A Study on Genetic Diversity of Populus tremula in China by Single-copy Nuclear Markers

DU Shu-hui; WANG Zhao-shan; BAOERJIANG Abuduhamiti; XING Shi-yan; ZHANG Jian-guo

Volume 29 Issue 1

Article Contents

Turn off MathJax

Article Navigation > Forest Research > 2016 > 29(1): 48-52

Citation:

A Study on Genetic Diversity of Populus tremula in China by Single-copy Nuclear Markers

1.
Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China
2.
College of Forestry, Shandong Agricultural University, Tai'an 271000, Shandong, China
3.
Altay Research Institute of Forestry, Altay 836500, Xinjiang, China

Received Date: 2015-01-05

Abstract

[Objective]This paper aims at investigating the genetic diversity and genetic differentiation of Populus tremula distributed in Xinjiang, China. [Method]Six single-copy nuclear gene markers of 72 P. tremula individuals from 4 populations in Xinjiang were amplified and sequenced. The parameters of genetic diversity and genetic differentiation were calculated. [Result]After aligning, the length of the six genes ranged between 459 bp and 747 bp and the average number of polymorphism sites was 14. Diversity parameters, π and θw reached 0.004 8 and 0.004 4, respectively. The mean value of gene diversity was 0.73. These indicated high level of genetic diversity of P. tremula. The results of Neutral tests using Tajima's D were not significant, which indicated all the six genes did not violate from neutrality. The results of AMOVA analysis showed that 89.72% of the total variance existed within populations. The average genetic differentiation parameter Fst and gene flow among populations reached 0.10 and 3.235, respectively. [Conclusion]High level of outcrossing rate and nucleotide mutation rate as well as long distance dispersal seed contributed to the high level of genetic diversity and low genetic differentiation in P. tremula in Xinjiang, China.
- Xinjiang,
- Populus tremula,
- sing-copy nuclear markers,
- genetic diversity,
- genetic differentiation

References

[1]	中国科学院中国植物志编辑委员会[M].《中国植物志》北京: 科学出版社, 1984, 20 (2): 12.
[2]	Ingvarsson P K. Nucleotide polymorphism and linkage disequilibrium within and among natural populations of European aspen (Populus tremula L., Salicaceae)[J]. Genetics, 2005, 169(2): 945-953.
[3]	Ingvarsson P K. Multilocus patterns of nucleotide polymorphism and the demographic history of Populus tremula[J]. Genetics, 2008, 180(1): 329-340.
[4]	Fussi B, Lexer C, Heinze B. Phylogeography of Populus alba (L.) and Populus tremula (L.) in Central Europe: secondary contact and hybridisation during recolonisation from disconnected refugia[J]. Tree Genetics & Genomes, 2010, 6(3): 439-450.
[5]	Wendel J F, Doyle J J. Phylogenetic incongruence: window into genome history and molecular evolution[J]. Molecular Systematics of Plants. London: Springer. 1998: 265-296.
[6]	Zhang LB, Ge S. Multilocus analysis of nucleotide variation and speciation in Oryza officinalis and its close relatives[J]. Molecular Biology and Evolution, 2007, 24(3):769-783.
[7]	Wang Z, Du S, Dayanandan S, et al. Phylogeny reconstruction and hybrid analysis of Populus (Salicaceae) based on nucleotide sequences of multiple single-copy nuclear genes and plastid fragments[J]. PloS One, 2014, 9(8): e103645.
[8]	Tuskan G A, Difazio S, Jansson S, et al. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)[J]. Science, 2006, 313(5793): 1596-1604.
[9]	Du S H, Wang Z H, Zhang J G. A novel set of 15 single-copy nuclear DNA markers for genetic studies of Salicaceae[J]. Genetics and Molecular Research, 2015, 13(3): 4911-4917.
[10]	李际红, 邢世岩, 王聪聪, 等.银杏基因组 DNA 甲基化修饰位点的 MSAP 分析[J]. 园艺学报, 2011, 38 (8): 1429-1436.
[11]	Thompson J D, Gibson T J, Plewniak F, et al. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools[J]. Nucleic Acids Research, 1997, 25(24): 4876-4882.
[12]	Hall TA 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. 95-98[Z].
[13]	Librado P, Rozas J. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data[J]. Bioinformatics, 2009, 25(11): 1451-1452.
[14]	Nei M. Molecular evolutionary genetics[M]. New York: Columbia University Press, 1987.
[15]	Nei M. Evolution of human races at the gene level, Human genetics, part A: The unfolding genome[M]. New York: Alan R. Liss, 1982: 167-181.
[16]	Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism[J]. Genetics, 1989, 123(3): 585-595.
[17]	Nei M, Li W H. Mathematical model for studying genetic variation in terms of restriction endonucleases[J]. Proceedings of the National Academy of Sciences, 1979, 76(10): 5269- 5273.
[18]	Watterson G A. On the number of segregating sites in genetical models without recombination[J]. Theoretical Population Biology, 1975, 7(2): 256-276.
[19]	Excoffier L, Laval G, Schneider S. Arlequin (version 3.0): an integrated software package for population genetics data analysis[J]. Evolutionary Bioinformatics, 2005, 1: 47.
[20]	Heuertz M, De Paoli E, Källman T, et al. Multilocus patterns of nucleotide diversity, linkage disequilibrium and demographic history of Norway spruce[Picea abies (L.) Karst][J]. Genetics, 2006, 174(4): 2095-2105.
[21]	Ismail M, Soolanayakanahally R Y, Ingvarsson P K, et al. Comparative nucleotide diversity across North American and European Populus species[J]. Journal of Molecular Evolution, 2012, 74: 257-272.
[22]	DiFazio S P, Slavov G T, Joshi C P. Populus: a premier pioneer system for plant genomics. Genetics, genomics and breeding of poplar[M]. Lebanon: Science Publishers, Inc. 2011: 1-28.
[23]	杜淑辉. 杨属分子系统发育及三个山杨物种的生物地理学研究[D]. 中国林业科学研究院博士学位论文,2014.
[24]	Wright S I, Gaut B S. Molecular population genetics and the search for adaptive evolution in plants[J]. Molecular Biology and Evolution, 2005, 22(3): 506-519.
[25]	Charlesworth D. Effects of inbreeding on the genetic diversity of populations[J]. Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences, 2003, 358(1434): 1051-1070.
[26]	Richardson J E, Pennington R T, Pennington T D, et al. Rapid diversification of a species-rich genus of neotropical rain forest trees[J]. Science, 2001, 293(5538): 2242-2245.
[27]	Hamrick J, Godt M. Effects of life history traits on genetic diversity in plant species[J]. Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences, 1996, 351(1345): 1291-1298.
[28]	Petit R J, Aguinagalde I, de Beaulieu J L, et al. Glacial refugia: hotspots but not melting pots of genetic diversity[J]. Science, 2003, 300(5625): 1563.
[29]	张建国.新疆杨属植物研究[M]. 北京: 科学出版社, 2014: 92-93.

Proportional views

通讯作者: 陈斌, bchen63@163.com

1.
沈阳化工大学材料科学与工程学院沈阳 110142

Get Citation

PDF

XML

Article views(3021) PDF downloads(833) Cited by()

Proportional views

A Study on Genetic Diversity of Populus tremula in China by Single-copy Nuclear Markers

1. Key Laboratory of Tree Breeding and Cultivation, State Forestry Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China

2. College of Forestry, Shandong Agricultural University, Tai'an 271000, Shandong, China

3. Altay Research Institute of Forestry, Altay 836500, Xinjiang, China

Received Date: 2015-01-05

Abstract: [Objective]This paper aims at investigating the genetic diversity and genetic differentiation of Populus tremula distributed in Xinjiang, China. [Method]Six single-copy nuclear gene markers of 72 P. tremula individuals from 4 populations in Xinjiang were amplified and sequenced. The parameters of genetic diversity and genetic differentiation were calculated. [Result]After aligning, the length of the six genes ranged between 459 bp and 747 bp and the average number of polymorphism sites was 14. Diversity parameters, π and θw reached 0.004 8 and 0.004 4, respectively. The mean value of gene diversity was 0.73. These indicated high level of genetic diversity of P. tremula. The results of Neutral tests using Tajima's D were not significant, which indicated all the six genes did not violate from neutrality. The results of AMOVA analysis showed that 89.72% of the total variance existed within populations. The average genetic differentiation parameter Fst and gene flow among populations reached 0.10 and 3.235, respectively. [Conclusion]High level of outcrossing rate and nucleotide mutation rate as well as long distance dispersal seed contributed to the high level of genetic diversity and low genetic differentiation in P. tremula in Xinjiang, China.

HTML

Reference (29)

[1]	中国科学院中国植物志编辑委员会[M].《中国植物志》北京: 科学出版社, 1984, 20 (2): 12.
[2]	Ingvarsson P K. Nucleotide polymorphism and linkage disequilibrium within and among natural populations of European aspen (Populus tremula L., Salicaceae)[J]. Genetics, 2005, 169(2): 945-953.
[3]	Ingvarsson P K. Multilocus patterns of nucleotide polymorphism and the demographic history of Populus tremula[J]. Genetics, 2008, 180(1): 329-340.
[4]	Fussi B, Lexer C, Heinze B. Phylogeography of Populus alba (L.) and Populus tremula (L.) in Central Europe: secondary contact and hybridisation during recolonisation from disconnected refugia[J]. Tree Genetics & Genomes, 2010, 6(3): 439-450.
[5]	Wendel J F, Doyle J J. Phylogenetic incongruence: window into genome history and molecular evolution[J]. Molecular Systematics of Plants. London: Springer. 1998: 265-296.
[6]	Zhang LB, Ge S. Multilocus analysis of nucleotide variation and speciation in Oryza officinalis and its close relatives[J]. Molecular Biology and Evolution, 2007, 24(3):769-783.
[7]	Wang Z, Du S, Dayanandan S, et al. Phylogeny reconstruction and hybrid analysis of Populus (Salicaceae) based on nucleotide sequences of multiple single-copy nuclear genes and plastid fragments[J]. PloS One, 2014, 9(8): e103645.
[8]	Tuskan G A, Difazio S, Jansson S, et al. The genome of black cottonwood, Populus trichocarpa (Torr. & Gray)[J]. Science, 2006, 313(5793): 1596-1604.
[9]	Du S H, Wang Z H, Zhang J G. A novel set of 15 single-copy nuclear DNA markers for genetic studies of Salicaceae[J]. Genetics and Molecular Research, 2015, 13(3): 4911-4917.
[10]	李际红, 邢世岩, 王聪聪, 等.银杏基因组 DNA 甲基化修饰位点的 MSAP 分析[J]. 园艺学报, 2011, 38 (8): 1429-1436.
[11]	Thompson J D, Gibson T J, Plewniak F, et al. The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools[J]. Nucleic Acids Research, 1997, 25(24): 4876-4882.
[12]	Hall TA 1999. BioEdit: a user-friendly biological sequence alignment editor and analysis program for Windows 95/98/NT. 95-98[Z].
[13]	Librado P, Rozas J. DnaSP v5: a software for comprehensive analysis of DNA polymorphism data[J]. Bioinformatics, 2009, 25(11): 1451-1452.
[14]	Nei M. Molecular evolutionary genetics[M]. New York: Columbia University Press, 1987.
[15]	Nei M. Evolution of human races at the gene level, Human genetics, part A: The unfolding genome[M]. New York: Alan R. Liss, 1982: 167-181.
[16]	Tajima F. Statistical method for testing the neutral mutation hypothesis by DNA polymorphism[J]. Genetics, 1989, 123(3): 585-595.
[17]	Nei M, Li W H. Mathematical model for studying genetic variation in terms of restriction endonucleases[J]. Proceedings of the National Academy of Sciences, 1979, 76(10): 5269- 5273.
[18]	Watterson G A. On the number of segregating sites in genetical models without recombination[J]. Theoretical Population Biology, 1975, 7(2): 256-276.
[19]	Excoffier L, Laval G, Schneider S. Arlequin (version 3.0): an integrated software package for population genetics data analysis[J]. Evolutionary Bioinformatics, 2005, 1: 47.
[20]	Heuertz M, De Paoli E, Källman T, et al. Multilocus patterns of nucleotide diversity, linkage disequilibrium and demographic history of Norway spruce[Picea abies (L.) Karst][J]. Genetics, 2006, 174(4): 2095-2105.
[21]	Ismail M, Soolanayakanahally R Y, Ingvarsson P K, et al. Comparative nucleotide diversity across North American and European Populus species[J]. Journal of Molecular Evolution, 2012, 74: 257-272.
[22]	DiFazio S P, Slavov G T, Joshi C P. Populus: a premier pioneer system for plant genomics. Genetics, genomics and breeding of poplar[M]. Lebanon: Science Publishers, Inc. 2011: 1-28.
[23]	杜淑辉. 杨属分子系统发育及三个山杨物种的生物地理学研究[D]. 中国林业科学研究院博士学位论文,2014.
[24]	Wright S I, Gaut B S. Molecular population genetics and the search for adaptive evolution in plants[J]. Molecular Biology and Evolution, 2005, 22(3): 506-519.
[25]	Charlesworth D. Effects of inbreeding on the genetic diversity of populations[J]. Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences, 2003, 358(1434): 1051-1070.
[26]	Richardson J E, Pennington R T, Pennington T D, et al. Rapid diversification of a species-rich genus of neotropical rain forest trees[J]. Science, 2001, 293(5538): 2242-2245.
[27]	Hamrick J, Godt M. Effects of life history traits on genetic diversity in plant species[J]. Philosophical Transactions of the Royal Society of London. Series B: Biological Sciences, 1996, 351(1345): 1291-1298.
[28]	Petit R J, Aguinagalde I, de Beaulieu J L, et al. Glacial refugia: hotspots but not melting pots of genetic diversity[J]. Science, 2003, 300(5625): 1563.
[29]	张建国.新疆杨属植物研究[M]. 北京: 科学出版社, 2014: 92-93.

A Study on Genetic Diversity of Populus tremula in China by Single-copy Nuclear Markers

Abstract

References

Proportional views

通讯作者: 陈斌, bchen63@163.com

Proportional views

A Study on Genetic Diversity of Populus tremula in China by Single-copy Nuclear Markers

HTML

Catalog

Export File

Citation

Format

Content