Identification of Rosa sterilis Based on AFLP Molecular Markers and DNA Barcodes

LI Dan; ZHOU An-pei; ZHANG De-guo; GAO Jian; HE Cheng-zhong; LI Yong-he

Volume 28 Issue 1

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Identification of Rosa sterilis Based on AFLP Molecular Markers and DNA Barcodes

1.
Southwest Forestry University, Kunming 650224, Yunnan, China
2.
Yunnan Academy of Biodiversity, Kunming 650224, Yunnan, China
3.
Rocky Desertification Comprehensive Treatment Office of Xing'ren County, Xing'ren 562300, Guizhou, China

Received Date: 2014-07-21

Abstract

Nineteen Rosa roxbunghii, R. sterilis and R. sterilis var. leioclada specimen collected from Xing'ren and Anshun in Guizhou of China were identified by AFLP molecular markers and DNA barcodes. The results of AFLP showed that genetic similarity coefficient among the 19 specimen ranged from 0.719 0 0.997 2 and the average was 0.936 5. The result of UPGMA cluster analysis showed that the 19 specimen could be divided into two groups. R. roxbunghii was distinct from the others and formed one group separately, which the others fall into another group. The result of DNA barcodes showed that there was not variable site in ITS sequences and 4 cpDNA sequences showed highly closed affinity. Based on combined sequences, the average error was 0.000 6, while the genetic distance between R. roxbunghii and the others was 0.005 8. The identification results of two methods were consistent. R. sterilis and R. roxbunghii were two segregated species. The R. sterilis collected from Xing'ren and R. sterilis var. leioclada collected from Anshun belong to the same species. The results of this study determined the phylogeny status of R. sterilis at the level of molecular and gene and laid the theoretical foundation for further collection, preservation, exploitation and application of R. sterilis germplasm resources.
- Rosa roxbunghii,
- Rosa sterilis,
- AFLP markers,
- ITS sequences,
- cpDNA sequences

References

[1]	时圣德. 贵州蔷薇属植物新分类群[J]. 贵州科学, 1985, 9(1): 8-9.
[2]	付慧晓, 王道平, 黄丽荣, 等. 刺梨和无籽刺梨挥发性香气成分分析[J]. 精细化工, 2012, 29(9): 875-878.
[3]	邓朝义, 方仕能, 黄勇. 贵州特有种子植物无子刺梨形态特征研究及分类学订正[J]. 种子, 2009, 28(9): 62-68.
[4]	韦景枫, 钟漫, 程友忠, 等. 无籽刺梨试管苗移栽及其影响因素的探讨[J]. 中国林副特产, 2010, 104(6): 30-31.
[5]	季祥彪, 李淑久. 贵州4种刺梨的比较形态解剖学研究[J]. 山地农业生物学报, 1998, 1(1): 28-33.
[6]	文晓鹏, 庞晓明, 邓秀新. 刺梨及部分近缘种的形态学形状及RAPD 标记分析[J]. 园艺学报, 2003, 30 (2): 204-206.
[7]	安明态, 程友忠, 钟漫, 等. 贵州蔷薇属一新变种--光枝无子刺梨[J]. 种子, 2009, 28(1): 6.
[8]	纵丹, 员涛, 周安佩, 等. 滇杨优树遗传多样性的 AFLP 分析[J]. 西北林学院学报, 2014, 29(4): 103-108.
[9]	Tautz D, Arctander P, Minelli A, et al. DNA points the way ahead in taxonomy[J]. Nature, 2002, 418: 479.
[10]	Hebert P D N, Cywinska A, Ball S L. Biological identifications through DNA barcodes[J]. Proceedings of the Royal Society of London. Series B: Biological Sciences, 2003, 270: 313-321.
[11]	Liu J, Shi L, Han J, et al. Identification of species in the angiosperm family Apiaceae using DNA barcodes[J]. Molecular Ecology Resources, 2014 Apr 16. doi: 10.1111/1755-0998.12262.
[12]	Weitschek E, Fiscon G, Felici G. Supervised DNA barcodes species classification: analysis, comparisons and results[J]. BioData Mining, 2014 Apr 11, 7(1):4. doi: 10.1186/1756-0381-7-4.
[13]	Li X, Yang Y, Henry R J, et al. Plant DNA barcoding: from gene to genome[J]. Biological Reviews, 2014 Mar 26, doi: 10.1111/brv.12104.
[14]	Vos P, Hogers R, Bleeker M, et al. AFLP: a new technique for DNA fingerprinting[J]. Nucleic acids research, 1995, 23(21): 4407-4414.
[15]	Tixier M H, Sourdille P, Rder M, et al. Detection of wheat microsatellites using a non radioactive silver-nitrate staining method[J]. Journal of Genetics and Breeding, 1997, 51(2): 175-178.
[16]	张富民, 葛颂. 群体遗传学研究中的数据处理方法I. RAPD 数据的 AMOVA分析[J]. 生物多样性, 2002, 10(4): 438-444.
[17]	Yeh F, Yang R C, Boyle T. POPGENE. A User-friendly Shareware for Population Genetic Analysis [M]. Edmonton: Molecular and Biotechnology Center, University of Alberta, 1997.
[18]	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.
[19]	Swofford D L.. PAUP* 4.0: Phylogenetic analysis using parsimony and other methods. Beta version 4.0 b10[M]. Sunderland: Sinauer Associates. 2002.
[20]	Kimura M. Estimation of evolutionary distances between homologous nucleotide sequences[J]. Proceedings of the National Academy of Sciences, 1981, 78(1): 454-458.
[21]	Kumar S, Tamura K, Nei M, et al. MEGA: molecular evolutionary genetics analysis, version 1.02[J]. Systematic Biology, 1995, 44(4): 576-577.
[22]	Lahaye R, Bank M V D, Bogarin D, et al. DNA barcoding the floras of biodiversity hotspots[J]. Proceedings of the National Academy of Sciences, 2008, 105(8): 2923-2928.
[23]	Lahaye R, Savolainen V, Duthoit S, et al. A test of psbK-psbI and atpF-atpH as potential plant DNA barcodes using the flora of the Kruger National Park as a model system (South Africa)[J]. Nature Precedings, 2008: 1-21.
[24]	Taberlet P, Gielly L, Pautou G, et al. Universal primers for amplification of three non-coding regions of chloroplast DNA[J]. Plant Molecular Biology, 1991, 17(5): 1105-1109.
[25]	White T J, Bruns T, Lee S, et al. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis M A eds., PCR protocols: a guide to methods and applications[M]. New York: Academic Press, 1990, 315-322.
[26]	黄建安, 李家贤, 黄意欢, 等. 茶树品种资源遗传多样性的AFLP研究[J]. 园艺学报, 2006, 33(2): 317-322.
[27]	赵琴, 刘君, 杨志民. AFLP 分子标记对 9 份狗牙根材料的鉴定分析[J]. 草地学报, 2012, 20(6): 1156-1162.
[28]	鲁凤娟. 利用 AFLP 分子标记鉴定库尔勒香梨的分类地位[J]. 江苏农业科学, 2010 (3): 40-41.
[29]	唐先华, 张晓艳. 睡莲类植物 ITS nrDNA 序列的分子系统发育分析[J]. 地球科学: 中国地质大学学报, 2003, 28(1): 97-101.
[30]	王晓锋, 刘娜娜, 季孔庶. 黄杨属植物 ITS 序列分子进化特点分析[J]. 分子植物育种, 2011, 9(4): 506-513.
[31]	Lahaye R, Van der Bank M, Bogarin D, et al. DNA barcoding the floras of biodiversity hotspots[J]. Proceedings of the National Academy of Sciences, 2008, 105 (8): 2923-2928.
[32]	Yang H Q, Dong Y R, Gu Z J, et al. A Preliminary Assessment of mat K, rbc L and trn H-psb A as DNA Barcodes for Calamus (Arecaceae) Species in China with a Note on ITS [C]//Annales Botanici Fennici. Finnish Zoological and Botanical Publishing Board, 2012, 49(5): 319-330.
[33]	宁淑萍, 颜海飞, 郝刚, 等. 植物 DNA 条形码研究进展[J]. 生物多样性, 2008, 16(5): 417-425.
[34]	Liu J I E, Moeller M, GAO L M, et al. DNA barcoding for the discrimination of Eurasian yews (Taxus L., Taxaceae) and the discovery of cryptic species[J]. Molecular Ecology Resources, 2011, 11(1): 89-100.
[35]	Zhang W, Fan X H, Zhu S F, et al. Species-specific identification from incomplete sampling: applying DNA barcodes to monitoring invasive solanum plants[J]. PloS One, 2013, 8(2): e55927.

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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

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Identification of Rosa sterilis Based on AFLP Molecular Markers and DNA Barcodes

1. Southwest Forestry University, Kunming 650224, Yunnan, China

2. Yunnan Academy of Biodiversity, Kunming 650224, Yunnan, China

3. Rocky Desertification Comprehensive Treatment Office of Xing'ren County, Xing'ren 562300, Guizhou, China

Received Date: 2014-07-21

Abstract: Nineteen Rosa roxbunghii, R. sterilis and R. sterilis var. leioclada specimen collected from Xing'ren and Anshun in Guizhou of China were identified by AFLP molecular markers and DNA barcodes. The results of AFLP showed that genetic similarity coefficient among the 19 specimen ranged from 0.719 0 0.997 2 and the average was 0.936 5. The result of UPGMA cluster analysis showed that the 19 specimen could be divided into two groups. R. roxbunghii was distinct from the others and formed one group separately, which the others fall into another group. The result of DNA barcodes showed that there was not variable site in ITS sequences and 4 cpDNA sequences showed highly closed affinity. Based on combined sequences, the average error was 0.000 6, while the genetic distance between R. roxbunghii and the others was 0.005 8. The identification results of two methods were consistent. R. sterilis and R. roxbunghii were two segregated species. The R. sterilis collected from Xing'ren and R. sterilis var. leioclada collected from Anshun belong to the same species. The results of this study determined the phylogeny status of R. sterilis at the level of molecular and gene and laid the theoretical foundation for further collection, preservation, exploitation and application of R. sterilis germplasm resources.

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Reference (35)

[1]	时圣德. 贵州蔷薇属植物新分类群[J]. 贵州科学, 1985, 9(1): 8-9.
[2]	付慧晓, 王道平, 黄丽荣, 等. 刺梨和无籽刺梨挥发性香气成分分析[J]. 精细化工, 2012, 29(9): 875-878.
[3]	邓朝义, 方仕能, 黄勇. 贵州特有种子植物无子刺梨形态特征研究及分类学订正[J]. 种子, 2009, 28(9): 62-68.
[4]	韦景枫, 钟漫, 程友忠, 等. 无籽刺梨试管苗移栽及其影响因素的探讨[J]. 中国林副特产, 2010, 104(6): 30-31.
[5]	季祥彪, 李淑久. 贵州4种刺梨的比较形态解剖学研究[J]. 山地农业生物学报, 1998, 1(1): 28-33.
[6]	文晓鹏, 庞晓明, 邓秀新. 刺梨及部分近缘种的形态学形状及RAPD 标记分析[J]. 园艺学报, 2003, 30 (2): 204-206.
[7]	安明态, 程友忠, 钟漫, 等. 贵州蔷薇属一新变种--光枝无子刺梨[J]. 种子, 2009, 28(1): 6.
[8]	纵丹, 员涛, 周安佩, 等. 滇杨优树遗传多样性的 AFLP 分析[J]. 西北林学院学报, 2014, 29(4): 103-108.
[9]	Tautz D, Arctander P, Minelli A, et al. DNA points the way ahead in taxonomy[J]. Nature, 2002, 418: 479.
[10]	Hebert P D N, Cywinska A, Ball S L. Biological identifications through DNA barcodes[J]. Proceedings of the Royal Society of London. Series B: Biological Sciences, 2003, 270: 313-321.
[11]	Liu J, Shi L, Han J, et al. Identification of species in the angiosperm family Apiaceae using DNA barcodes[J]. Molecular Ecology Resources, 2014 Apr 16. doi: 10.1111/1755-0998.12262.
[12]	Weitschek E, Fiscon G, Felici G. Supervised DNA barcodes species classification: analysis, comparisons and results[J]. BioData Mining, 2014 Apr 11, 7(1):4. doi: 10.1186/1756-0381-7-4.
[13]	Li X, Yang Y, Henry R J, et al. Plant DNA barcoding: from gene to genome[J]. Biological Reviews, 2014 Mar 26, doi: 10.1111/brv.12104.
[14]	Vos P, Hogers R, Bleeker M, et al. AFLP: a new technique for DNA fingerprinting[J]. Nucleic acids research, 1995, 23(21): 4407-4414.
[15]	Tixier M H, Sourdille P, Rder M, et al. Detection of wheat microsatellites using a non radioactive silver-nitrate staining method[J]. Journal of Genetics and Breeding, 1997, 51(2): 175-178.
[16]	张富民, 葛颂. 群体遗传学研究中的数据处理方法I. RAPD 数据的 AMOVA分析[J]. 生物多样性, 2002, 10(4): 438-444.
[17]	Yeh F, Yang R C, Boyle T. POPGENE. A User-friendly Shareware for Population Genetic Analysis [M]. Edmonton: Molecular and Biotechnology Center, University of Alberta, 1997.
[18]	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.
[19]	Swofford D L.. PAUP* 4.0: Phylogenetic analysis using parsimony and other methods. Beta version 4.0 b10[M]. Sunderland: Sinauer Associates. 2002.
[20]	Kimura M. Estimation of evolutionary distances between homologous nucleotide sequences[J]. Proceedings of the National Academy of Sciences, 1981, 78(1): 454-458.
[21]	Kumar S, Tamura K, Nei M, et al. MEGA: molecular evolutionary genetics analysis, version 1.02[J]. Systematic Biology, 1995, 44(4): 576-577.
[22]	Lahaye R, Bank M V D, Bogarin D, et al. DNA barcoding the floras of biodiversity hotspots[J]. Proceedings of the National Academy of Sciences, 2008, 105(8): 2923-2928.
[23]	Lahaye R, Savolainen V, Duthoit S, et al. A test of psbK-psbI and atpF-atpH as potential plant DNA barcodes using the flora of the Kruger National Park as a model system (South Africa)[J]. Nature Precedings, 2008: 1-21.
[24]	Taberlet P, Gielly L, Pautou G, et al. Universal primers for amplification of three non-coding regions of chloroplast DNA[J]. Plant Molecular Biology, 1991, 17(5): 1105-1109.
[25]	White T J, Bruns T, Lee S, et al. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: Innis M A eds., PCR protocols: a guide to methods and applications[M]. New York: Academic Press, 1990, 315-322.
[26]	黄建安, 李家贤, 黄意欢, 等. 茶树品种资源遗传多样性的AFLP研究[J]. 园艺学报, 2006, 33(2): 317-322.
[27]	赵琴, 刘君, 杨志民. AFLP 分子标记对 9 份狗牙根材料的鉴定分析[J]. 草地学报, 2012, 20(6): 1156-1162.
[28]	鲁凤娟. 利用 AFLP 分子标记鉴定库尔勒香梨的分类地位[J]. 江苏农业科学, 2010 (3): 40-41.
[29]	唐先华, 张晓艳. 睡莲类植物 ITS nrDNA 序列的分子系统发育分析[J]. 地球科学: 中国地质大学学报, 2003, 28(1): 97-101.
[30]	王晓锋, 刘娜娜, 季孔庶. 黄杨属植物 ITS 序列分子进化特点分析[J]. 分子植物育种, 2011, 9(4): 506-513.
[31]	Lahaye R, Van der Bank M, Bogarin D, et al. DNA barcoding the floras of biodiversity hotspots[J]. Proceedings of the National Academy of Sciences, 2008, 105 (8): 2923-2928.
[32]	Yang H Q, Dong Y R, Gu Z J, et al. A Preliminary Assessment of mat K, rbc L and trn H-psb A as DNA Barcodes for Calamus (Arecaceae) Species in China with a Note on ITS [C]//Annales Botanici Fennici. Finnish Zoological and Botanical Publishing Board, 2012, 49(5): 319-330.
[33]	宁淑萍, 颜海飞, 郝刚, 等. 植物 DNA 条形码研究进展[J]. 生物多样性, 2008, 16(5): 417-425.
[34]	Liu J I E, Moeller M, GAO L M, et al. DNA barcoding for the discrimination of Eurasian yews (Taxus L., Taxaceae) and the discovery of cryptic species[J]. Molecular Ecology Resources, 2011, 11(1): 89-100.
[35]	Zhang W, Fan X H, Zhu S F, et al. Species-specific identification from incomplete sampling: applying DNA barcodes to monitoring invasive solanum plants[J]. PloS One, 2013, 8(2): e55927.

Identification of Rosa sterilis Based on AFLP Molecular Markers and DNA Barcodes

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通讯作者: 陈斌, bchen63@163.com

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Identification of Rosa sterilis Based on AFLP Molecular Markers and DNA Barcodes

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