Genetic diversity in old populations of sessile oak from Calabria assessed by nuclear and chloroplast SSR
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摘要
In the framework of forest resources conservation, this study aims to understand the dynamic and the genetic structure of sessile oak forests in Calabria, Italy. Two old populations of sessile oak(Quercus petraea(Mattuschka) Liebl.) from two areas of Sila and Aspromonte massifs in Calabria were analyzed for genetic diversity and population structure based on 6 nuclear simple sequence repeat(nSSR) and 4 chloroplastic SSR(cpSSR) loci. The populations displayed high amount of genetic diversity, which was toughly structured according to their geographical origins. Number of alleles at SSR loci ranged from 11 to 20 with an average of 13.5 per locus. Gene diversity(expected heterozygosity, He) estimates ranged from 0.575 to 0.834 with a mean of 0.749. The observed heterozygosity(Ho) was on average 0.458 ranging from 0.150 to 0.682. Polymorphism information content(PIC) values ranged from 0.625 to 0.865 with an average of 0.787. The analysis of molecular variance(AMOVA) highlighted a significant higher estimated variance within populations compared to among populations. Finally, the analysis of haplotypes by using cpSSR suggested a higher diversification in the population from Sila. Hierarchical clustering analysis grouped the genotypes into two major clusters, which agreed with the geographic origin of populations, and was confirmed by the Discriminant Analysis of Principal Components(DAPC). The first cluster included plants/population from Sila massif, while the second encompassed mostly plants/population sampled in Aspromonte massif. Finally, model-based clustering by STRUCTURE analysis also supported the presence of clear genetic structuring in the collection with two major populations(K=2) supported to PCoA analysis as well. Finally, our data indicated the Aspromonte population as a marginal forest with fragmented distribution suggesting different strategies of preservation than in Sila massif.
In the framework of forest resources conservation, this study aims to understand the dynamic and the genetic structure of sessile oak forests in Calabria, Italy. Two old populations of sessile oak(Quercus petraea(Mattuschka) Liebl.) from two areas of Sila and Aspromonte massifs in Calabria were analyzed for genetic diversity and population structure based on 6 nuclear simple sequence repeat(nSSR) and 4 chloroplastic SSR(cpSSR) loci. The populations displayed high amount of genetic diversity, which was toughly structured according to their geographical origins. Number of alleles at SSR loci ranged from 11 to 20 with an average of 13.5 per locus. Gene diversity(expected heterozygosity, He) estimates ranged from 0.575 to 0.834 with a mean of 0.749. The observed heterozygosity(Ho) was on average 0.458 ranging from 0.150 to 0.682. Polymorphism information content(PIC) values ranged from 0.625 to 0.865 with an average of 0.787. The analysis of molecular variance(AMOVA) highlighted a significant higher estimated variance within populations compared to among populations. Finally, the analysis of haplotypes by using cpSSR suggested a higher diversification in the population from Sila. Hierarchical clustering analysis grouped the genotypes into two major clusters, which agreed with the geographic origin of populations, and was confirmed by the Discriminant Analysis of Principal Components(DAPC). The first cluster included plants/population from Sila massif, while the second encompassed mostly plants/population sampled in Aspromonte massif. Finally, model-based clustering by STRUCTURE analysis also supported the presence of clear genetic structuring in the collection with two major populations(K=2) supported to PCoA analysis as well. Finally, our data indicated the Aspromonte population as a marginal forest with fragmented distribution suggesting different strategies of preservation than in Sila massif.
In the framework of forest resources conservation, this study aims to understand the dynamic and the genetic structure of sessile oak forests in Calabria, Italy. Two old populations of sessile oak(Quercus petraea(Mattuschka) Liebl.) from two areas of Sila and Aspromonte massifs in Calabria were analyzed for genetic diversity and population structure based on 6 nuclear simple sequence repeat(nSSR) and 4 chloroplastic SSR(cpSSR) loci. The populations displayed high amount of genetic diversity, which was toughly structured according to their geographical origins. Number of alleles at SSR loci ranged from 11 to 20 with an average of 13.5 per locus. Gene diversity(expected heterozygosity, He) estimates ranged from 0.575 to 0.834 with a mean of 0.749. The observed heterozygosity(Ho) was on average 0.458 ranging from 0.150 to 0.682. Polymorphism information content(PIC) values ranged from 0.625 to 0.865 with an average of 0.787. The analysis of molecular variance(AMOVA) highlighted a significant higher estimated variance within populations compared to among populations. Finally, the analysis of haplotypes by using cpSSR suggested a higher diversification in the population from Sila. Hierarchical clustering analysis grouped the genotypes into two major clusters, which agreed with the geographic origin of populations, and was confirmed by the Discriminant Analysis of Principal Components(DAPC). The first cluster included plants/population from Sila massif, while the second encompassed mostly plants/population sampled in Aspromonte massif. Finally, model-based clustering by STRUCTURE analysis also supported the presence of clear genetic structuring in the collection with two major populations(K=2) supported to PCoA analysis as well. Finally, our data indicated the Aspromonte population as a marginal forest with fragmented distribution suggesting different strategies of preservation than in Sila massif.
引文
Alberto F,Niort J,Derory J,et al.(2010)Population differentiation of sessile oak at the altitudinal front of migration in the French Pyrenees.Molecular Ecology 19(13):2626-2639.https://doi.org/10.1111/j.1365-294x.2010.04631.x
Alberto FJ,Aitken SN,Alía R,et al.(2013)Potential for evolutionary responses to climate change-evidence from tree populations.Global Change Biology 19(6):1645-1661.https://doi.org/10.1111/gcb.12181
Alikhani L,Rahmani MS,Shabanian N,et al.(2014)Genetic variability and structure of Quercus brantii assessed by ISSR,IRAP and SCoT markers.Gene 552(1):176-183.https://doi.org/10.1016/j.gene.2014.09.034
Allendorf F,Luikart G(2007)Conservation and the Genetics of Populations.Blackwell Publishing.p 620.
Antonecchia G,Fortini P,Lepais O,et al.(2015)Genetic structure of a natural oak community in central Italy:Evidence of gene flow between three sympatric white oak species(Quercus,Fagaceae).Annals of Forest Research 57(2):1.https://doi.org/10.15287/afr.2015.415
Botstein D,White RL,Skolnick M,Davis RW(1980)Construction of a genetic linkage map in man using restriction fragment length polymorphisms.American Journal of Human Genetics 32:314-331.
Bruschi P,Venderamin GG,Bussotti F,Grossoni P(2003)Morphological and molecular diversity among Italian populations of Quercus petraea.Annals of Botany 91:707-716.https://doi.org/10.1093/aob/mcg075
Bruschi P,Vendramin GG,Bussotti F,Grossoni P(2000)Morphological and molecular differentiation between Quercus petraea(Matt.)Liebl.and Quercus pubescens Willd.(Fagaceae)in Northern and Central Italy.Annals of Botany 85:325-333.https://doi.org/10.1006/anbo.1999.1046
Bruvo R,Michiels NK,D’souza TG,et al.(2004)A simple method for the calculation of microsatellite genotype distances irrespective of ploidy level.Molecular Ecology 13:2101-2106.https://doi.org/10.1111/j.1365-294x.2004.02209.x
Chatwin WB,Carpenter KK,Jimenez FR,et al.(2014)Microsatellite primer development for post oak,Quercus stellata(fagaceae).Applications in Plant Sciences 2:1400070.https://doi.org/10.3732/apps.1400070
Chmielewski M,Meyza K,Chybicki IJ,et al.(2015)Chloroplast microsatellites as a tool for phylogeographic studies:the case of white oaks in Poland.IForest-Biogeosciences and Forestry8(6):765-771.https://doi.org/10.3832/ifor1597-008
Chybicki IJ,Burczyk J(2013)Seeing the forest through the trees:comprehensive inference on individual mating patterns in a mixed stand of Quercus robur and Q.petraea.Annals of Botany 112(3):561-574.https://doi.org/10.1093/aob/mct131
Cr?ciunesc AL,Curtu N,?oflete A(2016)Genetic diversity and differentiation among four Quercus robur and Q.petraea natural populations in Romania.Bulletin of the Transilvania University of Bra?ov 9(58):2.
Curtu AL,Gailing O,Finkeldey R(2007a)Evidence for hybridization and introgression within a species-rich oak(Quercus spp.)community.BMC Evolutionary Biology 7:218.https://doi.org/10.1186/1471-2148-7-218
Curtu AL,Gailing O,Leinemann L,et al.(2007b)Genetic variation and differentiation within a natural community of five oak species(Quercus spp.).Plant Biology 9(1):116-126.https://doi.org/10.1055/s-2006-924542
Deguilloux MF,Pemonge MH,Petit RJ(2004)Use of chloroplast microsatellites to differentiate oak populations.Annals of Forest Science 61(8):825-830.https://doi.org/10.1051/forest:2004078
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Excoffier LL,Smouse PE,Quattro JM(1992)Analysis of molecular variance inferred from metric distances among DNA haplotypes:application to human mitochondrial DNArestriction data.Genetics 131:479-491.
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González-Rodríguez A,Arias DM,Oyama K(2005)Genetic variation and differentiation of populations within the Quercus affinis Quercus laurina(Fagaceae)complex analyzed with RAPD markers.Canadian Journal of Botany 83:155-162.https://doi.org/10.1139/b04-162
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Jombart T,Ahmed I(2011)Adegenet 1.3-1:new tools for the analysis of genome-wide SNP data.Bioinformatics 27(21):3070-3071.https://doi.org/10.1093/bioinformatics/btr521
Kamvar ZN,Tabima JF,Grünwald NJ(2014)Poppr:an Rpackage for genetic analysis of populations with clonal,partially clonal,and/or sexual reproduction.PeerJ 2:e281.https://doi.org/10.7717/peerj.281
Kremer A,Dupouey JL,Deans JD,et al.(2002)Leaf morphological differentiation between Quercus robur and Quercus petraea is stable across western European mixed oak stands.Annals of Forest Science 59:777-787.https://doi.org/10.1051/forest:2002065
Kremer A,Petit RJ(1993)Gene diversity in natural populations of oak species.Annals of Forest Science 50:186-202.https://doi.org/10.1051/forest:19930717
Leberg PL(2002)Estimating allelic richness:Effects of sample size and bottlenecks.Molecular Ecology 11(11):2445-2449.https://doi.org/10.1046/j.1365-294X.2002.01612.x
Lind-Riehl JF(2014)Genetic variation,local adaptation and population structure in North American red oak species,Quercus rubra I.and Q.ellipsoidalis E.J.Hill.Dissertation,Michigan Technological University.http://digitalcommons.mtu.edu/etds/864
Lowe A,Harris S,Ashton P(2004)Ecological genetics:design,analysis and application.Blackwell Publishing,Oxford,UK.p344.
Marziliano PA,Coletta V,Scuderi A,et al.(2017)Forest structure of a maple old-growth stand:a case study on the Apennines mountains(Southern Italy).Journal of Mountain Science 14(7):1329-1340.https://doi.org/10.1007/s11629-016-4336-1
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Mercati F,Riccardi P,Leebens-Mack J,et al.(2013)Single nucleotide polymorphism isolated from a novel EST dataset in garden Asparagus(Asparagus officinalis L.).Plant Science203-204:115-123.https://doi.org/10.1016/j.plantsci.2013.01.002
Mercati F,Longo C,Poma D,et al.(2015)Genetic variation of an italian long shelf-life tomato(Solanum lycopersicon L.)collection by using SSR and morphological fruit traits.Genetic Resources and Crop Evolution 62:721-732.https://dai.org/10.1007/s10722-014-0191-5
Morán-López T,Forner A,Flores-Rentería D,et al.(2016)Some positive effects of the fragmentation of holm oak forests:Attenuation of water stress and enhancement of acorn production.Forest Ecology and Management 370:22-30.https://doi.org/10.1016/j.foreco.2016.03.042
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Porth I,El-Kassaby Y(2014)Assessment of the genetic diversity in forest tree populations using molecular markers.Diversity6(2):283-295.https://doi.org/10.3390/d6020283
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Alikhani L,Rahmani MS,Shabanian N,et al.(2014)Genetic variability and structure of Quercus brantii assessed by ISSR,IRAP and SCoT markers.Gene 552(1):176-183.https://doi.org/10.1016/j.gene.2014.09.034
Allendorf F,Luikart G(2007)Conservation and the Genetics of Populations.Blackwell Publishing.p 620.
Antonecchia G,Fortini P,Lepais O,et al.(2015)Genetic structure of a natural oak community in central Italy:Evidence of gene flow between three sympatric white oak species(Quercus,Fagaceae).Annals of Forest Research 57(2):1.https://doi.org/10.15287/afr.2015.415
Botstein D,White RL,Skolnick M,Davis RW(1980)Construction of a genetic linkage map in man using restriction fragment length polymorphisms.American Journal of Human Genetics 32:314-331.
Bruschi P,Venderamin GG,Bussotti F,Grossoni P(2003)Morphological and molecular diversity among Italian populations of Quercus petraea.Annals of Botany 91:707-716.https://doi.org/10.1093/aob/mcg075
Bruschi P,Vendramin GG,Bussotti F,Grossoni P(2000)Morphological and molecular differentiation between Quercus petraea(Matt.)Liebl.and Quercus pubescens Willd.(Fagaceae)in Northern and Central Italy.Annals of Botany 85:325-333.https://doi.org/10.1006/anbo.1999.1046
Bruvo R,Michiels NK,D’souza TG,et al.(2004)A simple method for the calculation of microsatellite genotype distances irrespective of ploidy level.Molecular Ecology 13:2101-2106.https://doi.org/10.1111/j.1365-294x.2004.02209.x
Chatwin WB,Carpenter KK,Jimenez FR,et al.(2014)Microsatellite primer development for post oak,Quercus stellata(fagaceae).Applications in Plant Sciences 2:1400070.https://doi.org/10.3732/apps.1400070
Chmielewski M,Meyza K,Chybicki IJ,et al.(2015)Chloroplast microsatellites as a tool for phylogeographic studies:the case of white oaks in Poland.IForest-Biogeosciences and Forestry8(6):765-771.https://doi.org/10.3832/ifor1597-008
Chybicki IJ,Burczyk J(2013)Seeing the forest through the trees:comprehensive inference on individual mating patterns in a mixed stand of Quercus robur and Q.petraea.Annals of Botany 112(3):561-574.https://doi.org/10.1093/aob/mct131
Cr?ciunesc AL,Curtu N,?oflete A(2016)Genetic diversity and differentiation among four Quercus robur and Q.petraea natural populations in Romania.Bulletin of the Transilvania University of Bra?ov 9(58):2.
Curtu AL,Gailing O,Finkeldey R(2007a)Evidence for hybridization and introgression within a species-rich oak(Quercus spp.)community.BMC Evolutionary Biology 7:218.https://doi.org/10.1186/1471-2148-7-218
Curtu AL,Gailing O,Leinemann L,et al.(2007b)Genetic variation and differentiation within a natural community of five oak species(Quercus spp.).Plant Biology 9(1):116-126.https://doi.org/10.1055/s-2006-924542
Deguilloux MF,Pemonge MH,Petit RJ(2004)Use of chloroplast microsatellites to differentiate oak populations.Annals of Forest Science 61(8):825-830.https://doi.org/10.1051/forest:2004078
Dumolin-Lapègue S,Demesure B,Fineschi S,Le Corre V,Petit RJ(1997)Phylogeographic structure of white oaks throughout the European continent.Genetics 146:1475-1487.
Evanno G,Regnaut S,Goudet J(2005)Detecting the number of clusters of individuals using the software structure:a simulation study.Molecular Ecology 14:2611-2620.https://doi.org/10.1111/j.1365-294x.2005.02553.x
Excoffier LL,Smouse PE,Quattro JM(1992)Analysis of molecular variance inferred from metric distances among DNA haplotypes:application to human mitochondrial DNArestriction data.Genetics 131:479-491.
FAO(2011)Global Forest Resources Assessment 2010.Food and Agricultural Organization of the United Nations Forestry Paper,Roma.pp 35-40.
Geburek T,Konrad H(2008)Why the conservation of forest genetic resources has not worked?Conservation Biology 22:267-274.https://doi.org/10.1111/j.1523-1739.2008.00900.x
González-Rodríguez A,Arias DM,Oyama K(2005)Genetic variation and differentiation of populations within the Quercus affinis Quercus laurina(Fagaceae)complex analyzed with RAPD markers.Canadian Journal of Botany 83:155-162.https://doi.org/10.1139/b04-162
Hamrick JL(2004)Response of forest trees to global environmental changes.Forest Ecology and Management197(1-3):323-335.https://doi.org/10.1016/j.foreco.2004.05.023
Hamrick JL,Godt MJW,Brown AHD,et al.(1990)Allozyme diversity in plant species.In:Clegg MT et al.(eds.),Plant population genetics.Breeding and genetic resources.Sinauer Associates,Sunderland,Massachusetts,USA.pp 43-63.
Hokanson SC,Isebrands JG,Jensen RJ,et al.(1993)Isozyme variation in oaks of the Apostle Islands in Wisconsin:genetic structure and levels of inbreeding in Quercus rubra and Q.ellipsoidalis(Fagaceae).American Journal of Botany 80(11):1349-1357.https://doi.org/10.1002/j.1537-2197.1993.tb15374.x
Honnay O,Jacquemyn H(2007)Susceptibility of common and rare plant species to the genetic consequences of habitat fragmentation.Conservation Biology 21(3):823-831.https://doi.org/10.1111/j.1523-1739.2006.00646.x
Jombart T,Ahmed I(2011)Adegenet 1.3-1:new tools for the analysis of genome-wide SNP data.Bioinformatics 27(21):3070-3071.https://doi.org/10.1093/bioinformatics/btr521
Kamvar ZN,Tabima JF,Grünwald NJ(2014)Poppr:an Rpackage for genetic analysis of populations with clonal,partially clonal,and/or sexual reproduction.PeerJ 2:e281.https://doi.org/10.7717/peerj.281
Kremer A,Dupouey JL,Deans JD,et al.(2002)Leaf morphological differentiation between Quercus robur and Quercus petraea is stable across western European mixed oak stands.Annals of Forest Science 59:777-787.https://doi.org/10.1051/forest:2002065
Kremer A,Petit RJ(1993)Gene diversity in natural populations of oak species.Annals of Forest Science 50:186-202.https://doi.org/10.1051/forest:19930717
Leberg PL(2002)Estimating allelic richness:Effects of sample size and bottlenecks.Molecular Ecology 11(11):2445-2449.https://doi.org/10.1046/j.1365-294X.2002.01612.x
Lind-Riehl JF(2014)Genetic variation,local adaptation and population structure in North American red oak species,Quercus rubra I.and Q.ellipsoidalis E.J.Hill.Dissertation,Michigan Technological University.http://digitalcommons.mtu.edu/etds/864
Lowe A,Harris S,Ashton P(2004)Ecological genetics:design,analysis and application.Blackwell Publishing,Oxford,UK.p344.
Marziliano PA,Coletta V,Scuderi A,et al.(2017)Forest structure of a maple old-growth stand:a case study on the Apennines mountains(Southern Italy).Journal of Mountain Science 14(7):1329-1340.https://doi.org/10.1007/s11629-016-4336-1
Mayes SG,McGinley MA,Werth CR(1998)Clonal population structure and genetic variation in sand-shinnery oak,Quercus havardii(Fagaceae).American Journal of Botany 85:1609-1617.https://doi.org/10.2307/2446489
Mercati F,Riccardi P,Leebens-Mack J,et al.(2013)Single nucleotide polymorphism isolated from a novel EST dataset in garden Asparagus(Asparagus officinalis L.).Plant Science203-204:115-123.https://doi.org/10.1016/j.plantsci.2013.01.002
Mercati F,Longo C,Poma D,et al.(2015)Genetic variation of an italian long shelf-life tomato(Solanum lycopersicon L.)collection by using SSR and morphological fruit traits.Genetic Resources and Crop Evolution 62:721-732.https://dai.org/10.1007/s10722-014-0191-5
Morán-López T,Forner A,Flores-Rentería D,et al.(2016)Some positive effects of the fragmentation of holm oak forests:Attenuation of water stress and enhancement of acorn production.Forest Ecology and Management 370:22-30.https://doi.org/10.1016/j.foreco.2016.03.042
Navascués M,Emerson BC(2005)Chloroplast microsatellites:Measures of genetic diversity and the effect of homoplasy.Molecular Ecology 14:1333-1341https://doi.org/10.1111/j.1365-294x.2005.02504.x
Neophytou C,Aravanopoulos FA,Fink S,et al.(2010)Detecting interspecific and geographic differentiation patterns in two interfertile oak species(Quercus petraea(Matt.)Liebl.and Q.robur L.)using small sets of microsatellite markers.Forest Ecology and Management 259(10):2026-2035.https://doi.org/10.1016/j.foreco.2010.02.013
Nixon KC(1993)Infrageneric classification of Quercus(Fagaceae)and typification of sectional names.Annals of Forest Science 50:25-34.https://doi.org/10.1051/forest:19930701
Peakall ROD,Smouse PE(2006)Genalex 6:genetic analysis in Excel.Population genetic software for teaching and research.Molecular Ecology Notes 6(1):288-295.https://doi.org/10.1111/j.1471-8286.2005.01155.x
Petit RJ,Latouche-HalléC,Pemonge MH,et al.(2002)Chloroplast DNA variation of oaks in France and the influence of forest fragmentation on genetic diversity.Forest Ecology and Management 156(1-3):115-129.https://doi.org/10.1016/s0378-1127(01)00638-7
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