DNA Extraction Method of Walnut Cotyledon Suitable for MSAP Analysis

ZHOU Bei-bei; CHEN Ling-na; ZHANG Jun-pei; PEI Dong

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DNA Extraction Method of Walnut Cotyledon Suitable for MSAP Analysis

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

Received Date: 2012-11-05

Abstract

To obtain high-quality DNA suitable for methylation-sensitive amplification polymorphism (MSAP), analysis, the mature cotyledon and tissue cultured cotyledon of walnut cultivar‘Liaoning-1’were used as the testing materials in the research of DNA isolation by 3 methods (SDS, high salt CTAB and modified high salt CTAB) and the mature leaf tissue was taken as the control. The concentration and intactness of the extracted DNA were determined using a spectrometer and by electrophoresis in 0.8% (w/v) agarose gels against standard solutions of lambda DNA. High quality DNA was extracted from leaf tissues using the high salt CTAB method and the modified high salt CTAB method. No detectable DNA was extracted from the mature cotyledon and cultured cotyledon using SDS method. The DNA with high quality but little quantity was extracted from the mature cotyledon but not the extract cultured cotyledon using the high salt CTAB method. The DNA with high quantity and quality suitable for MSAP analysis from both mature cotyledon and cultured cotyledon was extracted using the modified high salt CTAB method. The DNA extraction method of walnut cotyledon suitable for MSAP analysis was established, which could lay foundation for downstream molecular biology experiment and provide a reference to the polysaccharide removal research in DNA extraction procedure.
- Juglans regia,
- cotyledon,
- DNA extraction,
- polysaccharide,
- MSAP

References

[1]	Zwarts G S D M. Fatty acid content of New Zealand-grown walnuts (Juglans regia L.)[J]. International Journal of Food Sciences and Nutrition, 1999, 50(3): 189-194
[2]	王清民. 核桃不定根发生调控的组织和免疫化学研究[D]. 北京:中国林业科学研究院, 2007
[3]	裴东, 袁丽钗, 谷瑞升, 等. 核桃子叶不定根发生调控的研究[J]. 林业科学, 2003, 39(6): 33-39
[4]	Noyer J L, Causse S, Tomekpe K, et al. A new image of plantain diversity assessed by SSR, AFLP and MSAP markers[J]. Genetica, 2005, 124(1): 61-69
[5]	Kaufman B, Richards S, Dierig D A. DNA isolation method for high polysaccharide Lesquerella species[J]. Industrial Crops and Products, 1999, 9(2): 111-114
[6]	雷玲, 王红霞, 张志华, 等. 河北核桃叶片 DNA 提取方法的比较[J]. 华北农学报, 2010, 25(2): 145-148
[7]	常月梅. 核桃总 DNA 提取方法研究[J]. 经济林研究, 2005, 23(3): 34-35
[8]	周贝贝, 张俊佩, 王伟, 等. Fe³⁺ 浓度对核桃成熟子叶离体生根培养的影响[J]. 经济林研究, 2011, 29(1): 124-127
[9]	Driver R, Child D, Gott R, et al. Science in Schools at age 15: Report No: 2 Report to the DES, DENI, and the Welsh Office on the 1981 survey of 15 year olds[M]. Great Britain: Welsh Office Dept of Education and Science, 1984
[10]	Goldenberger D, Perschil I, Ritzler M, et al. A simple"universal" DNA extraction procedure using SDS and proteinase K is compatible with direct PCR amplification.[J]. Genome Research, 1995, 4(6): 368-370
[11]	Rohland N, Hofreiter M. Comparison and optimization of ancient DNA extraction[J]. Biotechniques, 2007, 42(3): 343-352
[12]	Aljanabi S M, Martinez I. Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques[J]. Nucleic acids research, 1997, 25(22): 4692-4693
[13]	Souza H, Muller L, Brando R L, et al. Isolation of high quality and polysaccharide-free DNA from leaves of Dimorphandra mollis (Leguminosae), a tree from the Brazilian Cerrado[J]. Genetics and Molecular Research, 2012, 11(1): 756-764
[14]	Zhang M, Xu C, von Wettstein D, et al. Tissue-specific differences in cytosine methylation and their association with differential gene expression in sorghum[J]. Plant physiology, 2011, 156(4): 1955-1966
[15]	Portis E, Acquadro A, Comino C, et al. Analysis of DNA methylation during germination of pepper (Capsicum annuum L.) seeds using methylation-sensitive amplification polymorphism (MSAP)[J]. Plant Science, 2004, 166(1): 169-178
[16]	Peraza-Echeverria S, Herrera-Valencia V A, Kay A J. Detection of DNA methylation changes in micropropagated banana plants using methylation-sensitive amplification polymorphism (MSAP)[J]. Plant Science, 2001, 161(2): 359-367
[17]	Zhang M, Xu C, Yan H, et al. Limited tissue culture-induced mutations and linked epigenetic modifications in F1 hybrids of Sorghum pure lines are accompanied by increased transcription of DNA methyltransferases and 5-methylcytosine glycosylases[J]. The Plant Journal, 2009, 57(4): 666-679
[18]	Long L, Lin X, Zhai J, et al. Heritable alteration in DNA methylation pattern occurred specifically at mobile elements in rice plants following hydrostatic pressurization[J]. Biochemical and biophysical research communications, 2006, 340(2): 369-376
[19]	Ma Q, Zhang J, Pei D. Genetic Analysis of Walnut Cultivars in China Using Fluorescent Amplified Fragment Length Polymorphism[J]. Journal of the American Society for Horticultural Science, 2011, 136(6): 422-428
[20]	陈庆山, 刘春燕, 吕东, 等. 大豆 DNA 提取基本原理的探讨[J]. 东北农业大学学报, 2004, 35(2): 254-256
[21]	Porebski S, Bailey L G, Baum B R. Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components[J]. Plant Molecular Biology Reporter, 1997, 15(1): 8-15
[22]	张丽, 黄学琴, 吴全忠, 等. 黑核桃叶片基因组 DNA 提取方法比较研究[J]. 中国农学通报, 2011, 27(28): 125-129
[23]	Fang G, Hammar S, Grumet R. A quick and inexpensive method for removing polysaccharides from plant genomic DNA.[J]. Biotechniques, 1992, 13(1): 52-56
[24]	Su X, Gibor A. A method for RNA isolation from marine macro-algae[J]. Analytical biochemistry, 1988, 174(2): 650-657
[25]	Lopez-Gomez R, Gomez-Lim M A. A method for extracting intact RNA from fruits rich in polysaccharides using ripe mango mesocarp[J]. HortScience, 1992, 27(5): 440-442
[26]	詹亚光, 曾凡锁. 富含多糖的白桦成熟叶片 DNA 的提取方法[J]. 东北林业大学学报, 2005, 33(3): 24-25

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通讯作者: 陈斌, bchen63@163.com

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沈阳化工大学材料科学与工程学院沈阳 110142

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DNA Extraction Method of Walnut Cotyledon Suitable for MSAP Analysis

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

Received Date: 2012-11-05

Abstract: To obtain high-quality DNA suitable for methylation-sensitive amplification polymorphism (MSAP), analysis, the mature cotyledon and tissue cultured cotyledon of walnut cultivar‘Liaoning-1’were used as the testing materials in the research of DNA isolation by 3 methods (SDS, high salt CTAB and modified high salt CTAB) and the mature leaf tissue was taken as the control. The concentration and intactness of the extracted DNA were determined using a spectrometer and by electrophoresis in 0.8% (w/v) agarose gels against standard solutions of lambda DNA. High quality DNA was extracted from leaf tissues using the high salt CTAB method and the modified high salt CTAB method. No detectable DNA was extracted from the mature cotyledon and cultured cotyledon using SDS method. The DNA with high quality but little quantity was extracted from the mature cotyledon but not the extract cultured cotyledon using the high salt CTAB method. The DNA with high quantity and quality suitable for MSAP analysis from both mature cotyledon and cultured cotyledon was extracted using the modified high salt CTAB method. The DNA extraction method of walnut cotyledon suitable for MSAP analysis was established, which could lay foundation for downstream molecular biology experiment and provide a reference to the polysaccharide removal research in DNA extraction procedure.

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Reference (26)

[1]	Zwarts G S D M. Fatty acid content of New Zealand-grown walnuts (Juglans regia L.)[J]. International Journal of Food Sciences and Nutrition, 1999, 50(3): 189-194
[2]	王清民. 核桃不定根发生调控的组织和免疫化学研究[D]. 北京:中国林业科学研究院, 2007
[3]	裴东, 袁丽钗, 谷瑞升, 等. 核桃子叶不定根发生调控的研究[J]. 林业科学, 2003, 39(6): 33-39
[4]	Noyer J L, Causse S, Tomekpe K, et al. A new image of plantain diversity assessed by SSR, AFLP and MSAP markers[J]. Genetica, 2005, 124(1): 61-69
[5]	Kaufman B, Richards S, Dierig D A. DNA isolation method for high polysaccharide Lesquerella species[J]. Industrial Crops and Products, 1999, 9(2): 111-114
[6]	雷玲, 王红霞, 张志华, 等. 河北核桃叶片 DNA 提取方法的比较[J]. 华北农学报, 2010, 25(2): 145-148
[7]	常月梅. 核桃总 DNA 提取方法研究[J]. 经济林研究, 2005, 23(3): 34-35
[8]	周贝贝, 张俊佩, 王伟, 等. Fe³⁺ 浓度对核桃成熟子叶离体生根培养的影响[J]. 经济林研究, 2011, 29(1): 124-127
[9]	Driver R, Child D, Gott R, et al. Science in Schools at age 15: Report No: 2 Report to the DES, DENI, and the Welsh Office on the 1981 survey of 15 year olds[M]. Great Britain: Welsh Office Dept of Education and Science, 1984
[10]	Goldenberger D, Perschil I, Ritzler M, et al. A simple"universal" DNA extraction procedure using SDS and proteinase K is compatible with direct PCR amplification.[J]. Genome Research, 1995, 4(6): 368-370
[11]	Rohland N, Hofreiter M. Comparison and optimization of ancient DNA extraction[J]. Biotechniques, 2007, 42(3): 343-352
[12]	Aljanabi S M, Martinez I. Universal and rapid salt-extraction of high quality genomic DNA for PCR-based techniques[J]. Nucleic acids research, 1997, 25(22): 4692-4693
[13]	Souza H, Muller L, Brando R L, et al. Isolation of high quality and polysaccharide-free DNA from leaves of Dimorphandra mollis (Leguminosae), a tree from the Brazilian Cerrado[J]. Genetics and Molecular Research, 2012, 11(1): 756-764
[14]	Zhang M, Xu C, von Wettstein D, et al. Tissue-specific differences in cytosine methylation and their association with differential gene expression in sorghum[J]. Plant physiology, 2011, 156(4): 1955-1966
[15]	Portis E, Acquadro A, Comino C, et al. Analysis of DNA methylation during germination of pepper (Capsicum annuum L.) seeds using methylation-sensitive amplification polymorphism (MSAP)[J]. Plant Science, 2004, 166(1): 169-178
[16]	Peraza-Echeverria S, Herrera-Valencia V A, Kay A J. Detection of DNA methylation changes in micropropagated banana plants using methylation-sensitive amplification polymorphism (MSAP)[J]. Plant Science, 2001, 161(2): 359-367
[17]	Zhang M, Xu C, Yan H, et al. Limited tissue culture-induced mutations and linked epigenetic modifications in F1 hybrids of Sorghum pure lines are accompanied by increased transcription of DNA methyltransferases and 5-methylcytosine glycosylases[J]. The Plant Journal, 2009, 57(4): 666-679
[18]	Long L, Lin X, Zhai J, et al. Heritable alteration in DNA methylation pattern occurred specifically at mobile elements in rice plants following hydrostatic pressurization[J]. Biochemical and biophysical research communications, 2006, 340(2): 369-376
[19]	Ma Q, Zhang J, Pei D. Genetic Analysis of Walnut Cultivars in China Using Fluorescent Amplified Fragment Length Polymorphism[J]. Journal of the American Society for Horticultural Science, 2011, 136(6): 422-428
[20]	陈庆山, 刘春燕, 吕东, 等. 大豆 DNA 提取基本原理的探讨[J]. 东北农业大学学报, 2004, 35(2): 254-256
[21]	Porebski S, Bailey L G, Baum B R. Modification of a CTAB DNA extraction protocol for plants containing high polysaccharide and polyphenol components[J]. Plant Molecular Biology Reporter, 1997, 15(1): 8-15
[22]	张丽, 黄学琴, 吴全忠, 等. 黑核桃叶片基因组 DNA 提取方法比较研究[J]. 中国农学通报, 2011, 27(28): 125-129
[23]	Fang G, Hammar S, Grumet R. A quick and inexpensive method for removing polysaccharides from plant genomic DNA.[J]. Biotechniques, 1992, 13(1): 52-56
[24]	Su X, Gibor A. A method for RNA isolation from marine macro-algae[J]. Analytical biochemistry, 1988, 174(2): 650-657
[25]	Lopez-Gomez R, Gomez-Lim M A. A method for extracting intact RNA from fruits rich in polysaccharides using ripe mango mesocarp[J]. HortScience, 1992, 27(5): 440-442
[26]	詹亚光, 曾凡锁. 富含多糖的白桦成熟叶片 DNA 的提取方法[J]. 东北林业大学学报, 2005, 33(3): 24-25

DNA Extraction Method of Walnut Cotyledon Suitable for MSAP Analysis

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DNA Extraction Method of Walnut Cotyledon Suitable for MSAP Analysis

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