Development of a stable SCAR marker for rapid identification of Ganoderma lucidum Hunong 5 cultivar using DNA pooling method and inter-simple sequence repeat markers

doi:10.1016/S2095-3119(17)61825-2

Journal of Integrative Agriculture ›› 2018, Vol. 17 ›› Issue (01): 130-138.DOI: 10.1016/S2095-3119(17)61825-2

收稿日期:2017-04-06 出版日期:2018-01-20 发布日期:2018-01-04

Development of a stable SCAR marker for rapid identification of Ganoderma lucidum Hunong 5 cultivar using DNA pooling method and inter-simple sequence repeat markers

CHAO Wen-zheng^{1, 2}, TANG Chuan-hong^{2, 3}, ZHANG Jing-song², YU Ling¹, Honda Yoichi³

¹ School of Perfume and Aroma Technology, Shanghai Institute of Technology, Shanghai 201418, P.R.China
² Key Laboratory of Edible Fungus Resources and Utilization (South), Ministry of Agriculture/National Engineering Research Center of Edible Fungi/National R&D Center for Edible Fungi Processing/Key Laboratory of Agriculture Genetics and Breeding of Shanghai, Institute of Edible Fungi, Shanghai Academy of Agricultural Sciences, Shanghai 201403, P.R.China
³ Laboratory of Forest Biochemistry, Graduate School of Agriculture, Kyoto University, Kyoto 6068502, Japan

Received:2017-04-06 Online:2018-01-20 Published:2018-01-04
Contact: Correspondence TANG Chuan-hong,E-mail:tangchuanhong123@163.com;ZHANG Jing-song, Tel: +86-21-62200746,Fax:+86-21-62201530, E-mail: zhangjs888@163.com
Supported by:
This work was financially supported by the National Natural Science Foundation of China (31401933) and the Shanghai Municipal Committee of Agriculture, China (G2014070107).

摘要/Abstract

Abstract: The cultivar Ganoderma lucidum Hunong 5 was obtained using cross-breeding. Hunong 5 has high commercial value due to its high polysaccharide and triterpene content. This is the first report of using a DNA pooling method to develop a stable sequence characterized amplified region (SCAR) marker for rapid identification of the G. lucidum Hunong 5 cultivar. The SCAR marker was developed by first generating and sequencing a distinctive inter simple sequence repeat (ISSR) fragment (882 bp) from G. lucidum Hunong 5 cultivar. A stable SCAR primer pair GLH5F/GLH5R were obtained to identify the cultivar and the SCAR marker is a DNA fragment of 773 bp.

Key words: DNA pooling , Ganoderma lucidum , Hunong 5 cultivar , ISSR marker , SCAR marker

. [J]. Journal of Integrative Agriculture, 2018, 17(01): 130-138.

CHAO Wen-zheng, TANG Chuan-hong, ZHANG Jing-song, YU Ling, Honda Yoichi. Development of a stable SCAR marker for rapid identification of Ganoderma lucidum Hunong 5 cultivar using DNA pooling method and inter-simple sequence repeat markers[J]. Journal of Integrative Agriculture, 2018, 17(01): 130-138.

参考文献

Albani M C, Battey N H, Wilkinson M J. 2004. The development of ISSR-derived SCAR markers around the SEASONAL FLOWERING LOCUS (SFL) in Fragaria vesca. Theoretical and Applied Genetics, 109, 571–579.

Ashfaqur R, Andrew H, Daniel S, John M H. 2015. Allele frequency calibration for SNP based genotyping of DNA pools: A regression based local-global error fusion method. Computers in Biology and Medicine, 61, 48–55.

Boh B, Berovic M, Zhang J, Zhi B L. 2007. Ganoderma lucidum and its pharmaceutically active compounds. Biotechnology Annual Review, 13, 265–301.

Che K P, Xu Y, Liang C Y, Gong G Y, Weng M L, Zhang H Y, Jin D M, Wang B. 2003. AFLP fingerprint and SCAR markers of watermelon core collection. Acta Botanica Sinica, 6, 731–735.

Chen J L, Long Y, Khan M A, Wei C L, Shelly Fu, Fu J J. 2015. Development and significance of RAPD-SCAR markers for identification of Litchi chinensis Sonn. by improved RAPD amplification and molecular cloning. Electronic Journal of Biotechnology, 1, 35–39.

Chen X, Romaine C P, Ospina-Giraldo M D, Royse D J. 1999. A polymerase chain reaction-based test for the identification of Trichoderma harzianum, biotypes 2 and 4, responsible for the worldwide green mold epidemic in cultivated Agaricus bisporus. Applied Microbiology & Biotechnology, 52, 246–250.

Cui J X, Du H L, Zhang X Q. 2005. Rapidly screening SNPs and estimating allelic frequencies by DNA pooling and sequencing. Acta Genetic Sinica, 4, 372–377. (in Chinese)

Darvasi A, Soller M. 1994. Selective DNA pooling for determination of linkage between a molecular marker and a quantitative trait locus. Genetics, 138, 1365–1373.

El-Mekkawy S, Meselhy M R, Nakamura N, Tezuka Y, Hattori M, Kakiuchi N, Shimotohno K, Kawahata T, Otaka T. 1998. Anti-HIV-1 and anti-HIV-protease substances from Ganoderma lucidum. Phytochemistry, 49, 1651–1657.

Fang Q H, Zhong J J. 2002. Effect of initial pH on production of ganoderic acid and polysaccharide by submerged fermentation of Ganoderma lucidum. Process Biochemistry, 37, 769–774.

Fu L Z, Wu X Q, Li M Y, Cheng J W, He L, Wu Q Q, Li H B, Wei H L, Cao Q. 2009. Analysis and evaluation of polysaccharides and triterpenes contents of fruitbody of Ganoderma lucidum strains. Edible Fungi of China, 4, 38–40. (in Chinese)

Gao Y, Chen G, Daiy X, Gao Y, Chen G, Daiy X, Yey J, Zhou S. 2004. A Phase I/II study of Ling Zhi mushroom Ganoderma lucidum (W.Curt.:Fr.) lloyd (Aphyllophoromycetideae) extract in patients with coronary heart disease. International Journal of Medicinal Mushrooms, 6, 33–40.

Gardes M, Bruns T D. 1993. ITS primers with enhanced specificity for basidiomycetes-application to the identification of mycorrhizae and rusts. Molecular Ecology, 2, 112–118.

Hoogendoorn B, Norton N, Kirov G, Williams N, Hamshere M, Spurlock G, Austin J, Stephens M K, Buckland P R, Owen M J, O’Donovan M C. 2000. Cheap, accurate and rapid allele frequency estimation of single nucleotide polymorphisms by primer extension and DHPLC in DNA pools. Human Genetics, 107, 488–493.

Hseu R S, Wang H H, Wang H F, Moncalvo J M. 1996. Differentiation and grouping of isolates of the Ganoderma lucidum complex by random amplified polymorphic DNA-PCR compared with grouping on the basis of internal transcribed spacer sequences. Applied and Environmental Microbiology, 62, 1354–1363.

Kulkarni R K. 1991. DNA polymorphisms in Lentinula edodes, the shiitake mushroom. Applied and Environmental Microbiology, 57, 1735–1739.

Li H B, Wu X Q, Peng H Z, Fu L Z, Wei H L, Wu Q Q, Jin Q Y, Li N. 2008. New available SCAR markers: Potentially useful in distinguishing a commercial strain of the superior type from other strains of Lentinula edodes. Applied Microbiology Biotechnology, 81, 303–309.

Li X Z, Yuan X J, Jiang S, Du H, Pan J S, Wu A Z, Cai R. 2007. Development of sequence characterized amplified region (SCAR) markers in cucumber. Molecular Plant Breeding, 3, 393–402.

Lin X S, Li K B, Chen T Q, He X J, Lin Y Q, Zeng X S, Yu Y R. 2001. A study on the cultivation properties of eleven strains of Ganoderma lucidum and their esterase isozymes. Acta Agriculturae University Jiangxiensis, 1, 81–84. (in Chinese)

Lindroos K, Sigurdsson S, Johansson K, Rönnblom L, Syvänen A C. 2002. Multiplex SNP genotyping in pooled DNA samples by a four-colour microarray system. Nucleic Acids Research, 30, e70.

Merlera G G, Muñoz S, Coelho I, Cavaglieri L R, Torres A M, Reynoso M M. 2015. Diversity of black Aspergilli isolated from raisins in Argentina: Polyphasic approach to species identification and development of SCAR markers for Aspergillus ibericus. International Journal of Food Microbiology, 210, 92–101.

Moncalvo J M, Wang H F, Hseu R S. 1995. Phylogeny of the Ganoderma lucidum complex based on ribosomal DNA sequences. Comparison with traditional taxonomic characters. Mycological Research, 12, 1489–1499.

Murata H, Babasaki K, Yamada A. 2005. Highly polymorphic DNA markers to specify strains of the ectomycorrhizal basidiomycete Tricholoma matsutake based on σmarY1, the long terminal repeat of gypsy-type retroelement marY1. Mycorrhiza, 15, 179–186.

Noguchi M, Kakuma T, Tomiyasu K, Yamada A, Itoh K, Konishi F, Kumamoto S, Shimizu K, Kondo R, Matsuoka K. 2008. Randomized clinical trial of an ethanol extract of ganoderma lucidum, in men with lower urinary tract symptoms. Asian Journal of Andrology, 10, 777–785.

Nusaibah S A, Rajinder S, Idris A S. 2010. Somatic incompatibility and AFLP analysis of four species of Ganoderma strain from oil palm. Journal of Oil Palm Research, 22, 814–821.

Qin L H, Tang Q, Chen M J, Pan Y J. 2006. Use of intersimple sequence repeats markers to develop strain-specific SCAR markers for Lentinula edodes. FEMS Microbiology Letters, 257, 112–116.

Piergiorge R M, Pontes M N, Duarte A V B, Gusmão J. 2014. Haplotype-specific single-locus multiplex PCR assay for molecular identification of sea-bob shrimp, Xiphopenaeus kroyeri (Heller, 1862), cryptic species from the Southwest Atlantic using a DNA pooling strategy for simultaneous identification of multiple samples. Biochemical Systematics & Ecology, 54, 348–353.

Sham P, Bader J S, Craig I, O’Donovan M, Owen M. 2002. DNA Pooling: A tool for large-scale association studies. Nature Reviews Genetics, 3, 862–871.

Sliva D. 2006. Ganoderma lucidum in cancer research. Leukemia Research, 30, 767–768.

Silva S N, Guerreiro D, Gomes M, Azevedo A P, Bezerra D C G, Rueff J, Gaspar J F. 2012. SNPs/Pools: A methodology for the identification of relevant SNPs in breast cancer epidemiology. Oncology Reports, 27, 511–516.

Su H, Wang L, Liu L, Chi X, Zhang Y. 2008. Use of inter-simple sequence repeat markers to develop strain-specific SCAR markers for Flammulina velutipes. Journal of Applied Genetics, 49, 233–235.

Sun S J, Gao W, Lin S Q, Zhu J, Xie B G, Lin Z B. 2006. Analysis of genetic diversity in Ganoderma population with a novel molecular marker SRAP. Applied Microbiology & Biotechnology, 72, 537–553.

Suprasert P, Apichartpiyakul C, Sakonwasun C, Nitisuwanraksa P, Phuackchantuck R. 2014. Clinical characteristics of gynecologic cancer patients who respond to salvage treatment with Lingzhi. Asian Pacific Journal Cancer Prevention, 15, 4193–4196.

Wang J B. 2002. ISSR markers and their applications in plant genetics. Hereditas, 24, 613–616. (in Chinese)

Wang S H, Liang C J, Weng Y W, Chen Y H, Hsu H Y, Chien H F, Tsai J S, Tseng Y C, Li C Y, Chen Y L. 2012. Ganoderma lucidum polysaccharides prevent platelet-derived growth factor-stimulated smooth muscle cell proliferation in vitro and neointimal hyperplasia in the endothelial-denuded artery in vivo. Journal of Cellular Physiology, 227, 3063–3071.

White T J, Bruns T, Lee S, Taylor J W. 1990. Amplification and direct sequencing of fungal ribosomal RNA genes for phylogenetics. In: PCR Protocols: A Guide to Methods and Applications. Academic Press, SanDiego. pp. 315–322.

Wu T S, Shi L S, Kuo S C. 2001. Cytotoxicity of Ganoderma lucidum triterpenes. Journal of Natural Products, 64, 1121–1122.

Wu X Q, Fu L Z, Cheng J W, He L, Li W Q, Li H B, Wei H L, Cao Q. 2009. Analysis and evaluation of polysaccharides and triterpenes contents of submerged culturing mycelium of strains of Ganoderma lucidum. Forest By-Product and Speciality in China, 5, 1–3. (in Chinese)

Xiao Z T, Yan Y, He H Q, Tan Z Y, Guo J X, Li S W, Ye Y C. 2009. Comparative study of twenty-eight Ganoderma lucidum strains. Guangdong Agricultural Sciences, 9, 58–60. (in Chinese)

Xu J W, Xu Y N, Zhong J J. 2010a. Production of individual ganoderic acids and expression of biosynthetic genes in liquid static and shaking cultures of Ganoderma lucidum. Applied Microbiology & Biotechnology, 85, 941–948.

Xu J W, Zhao W, Zhong J J. 2010b. Biotechnological production and application of ganoderic acids. Applied Microbiology & Biotechnology, 87, 457–466.

Zhang R, Huang C, Zheng S, Zhang J, Ng T B, Jiang R, Zuo X, Wang H. 2007. Strain-typing of Lentinula edodes in China with inter simple sequence repeat markers. Applied Microbiology & Biotechnology, 74, 140–145.

Zhang Y, Lin Z, Hu Y, Zhang Y, Lin Z, Hu Y, Wang F. 2008. Effect of ganoderma lucidum capsules on T-lymphocyte subsets in soccer players of living high-training low. British Journal of Sports Medicine, 42, 819–822.

Zhao H, Zhang Q, Zhao L, Huang X, Wang J, Kang X. 2012. Spore powder of Ganoderma lucidum improves cancer-related fatigue in breast cancer patients undergoing endocrine therapy: A pilot clinical trial. Evidence-Based Complementary and Alternative Medicine, 2012, 809614.

Zhao J D. 1989. The Ganodermataceae in China. Science Press, Beijing. pp. 1-76. (in Chinese)

Zheng L Y, Jia D H, Fei X F, Luo X, Yang Z R. 2009. An assessment of the genetic diversity within Ganoderma strains with AFLP and ITS PCR-RFLP. Microbiological Research, 164, 312–321.

Zietkiewicz E, Rafalski A, Labuda D. 1994. Genome fingerprinting by simple sequence repeats (SSR)-anchored polymerase chain reaction amplification. Genomics, 20, 176–183.

Development of a stable SCAR marker for rapid identification of Ganoderma lucidum Hunong 5 cultivar using DNA pooling method and inter-simple sequence repeat markers

PDF

可视化

摘要/Abstract

引用本文

使用本文

参考文献

相关文章 0

编辑推荐

Metrics