nubicola L.)from Motuo in Tibet Plateau based on simple sequence repeats(SSRs)[J].Biochem Syst Ecol,63(2):113-118.
MING TL,BARTHOLOMEW B,2007.Theaceae[M]//Flora Reipublicae Popularis Sinicae[M].Beijing:Science Press:368-372.
NYBOM H,2004.Comparison of different nuclear DNA markers for estimating intraspecific genetic diversity in plants[J].Mol Ecol,13(5):1143-1155.
PEAKALL R,SMOUSE PE,2012.Gen AlEx 6.5:Genetic analysis in Excel.Population genetic software for teaching and research-an update[J].Bioinformatics,28(28):2537-2539.
PENG GQ,TANG SQ,2017.Fine-scale spatial genetic structure and gene flow of Camellia flavida,a shadetolerant shrub in karst[J].Acta Ecol Sin,37(21):7313-7323.[彭国清,唐绍清,2017.喀斯特耐阴灌木淡黄金花茶的精细空间遗传结构与基因流[J].生态学报,37(21):7313-7323.]
PRITCHARD JK,STEPHENS M,DONNELLY P,2000.Inference of population structure using multilocus genotype data[J].Genetics,155(2):945-959.
QIN HN,YANG Y,DONG SY,et al.,2017.Threatened species list of China’s higher plants[J].Biodivers Sci,25(7):696-744.[覃海宁,杨永,董仕勇,等,2017.中国高等植物受威胁物种名录[J].生物多样性,25(7):696-744.]
RICE WR,1989.Analyzing tables of statistical tests[J].Evolution,43(1):223-225.
ROUSSET F,2008.Genepop'007:A complete re-implementation of the genepop software for Windows and Linux[J].Mol Ecol Resour,8(1):103-106.
RYALL CL,1998.Principles of conservation biology[J].Environmentalist,19(2):171.
SEGARRA-MORAGUES JG,PALOP-ESTEBAN M,GONZLEZ-CANDELAS F,et al.,2005.On the verge of extinction:Genetics of the critically endangered Iberian plant species,Borderea chouardii(Dioscoreaceae)and implications for conservation management[J].Mol Ecol,14(4):969-982.
SPIELMAN D,BROOK BW,FRANKHAM R,2004.Most species are not driven to extinction before genetic factors impact them[J].Proc Natl Acad Sci USA,101(42):15261-15264.
SU Z,RICHARDSON BA,ZHUO L,et al.,2017.Genetic diversity and structure of an endangered desert shrub and the implications for conservation[J].Aob Plants,9(3):plx016.
UENO S,TOMARU N,YOSHIMARU H,et al.,2000.Genetic structure of Camellia japonica L.in an old-growth evergreen forest,Tsushima,Japan[J].Mol Ecol,9(6):647-656.
WEI SJ,LU YB,YE QQ,et al.,2017.Populationgenetic structure and phylogeography of Camellia flavida(Theaceae)based on chloroplast and nuclear DNA sequences[J].Front Plant Sci,8:718.
WRIGHT S,1968.Evolution and the genetics of populations[M].Chicago:University of Chicago Press:1191-1192.
WRIGHT S,1931.Evolution in Mendelian populations[J].Genetics,16(2):97-159.
YANG HS,LI XP,LIU DJ,et al.,2016.Genetic diversity and population structure of the endangered medicinal plant Phellodendron amurense in China revealed by SSR markers[J].Biochem Syst Ecol,66:286-292.
YAO MZ,MA CL,QIAO TT,et al.,2012.Diversity distribution and population structure of tea germplasms in China revealed by EST-SSR markers[J].Tree Genet Genom,8(1):205-220.
YE QQ,XUE YG,2013.Classification of Camellia chrysanthoides,C.micrantha,C.parvipetala and C.xiashiensis[M]//LIANG SC,MA JM.Guangxi Dongzhiwu Shengtaixue Yanjiu.Beijing:China Forestry Press:23-27.[叶泉清,薛跃规,2013.薄叶金花茶、小花金花茶、小瓣金花茶、夏石金花茶分类的探讨[M]//梁士楚,马姜明.广西动植物生态学研究.北京:中国林业出版社:23-27.]
ZHAO DW,YANG JB,YANG SX,et al.,2014.Genetic diversity and domestication origin of tea plant Camellia taliensis(Theaceae)as revealed by microsatellite markers[J].BMCPlant Biol,14(1):14.
ZHAO Y,TANG M,BI YF,2017.Nuclear genetic diversity and population structure of a vulnerable and endemic orchid(Cymbidium tortisepalum)in Northwestern Yunnan,China[J].Sci Hortic-amsterdam,219:22-30.