大花序桉SSR位点多样性和群体结构分析
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摘要
为了获得大花序桉群体变异的可靠信息,本研究基于桉树29个基因组简单序列重复(SSR)标记,筛选了既不偏离哈温平衡、又非群体间分化系数(Fst)离群值的中性SSR用于大花序桉14个群体的遗传多样性和群体结构分析。基于11个中性SSR位点,群体的每位点等位片段数(Na)和特有等位片段数(Npa)平均分别为6.88和4.5,观测杂合度(Ho)和期望杂合度(He)平均分别为0.749和0.780,证明群体多样性较高;固定化指数(F)平均为0.040,表明群体内近交水平极低。位点平均Fst为0.120,分子方差分析(AMOVA)中群体间变异只占总方差分量的3.1%,表明群体为中等到低的分化水平。主坐标分析、聚类分析和群体结构分析都将昆士兰州北部与中部群体(各7个)分为不同的亚群体。这为大花序桉种质资源保存和育种策略制定提供了理论的参考依据。
In order to obtain reliable information on population variation in Eucalyptus cloeziana F. Meull., 11 neutral simple sequence repeats(SSR) markers that neither showed between-population differentiation(Fst) outliers nor departed from Hardy-Weinberg equilibrium were screened out from 29 genomic SSRs for analyses of genetic diversity and population structure of the species. Based on the 11 neutral SSR loci, the number of alleles(Na), the number of private alleles(Npa), observed heterozygosity(Ho) and expected heterozygosity(He) were av eraged at 6.88, 4.5, 0.749 and 0.780, respectively, demonstrating high levels of genetic diversity. Mean fixation index(F) was 0.040, indicating a very low degree of inbreeding. Overall Fstwas 0.120 and analysis of molecular variance(AMOVA) showed that among-population variance took only 3.1% of the total variance, suggesting moderate to relatively low levels of population differentiation. Principal coordinate analysis, cluster analysis and structure analysis resulted consistently in obvious separation of the seven northern populations from the seven middle populations from Queensland. The results will be helpful for germplasm conservation and breeding strategy making in E. cloeziana.
In order to obtain reliable information on population variation in Eucalyptus cloeziana F. Meull., 11 neutral simple sequence repeats(SSR) markers that neither showed between-population differentiation(Fst) outliers nor departed from Hardy-Weinberg equilibrium were screened out from 29 genomic SSRs for analyses of genetic diversity and population structure of the species. Based on the 11 neutral SSR loci, the number of alleles(Na), the number of private alleles(Npa), observed heterozygosity(Ho) and expected heterozygosity(He) were av eraged at 6.88, 4.5, 0.749 and 0.780, respectively, demonstrating high levels of genetic diversity. Mean fixation index(F) was 0.040, indicating a very low degree of inbreeding. Overall Fstwas 0.120 and analysis of molecular variance(AMOVA) showed that among-population variance took only 3.1% of the total variance, suggesting moderate to relatively low levels of population differentiation. Principal coordinate analysis, cluster analysis and structure analysis resulted consistently in obvious separation of the seven northern populations from the seven middle populations from Queensland. The results will be helpful for germplasm conservation and breeding strategy making in E. cloeziana.
引文
Allendorf F.W.,and Seeb L.W.,2000,Concordance of genetic divergence among sockeye salmon populations at allozyme,nuclear DNA,and mitochondrial DNA markers,Evolution,54(2):640-651
Antao T.,Lopes A.,Lopes R.J.,Bejapereira A.,and Luikart G.,2008,LOSITAN:A workbench to detect molecular adaptation based on a Fst-outlier method,BMC Bioinformatics,9:323
Botstein D.,White R.L.,Skolnick M.,and Davis R.W.,1980,Construction of a genetic linkage map in man using restriction fragment length polymorphisms,Am.J.Hum.Genet.,32(3):314-331
Bradbury D.,Smithson A.,and Krauss S.L.,2013,Signatures of diversifying selection at EST-SSR loci and association with climate in natural Eucalyptus populations,Mol.Ecol.,22(20):5112-5129
Bragg J.G.,Supple M.A.,Andrew R.L.,and Borevitz J.O.,2015,Genomic variation across landscapes:insights and applications,New Phytol.,207(4):953-967
Brondani R.P.,Williams E.R.,Brondani C.,and Grattapaglia D.,2006,A micros atellite-based consensus linkage map for species of Eucalyptus and a novel set of 230 microsatellite markers for the genus,BMC Plant Biol.,6:20
Brooker M.I.H.,2000,A n ew classification of the genus Eucalyptus L'Hér.(Myrtaceae),Aust.Syst.Bot.,13(1):79-148
Butcher P.A.,McDonald M.W.,and Bell J.C.,2009,Congruence between environmental parameters,morphology and genetic structure in Australia's most widely distributed eucalypt,Eucalyptus camaldulensis,Tree Genet.Genomes,5(1):189-210
Deng Z.Y.,2012,Genetic structure of Eucalyptus cloeziana by SSR markers,Thesis for M.S.,Guangxi University,Supervisor:Xiang D.Y.,pp.26-30(邓紫宇,2012,利用SSR分子标记研究大花序桉遗传结构,硕士学位论文,广西大学,导师:项东云,pp.26-30)
Earl D.A.,and vonHoldt B.M.,2012,STRUCTURE HARVE-STER:a website and program for visualizing STRUCTUREoutpu t and implementing the Evanno method,Conserv.Genet.Resour.,4(2):359-361
Ellis J.R.,and Burke J.M.,2007,EST-SSRs as a resource for population genetic analyses,Heredity,99(2):125-132
Evanno G.,Regnaut S.,and Goudet J.,2005,Detecting the number of clusters of individuals using the software STRUC-TURE:a simulation study,Mol.Ecol.,14(8):2611-2620
Excoffier L.,and Lischer H.E.L.,2010,Arlequin suite ver 3.5:a new series of programs to perform population genetics analyses under linux and windows,Mol.Ecol.Resour.,10(3):564-567
Falush D.,Stephens M.,and Pritchard J.K.,2003,Inference of population structure using multilocus genotype data:linked loci and correlated allele frequencies,Genetics,164(4):1567-1587
Kalinowski S.T.,Taper M.L.,and Marshall T.C.,2007,Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment,Mol.Ecol.,16(5):1099-1106
Larsson L.C.,Laikre L.,Palm S.,Andre C.,Carvalho G.R.,and Ryman N.,2007,Concordance of allozyme and microsatellite differentiation in a marine fish,but evidence of selection at a microsatellite locus,Mol.Ecol.,16(6):1135-1147
Li C.,Sun Y.,Huang H.W.,and Cannon C.H.,2014,Footprints of divergent selection in natural populations of Castanopsis fargesii(Fagaceae),Heredity,113(6):533-541
Li C.R.,Weng Q.J.,Chen J.B.,Li M.,Zhou C.P.,Chen S.K.,Zhou W.,Guo D.Q.,Lu C.X.,Chen J.C.,Xiang D.Y.,and Gan S.M.,2017,Genetic parameters for growth and wood mechanical properties in Eucalyptus cloeziana F.Muell.,New For.,48(1):33-49
Li F.G.,and Gan S.M.,2011,An optimised protocol for fluorescent-dUTP based SSR genotyping and its application to genetic mapping in Eucalyptus,Silvae Genet.,60(1):18-25
Li F.G.,Zhou C.P.,Weng Q.J.,Li M.,Yu X.L.,Guo Y.,Wang Y.,Zhang X.H.,and Gan S.M.,2015,Comparative genomics analyses reveal extensive chromosome colinearity and novel quantitative trait loci in Eucalyptus,PLoS One,10:e0145144
Luikart G.,England P.R.,Tallmon D.,Jordan S.,and Taberlet P.,2003,The power and promise of population genomics:from genotyping to genome typing,Nat.Rev.Genet.,4(12):981-994
Manel S.,Schwartz M.K.,Luikart G.,and Taberlet P.,2003,Landscape genetics:combining landscape ecology and population genetics,Trend.Ecol.Evol.,18(4):189-197
Marshall T.C.,Slate J.,Kruuk L.E.B.,and Pemberton J.M.,1998,Statistical confidence for likelihood-based paternity inference in natural populations,Mol.Ecol.,7(5):639-655
Ngugi M.R.,Doley D.,Hunt M.A.,Ryan P.,and Dart P.,2004,Physiological responses to water stress in Eucalyptus cloeziana and E.argophloia seedlings,Trees,18(4):381-389
Payn K.G.,Dvorak W.S.,Janse B.J.H.,and Myburg A.A.,2008,Microsatellite diversity and genetic structure of the commercially important tropical tree species Eucalyptus urophylla,endemic to seven islands in eastern Indonesia,Tree Genet.Genomes,4(3):519-530
Peakall R.,and Smouse P.E.,2006,GenAlEx 6:genetic analysis in Excel.,Population genetic software for teaching and research,Mol.Ecol.Notes,6(1):288-295
Powell W.,Machray G.C.,and Provan J.,1996,Polymorphism revealed by simple sequence repeats,Trend.Plant Sci.,1(7):215-222
Rohlf F.J.,ed.,2000,NTSYS-Pc:numerical taxonomy and multivariate analysis system(Version 2.1),Exeter Software,New York,USA,pp.1-38
Rousset F.,2008,Genepop'007:a complete re-implementation of the Genepop software for Windows and Linux,Mol.Ecol.Resour.,8(1):103-106
Schlotterer C.,2000,Evolutionary dynamics of microsatellite DNA,Chromosoma,109(6):365-371
Shepherd M.,Sexton T.R.,Thomas D.,Henson M.,and Henry R.J.,2010,Geographical and historical determinants of microsatellite variation in Eucalyptus pilularis,Can.J.For.Res.,40(6):1051-1063
Song Z.J.,Yang H.Y.,Weng Q.J.,Zhou C.P.,Li F.G.,Li M.,Lu W.H.,Luo J.Z.,and Gan S.M.,2016,Genetic diversity and selective loci in Eucalyptus tereticornis populations,Linye Kexue(Scientia Silvae Sinicae),52(9):39-47(宋志姣,杨合宇,翁启杰,周长品,李发根,李梅,卢万鸿,罗建中,甘四明,2016,细叶桉群体的遗传多样性和受选择位点,林业科学,52(9):39-47)
Song Z.J.,Zhang M.M.,Li F.G.,Weng Q.J.,Zhou C.P.,Li M.,Li J.,Huang H.H.,Mo X.Y.,and Gan S.M.,2016,Genome scans for divergent selection in natural populations of the widespread hardwood species Eucalyptus grandis(Myrtaceae)using microsatellites,Sci.Rep.,6:34941
Sork V.L.,2018,Genomic studies of local adaptation in natural plant populations,J.Hered.,109(1):3-15
Steane D.A.,Conod N.,Jones R.C.,Vaillancourt R.E.,and Potts B.M.,2006,A comparative analysis of population structure of a forest tree,Eucalyptus globulus(Myrtaceae),using microsatellite markers and quantitative traits,Tree Genet.Genomes,2(1):30-38
Tautz D.,1989,Hypervariability of simple sequences as a general source for polymorphic DNA markers,Nucleic Acids Res.,17(16):6463-6471
Varshney R.K.,Graner A.,and Sorrells M.E.,2005,Genic microsatellite markers in plants:features and applications,Trend.Biotechnol.,23(1):48-55
White T.,Adams T.,and Neale D.,2007,Forest genetics,CABIPublishing,Wallingford,UK,pp.149-186
Ye L.,Chen J.B.,Xiang D.Y.,Chen J.C.,Shen W.H.,Zhang,Z.Y.,Tang Q.L.,and Wu R.S.,2007,Primary research on provenance and family trials of Eucalyptus cloeziana,Guangxi Linye Kexue(Guangxi Forestry Science),36(4):187-191(叶露,陈健波,项东云,陈剑成,申文辉,张照远,唐庆兰,伍荣善,2007,大花序桉种源/家系试验的早期研究,广西林业科学,36(4):187-191)
Antao T.,Lopes A.,Lopes R.J.,Bejapereira A.,and Luikart G.,2008,LOSITAN:A workbench to detect molecular adaptation based on a Fst-outlier method,BMC Bioinformatics,9:323
Botstein D.,White R.L.,Skolnick M.,and Davis R.W.,1980,Construction of a genetic linkage map in man using restriction fragment length polymorphisms,Am.J.Hum.Genet.,32(3):314-331
Bradbury D.,Smithson A.,and Krauss S.L.,2013,Signatures of diversifying selection at EST-SSR loci and association with climate in natural Eucalyptus populations,Mol.Ecol.,22(20):5112-5129
Bragg J.G.,Supple M.A.,Andrew R.L.,and Borevitz J.O.,2015,Genomic variation across landscapes:insights and applications,New Phytol.,207(4):953-967
Brondani R.P.,Williams E.R.,Brondani C.,and Grattapaglia D.,2006,A micros atellite-based consensus linkage map for species of Eucalyptus and a novel set of 230 microsatellite markers for the genus,BMC Plant Biol.,6:20
Brooker M.I.H.,2000,A n ew classification of the genus Eucalyptus L'Hér.(Myrtaceae),Aust.Syst.Bot.,13(1):79-148
Butcher P.A.,McDonald M.W.,and Bell J.C.,2009,Congruence between environmental parameters,morphology and genetic structure in Australia's most widely distributed eucalypt,Eucalyptus camaldulensis,Tree Genet.Genomes,5(1):189-210
Deng Z.Y.,2012,Genetic structure of Eucalyptus cloeziana by SSR markers,Thesis for M.S.,Guangxi University,Supervisor:Xiang D.Y.,pp.26-30(邓紫宇,2012,利用SSR分子标记研究大花序桉遗传结构,硕士学位论文,广西大学,导师:项东云,pp.26-30)
Earl D.A.,and vonHoldt B.M.,2012,STRUCTURE HARVE-STER:a website and program for visualizing STRUCTUREoutpu t and implementing the Evanno method,Conserv.Genet.Resour.,4(2):359-361
Ellis J.R.,and Burke J.M.,2007,EST-SSRs as a resource for population genetic analyses,Heredity,99(2):125-132
Evanno G.,Regnaut S.,and Goudet J.,2005,Detecting the number of clusters of individuals using the software STRUC-TURE:a simulation study,Mol.Ecol.,14(8):2611-2620
Excoffier L.,and Lischer H.E.L.,2010,Arlequin suite ver 3.5:a new series of programs to perform population genetics analyses under linux and windows,Mol.Ecol.Resour.,10(3):564-567
Falush D.,Stephens M.,and Pritchard J.K.,2003,Inference of population structure using multilocus genotype data:linked loci and correlated allele frequencies,Genetics,164(4):1567-1587
Kalinowski S.T.,Taper M.L.,and Marshall T.C.,2007,Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment,Mol.Ecol.,16(5):1099-1106
Larsson L.C.,Laikre L.,Palm S.,Andre C.,Carvalho G.R.,and Ryman N.,2007,Concordance of allozyme and microsatellite differentiation in a marine fish,but evidence of selection at a microsatellite locus,Mol.Ecol.,16(6):1135-1147
Li C.,Sun Y.,Huang H.W.,and Cannon C.H.,2014,Footprints of divergent selection in natural populations of Castanopsis fargesii(Fagaceae),Heredity,113(6):533-541
Li C.R.,Weng Q.J.,Chen J.B.,Li M.,Zhou C.P.,Chen S.K.,Zhou W.,Guo D.Q.,Lu C.X.,Chen J.C.,Xiang D.Y.,and Gan S.M.,2017,Genetic parameters for growth and wood mechanical properties in Eucalyptus cloeziana F.Muell.,New For.,48(1):33-49
Li F.G.,and Gan S.M.,2011,An optimised protocol for fluorescent-dUTP based SSR genotyping and its application to genetic mapping in Eucalyptus,Silvae Genet.,60(1):18-25
Li F.G.,Zhou C.P.,Weng Q.J.,Li M.,Yu X.L.,Guo Y.,Wang Y.,Zhang X.H.,and Gan S.M.,2015,Comparative genomics analyses reveal extensive chromosome colinearity and novel quantitative trait loci in Eucalyptus,PLoS One,10:e0145144
Luikart G.,England P.R.,Tallmon D.,Jordan S.,and Taberlet P.,2003,The power and promise of population genomics:from genotyping to genome typing,Nat.Rev.Genet.,4(12):981-994
Manel S.,Schwartz M.K.,Luikart G.,and Taberlet P.,2003,Landscape genetics:combining landscape ecology and population genetics,Trend.Ecol.Evol.,18(4):189-197
Marshall T.C.,Slate J.,Kruuk L.E.B.,and Pemberton J.M.,1998,Statistical confidence for likelihood-based paternity inference in natural populations,Mol.Ecol.,7(5):639-655
Ngugi M.R.,Doley D.,Hunt M.A.,Ryan P.,and Dart P.,2004,Physiological responses to water stress in Eucalyptus cloeziana and E.argophloia seedlings,Trees,18(4):381-389
Payn K.G.,Dvorak W.S.,Janse B.J.H.,and Myburg A.A.,2008,Microsatellite diversity and genetic structure of the commercially important tropical tree species Eucalyptus urophylla,endemic to seven islands in eastern Indonesia,Tree Genet.Genomes,4(3):519-530
Peakall R.,and Smouse P.E.,2006,GenAlEx 6:genetic analysis in Excel.,Population genetic software for teaching and research,Mol.Ecol.Notes,6(1):288-295
Powell W.,Machray G.C.,and Provan J.,1996,Polymorphism revealed by simple sequence repeats,Trend.Plant Sci.,1(7):215-222
Rohlf F.J.,ed.,2000,NTSYS-Pc:numerical taxonomy and multivariate analysis system(Version 2.1),Exeter Software,New York,USA,pp.1-38
Rousset F.,2008,Genepop'007:a complete re-implementation of the Genepop software for Windows and Linux,Mol.Ecol.Resour.,8(1):103-106
Schlotterer C.,2000,Evolutionary dynamics of microsatellite DNA,Chromosoma,109(6):365-371
Shepherd M.,Sexton T.R.,Thomas D.,Henson M.,and Henry R.J.,2010,Geographical and historical determinants of microsatellite variation in Eucalyptus pilularis,Can.J.For.Res.,40(6):1051-1063
Song Z.J.,Yang H.Y.,Weng Q.J.,Zhou C.P.,Li F.G.,Li M.,Lu W.H.,Luo J.Z.,and Gan S.M.,2016,Genetic diversity and selective loci in Eucalyptus tereticornis populations,Linye Kexue(Scientia Silvae Sinicae),52(9):39-47(宋志姣,杨合宇,翁启杰,周长品,李发根,李梅,卢万鸿,罗建中,甘四明,2016,细叶桉群体的遗传多样性和受选择位点,林业科学,52(9):39-47)
Song Z.J.,Zhang M.M.,Li F.G.,Weng Q.J.,Zhou C.P.,Li M.,Li J.,Huang H.H.,Mo X.Y.,and Gan S.M.,2016,Genome scans for divergent selection in natural populations of the widespread hardwood species Eucalyptus grandis(Myrtaceae)using microsatellites,Sci.Rep.,6:34941
Sork V.L.,2018,Genomic studies of local adaptation in natural plant populations,J.Hered.,109(1):3-15
Steane D.A.,Conod N.,Jones R.C.,Vaillancourt R.E.,and Potts B.M.,2006,A comparative analysis of population structure of a forest tree,Eucalyptus globulus(Myrtaceae),using microsatellite markers and quantitative traits,Tree Genet.Genomes,2(1):30-38
Tautz D.,1989,Hypervariability of simple sequences as a general source for polymorphic DNA markers,Nucleic Acids Res.,17(16):6463-6471
Varshney R.K.,Graner A.,and Sorrells M.E.,2005,Genic microsatellite markers in plants:features and applications,Trend.Biotechnol.,23(1):48-55
White T.,Adams T.,and Neale D.,2007,Forest genetics,CABIPublishing,Wallingford,UK,pp.149-186
Ye L.,Chen J.B.,Xiang D.Y.,Chen J.C.,Shen W.H.,Zhang,Z.Y.,Tang Q.L.,and Wu R.S.,2007,Primary research on provenance and family trials of Eucalyptus cloeziana,Guangxi Linye Kexue(Guangxi Forestry Science),36(4):187-191(叶露,陈健波,项东云,陈剑成,申文辉,张照远,唐庆兰,伍荣善,2007,大花序桉种源/家系试验的早期研究,广西林业科学,36(4):187-191)