滇杨种群遗传多样性与遗传结构
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摘要
滇杨(Populus yunnanensis)是我国西南地区的特有树种,具有速生、易无性繁殖、适应性强等优良特性,是典型的南方型杨属树种。研究滇杨遗传多样性及种群结构对其种质资源的收集、保存和利用具有重要的意义。本研究从我国滇杨主要分布区云南和四川共采集了6个种群,包括云南的昭通(ZT)、会泽(HZ)、嵩明(SM)、洱源(EY)、拉市海(LS)以及四川的美姑(MG),共64个个体,利用34对SSR分子标记和3对cp DNA叶绿体标记开展遗传多样性与遗传结构研究。SSR引物共检测到154个等位基因,平均等位基因数为4.529,观测杂合度(Ho)与期望杂合度(He)分别为0.552和0.472,遗传分化系数(Fst)平均值为0.238,多态性信息含量指数(PIC)平均值为0.421,基因流(Nm)为0.806。滇杨的遗传结构分析(DAPC)与遗传距离的主坐标分析(PCo A)、UPGMA聚类分析均将6个种群划分为3个亚类:第?亚类包括昭通种群、会泽种群和嵩明种群的4个个体,第??亚类包括嵩明种群的6个个体以及洱源种群和拉市海种群,第III亚类为美姑种群;嵩明种群包含第?和第??两个亚类的混合遗传成分。3个cp DNA联合序列中共检测到35个变异位点,分为13个单倍型,其中单倍型H5在种群中分布最为广泛,其余的单倍型均为种群特有的单倍型。分子方差分析(AMOVA)表明种群内的遗传变异大于种群间变异。研究表明滇杨不同种群的遗传分化具有地域性,可选择就地保护;昭通种群遗传多样性最高,且包含7种叶绿体单倍型,单倍型类型最多,应优先保护。
Populus yunnanensis is an endemic tree species to Southwestern China. It is a typical southern Populus species that is fast-growing species with easy to clone propagules and is highly adaptable. It is important to research the genetic diversity and population structure of P. yunnanensis for the collection, preservation and utilization of the germplasm resources. In this study, 64 individuals were collected from six populations, spaning the main distribution areas of P. yunnanensis, including Zhaotong(ZT), Huize(HZ), Songming(SM), Eryuan(EY), Lashihai(LS) and Sichuan Meigu(MG). A total of 34 pairs of SSR primers and three pairs of cpDNA primers were used to determine out the genetic diversity and genetic structure. A total of 154 alleles were detected by SSR primers in P. yunnanensis. The average number of alleles was 4.529. The observed heterozygosity(Ho) and expected heterozygosity(He) were 0.552 and 0.472, respectively. And the average genetic differentiation coefficient(Fst) was 0.238. The average polymorphism information content(PIC) was 0.421 and the gene flow(Nm) was 0.806. The results of the DAPC, PCoA and UPGMA analyses showed that the six populations can be divided into three sub-categories: Group ? included ZT, HZ and four individuals of SM. Group II included EY, LS and the six remaining individuals of SM; and group III included MG; SM population include mixed genetic components from ? and ??. A total of 35 variable sites were detected in the three cpDNA combinations, forming 13 haplotypes. Among them, haplotype H5 was the most widely distributed in the population,while the remaining ones were of private haplotypes. Analysis of molecular variance(AMOVA) showed that genetic variation within the population was greater than between populations. The study clarifies that P. yunnanensis has geographical distribution characteristics and is suited to in situ conservation. As ZT population has the highest genetic diversity and contains seven chloroplast haplotypes, it should be given protection priority.
Populus yunnanensis is an endemic tree species to Southwestern China. It is a typical southern Populus species that is fast-growing species with easy to clone propagules and is highly adaptable. It is important to research the genetic diversity and population structure of P. yunnanensis for the collection, preservation and utilization of the germplasm resources. In this study, 64 individuals were collected from six populations, spaning the main distribution areas of P. yunnanensis, including Zhaotong(ZT), Huize(HZ), Songming(SM), Eryuan(EY), Lashihai(LS) and Sichuan Meigu(MG). A total of 34 pairs of SSR primers and three pairs of cpDNA primers were used to determine out the genetic diversity and genetic structure. A total of 154 alleles were detected by SSR primers in P. yunnanensis. The average number of alleles was 4.529. The observed heterozygosity(Ho) and expected heterozygosity(He) were 0.552 and 0.472, respectively. And the average genetic differentiation coefficient(Fst) was 0.238. The average polymorphism information content(PIC) was 0.421 and the gene flow(Nm) was 0.806. The results of the DAPC, PCoA and UPGMA analyses showed that the six populations can be divided into three sub-categories: Group ? included ZT, HZ and four individuals of SM. Group II included EY, LS and the six remaining individuals of SM; and group III included MG; SM population include mixed genetic components from ? and ??. A total of 35 variable sites were detected in the three cpDNA combinations, forming 13 haplotypes. Among them, haplotype H5 was the most widely distributed in the population,while the remaining ones were of private haplotypes. Analysis of molecular variance(AMOVA) showed that genetic variation within the population was greater than between populations. The study clarifies that P. yunnanensis has geographical distribution characteristics and is suited to in situ conservation. As ZT population has the highest genetic diversity and contains seven chloroplast haplotypes, it should be given protection priority.
引文
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Du QZ,Wang B,Wei ZZ,Zhang DQ,Li BL(2012)Genetic diversity and population structure of Chinese white poplar(Populus tomentosa)revealed by SSR markers.Journal of Heredity,103,853-862.
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Jiang DC,Wu GL,Mao KS,Feng JJ(2015)Structure of genetic diversity in marginal populations of black poplar(Populus nigra L.).Biochemical Systematics and Ecology,61,297-302.
Jombart T,Devillard S,Balloux F(2010)Discriminant analysis of principal components:A new method for the analysis of genetically structured populations.BMC Genetics,11,94.
Kumar S,Stecher G,Tamura K(2016)MEGA7:Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets.Molecular Biology and Evolution,33,1870-1874.
Peakall R,Smouse PE(2006)GENALEX 6:Genetic analysis in Excel.Population genetic software for teaching and research.Molecular Ecology Notes,6,288-295.
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Qiu YX,Fu CX,Comes HP(2011)Plant molecular phylogeography in China and adjacent regions:Tracing the genetic imprints of Quaternary climate and environmental change in the world’s most diverse temperate flora.Molecular Phylogenetics and Evolution,59,225-244.
Retief JD(1999)Phylogenetic analysis using PHYLIP.Methods in Molecular Biology,132,243-258.
Roy JK,Lakshmikumaran MS,Balyan HS,Gupta PK(2004)AFLP-based genetic diversity and its comparison with diversity based on SSR,SAMPL,and phenotypic traits in bread wheat.Biochemical Genetics,42,43-59.
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Schuelke M(2000)An economic method for the fluorescent labeling of PCR fragments.Nature Biotechnology,18,233-234.
Semerikova SA,Semerikov VL(2014)Molecular phylogenetic analysis of the genus Abies(Pinaceae)based on the nucleotide sequence of chloroplast DNA.Genetika,50,12-25.
Shang ZH,Yao AX(2002)Biological genetic diversity research methods and their protective measures.Journal of Ningxia Agricultural College,23(1),66-69.(in Chinese)[尚占环,姚爱兴(2002)生物遗传多样性研究方法及其保护措施.宁夏农学院学报,23(1),66-69.]
Shen XF,Wu ML,Liao BS,Liu ZX,Bai R,Xiao SM,Li XW,Zhang BL,Xu J,Chen SL(2017)Complete chloroplast genome sequence and phylogenetic analysis of the medicinal plant Artemisia annua.Molecules,22,1330.
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Wan XQ,Zhang F,Zhong Y,Wang CL,Ding YH,Hu TX,Zhai MP,Qian ZL(2009)Conservation and application of the genetic resource of native poplars in Southwest China.Scientia Silvae Sinicae,45(4),139-144.(in Chinese with English abstract)[万雪琴,张帆,钟宇,王长亮,丁云海,胡庭兴,翟明普,钱宗亮(2009)中国西南地区乡土杨树基因资源的保护与利用.林业科学,45(4),139-144.]
Wang J,Li ZJ,Guo QH,Ren GP,Wu YX(2011)Genetic variation within and between populations of a desert poplar(Populus euphratica)revealed by SSR markers.Annals of Forest Science,68,1143-1149.
Wang JL,Gao QB,Fu PC,Gulzar K,Chen SL,Zhang FQ(2014)Phylogeography of Spiraea mongolica(Rosaceae)on the Qinghai-Tibetan Plateau and adjacent highlands.Acta Botanica Boreali-Occidentalia Sinica,10,1981-1991.(in Chinese with English abstract)[王久利,高庆波,付鹏程,Gulzar K,陈世龙,张发起(2014)青藏高原及其毗邻山区蒙古绣线菊谱系地理学研究.西北植物学报,34,1981-1991.]
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Bai WN,Zhang DY(2014)Current status and future directions in plant phylogeography.Chinese Bulletin of Life Sciences,26,125-137.(in Chinese with English abstract)[白伟宁,张大勇(2014)植物亲缘地理学的研究现状与发展趋势.生命科学,26,125-137.]
Bandelt HJ,Forster P,R?hl A(1999)Median-joining networks for inferring intraspecific phylogenies.Molecular Biology and Evolution,16,37-48.
Burland TG(2000)DNASTAR’s Lasergene sequence analysis software.Methods in Molecular Biology,132,71-91.
Chen K(2007)Genetic Relationships among Poplar Species in Section Tacamahaca Spach from Western Sichuan of China.PhD dissertation,Chengdu Institute of Biology,Chinese Academy of Sciences,Chengdu.(in Chinese with English abstract)[陈珂(2007)川西青杨组(Section Tacamahaca Spach)不同种的亲缘关系分析.博士学位论文,中国科学院成都生物研究所,成都.]
Chen XM,He ZH,Shi JR,Xia LQ,Rick W,Zhou Y,Jiang GL(2003)Genetic diversity of high quality winter wheat varieties(lines)based on SSR markers.Acta Agronomica Sinica,29,13-19.(in Chinese with English abstract)[陈新民,何中虎,史建荣,夏兰芹,Ward Rick,周阳,蒋国梁(2003)利用SSR标记进行优质冬小麦品种(系)的遗传多样性研究.作物学报,29,13-19.]
Chen XY(2000)Effects of habitat fragmentation on genetic structure of plant populations and implications for the biodiversity conservation.Acta Ecologica Sinica,20,884-892.(in Chinese with English abstract)[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.生态学报,20,884-892.]
Crandall KA,Templeton AR(1993)Empirical tests of some predictions from coalescent theory with applications to intraspecific phylogeny reconstruction.Genetics,134,959-969.
DiFazio S,Slavov G,Rodgers-Melnick E,Martin J,Schackwitz W,Priya R,Tuskan G(2011)Inferring the evolutionary history of Populus trichocarpa from whole genome resequencing data.BMC Proceedings,5,O1.
Du QZ,Wang B,Wei ZZ,Zhang DQ,Li BL(2012)Genetic diversity and population structure of Chinese white poplar(Populus tomentosa)revealed by SSR markers.Journal of Heredity,103,853-862.
Ferradini N,Lancioni H,Torricelli R,Russi L,Ragione ID,Cardinali I,Marconi G,Gramaccia M,Concezzi L,Achilli A,Veronesi F,Albertini E(2017)Characterization and phylogenetic analysis of ancient Italian landraces of pear.Frontiers in Plant Science,8,751.
Golding GB(1987)The detection of deleterious selection using ancestors inferred from a phylogenetic history.Genetics Research,49,71-82.
Gong GT(2004)The geographic distribution and origin of Populus L.Journal of Sichuan Forestry Science and Technology,25(2),25-30.(in Chinese with English abstract)[龚固堂(2004)杨属地理分布与起源初探.四川林业科技,25(2),25-30.]
Hamrick JL,Godt MJW,Sherman-Broyles SL(1992)Factors influencing levels of genetic diversity in woody plant species.New Forests,6,95-124.
He CZ,Che PY,Peng CY,Zhou XT,Duan AA,Wang DX,Xin PY(2010)A survey of research progress on gene resources of Populus yunnanensis.Journal of Southwest Forestry University,30(1),83-88.(in Chinese with English abstract)[何承忠,车鹏燕,周修涛,段安安,王德新,辛培尧(2010)滇杨基因资源及其研究概况.西南林业大学学报,30(1),83-88.]
He CZ,Zhang ZY,Duan AA,Feng XL(2009)Genetic Diversity Analysis of Populus yunnanensis by AFLP Markers.China Forestry Publishing House,Beijing.(in Chinese)[何承忠,张志毅,段安安,冯夏莲(2009)滇杨基因资源遗传多样性的AFLP分析.中国林业出版社,北京.]
Jia HX,Ji HJ,Hu JJ,Lu MZ(2015)Fingerprints of SSR markers and ploidy detection for new Populus varieties.Scientia Silvae Sinicae,51(2),69-79.(in Chinese with English abstract)[贾会霞,姬慧娟,胡建军,卢孟柱(2015)杨树新品种的SSR指纹图谱构建和倍性检测.林业科学,51(2),69-79.]
Jiang DC,Wu GL,Mao KS,Feng JJ(2015)Structure of genetic diversity in marginal populations of black poplar(Populus nigra L.).Biochemical Systematics and Ecology,61,297-302.
Jombart T,Devillard S,Balloux F(2010)Discriminant analysis of principal components:A new method for the analysis of genetically structured populations.BMC Genetics,11,94.
Kumar S,Stecher G,Tamura K(2016)MEGA7:Molecular Evolutionary Genetics Analysis version 7.0 for bigger datasets.Molecular Biology and Evolution,33,1870-1874.
Peakall R,Smouse PE(2006)GENALEX 6:Genetic analysis in Excel.Population genetic software for teaching and research.Molecular Ecology Notes,6,288-295.
Peng YH(2006)Population Genetic Survey of Populus cathayana Rehd.Originating from eastern edge of Qinghai-Tibetan Plateau of China.PhD dissertation,Chengdu Institute of Biology,Chinese Academy of Sciences,Chengdu.(in Chinese with English abstract)[彭幼红(2006)青藏高原东缘青杨(Populus cathayana Rehd.)遗传多样性研究.博士学位论文,中国科学院研究生院成都生物研究所,成都.]
Polzin T,Daneshmand SV(2003)On Steiner trees and minimum spanning trees in hypergraphs.Operations Research Letters,31,12-20.
Posada D,Crandall KA(2001)Intraspecific gene genealogies:Trees grafting into networks.Trends in Ecology&Evolution,16,37-45.
Qiu YX,Fu CX,Comes HP(2011)Plant molecular phylogeography in China and adjacent regions:Tracing the genetic imprints of Quaternary climate and environmental change in the world’s most diverse temperate flora.Molecular Phylogenetics and Evolution,59,225-244.
Retief JD(1999)Phylogenetic analysis using PHYLIP.Methods in Molecular Biology,132,243-258.
Roy JK,Lakshmikumaran MS,Balyan HS,Gupta PK(2004)AFLP-based genetic diversity and its comparison with diversity based on SSR,SAMPL,and phenotypic traits in bread wheat.Biochemical Genetics,42,43-59.
Rozas J,Sánchez-DelBarrio JC,Messeguer X,Rozas R(2003)Dna SP,DNA polymorphism analyses by the coalescent and other methods.Bioinformatics,19,2496-2497.
Schuelke M(2000)An economic method for the fluorescent labeling of PCR fragments.Nature Biotechnology,18,233-234.
Semerikova SA,Semerikov VL(2014)Molecular phylogenetic analysis of the genus Abies(Pinaceae)based on the nucleotide sequence of chloroplast DNA.Genetika,50,12-25.
Shang ZH,Yao AX(2002)Biological genetic diversity research methods and their protective measures.Journal of Ningxia Agricultural College,23(1),66-69.(in Chinese)[尚占环,姚爱兴(2002)生物遗传多样性研究方法及其保护措施.宁夏农学院学报,23(1),66-69.]
Shen XF,Wu ML,Liao BS,Liu ZX,Bai R,Xiao SM,Li XW,Zhang BL,Xu J,Chen SL(2017)Complete chloroplast genome sequence and phylogenetic analysis of the medicinal plant Artemisia annua.Molecules,22,1330.
Tippmann HF(2004)Analysis for free:Comparing programs for sequence analysis.Briefings in Bioinformatics,5,82-87.
Wan XQ,Zhang F,Zhong Y,Wang CL,Ding YH,Hu TX,Zhai MP,Qian ZL(2009)Conservation and application of the genetic resource of native poplars in Southwest China.Scientia Silvae Sinicae,45(4),139-144.(in Chinese with English abstract)[万雪琴,张帆,钟宇,王长亮,丁云海,胡庭兴,翟明普,钱宗亮(2009)中国西南地区乡土杨树基因资源的保护与利用.林业科学,45(4),139-144.]
Wang J,Li ZJ,Guo QH,Ren GP,Wu YX(2011)Genetic variation within and between populations of a desert poplar(Populus euphratica)revealed by SSR markers.Annals of Forest Science,68,1143-1149.
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