尖镰孢EST-SSR信息分析及分子标记建立

doi:10.3864/j.issn.0578-1752.2014.20.006

Abstract

Abstract: 【Objective】 The objective of this study is to investigate the distribution of Fusarium oxysporum SSRs (simple sequence repeat) derived from ESTs (expressed sequence tag) and to develop EST-SSR markers. These researches could provide technical supports for the genetic diversity analysis of Fusarium. 【Method】 All the 9 304 EST sequences of F. oxysporum were obtained from NCBI. SSRIT (simple sequence repeat identification tool) was used to search SSRs in these sequences and Primer Premier 5.0 was used to design primers. Fourteen pairs of primers were used to analyze the genetic diversity of 23 F. oxysporum strains from different hosts and areas, and the PCR products of these primers were detected by PAGE.【Result】A total of 92 SSRs were identified from 90 F. oxysporum EST sequences, with the frequency of 1.0%. The dinucleotide repeats (59.78%) were most abundant followed by tri-(17.39%) and penta-nucleotide repeats (11.96%). AC/GT (0.51%) occurred more often than any other repeat motif. Among the 30 synthesized primers, 20 (66.7%) amplified distinct bands, and 14 (46.7%) amplified expected polymorphic products. The genetic diversity analysis based on the SSR data showed that a total of 62 bands were amplified by 14 selected SSR primers, 59 (95.2%) of which were polymorphic, with an average of 4.2 bands per primer. The genetic similarity ranged from 0.487 to 0.933, with an average of 0.686. The genetic variation of the strains was obvious. The cluster analysis based on the SSR data showed that except No.14 strain, F. oxysporum strains were distinctly clustered into different groups according to their hosts at 0.781.【Conclusion】Exploitation of SSR markers from F. oxysporum ESTs is convenient and practicable. Fourteen EST-SSR markers identified in this study would be useful for genetic variation study of F. oxysporum.

Key words: Fusarium oxysporum, expressed sequence tag (EST), simple sequence repeat (SSR), genetic diversity

LI Xin-feng, ZHANG Zuo-gang, WANG Jian-ming, GAO Jun-ming, TIAN Hong-xian. EST-SSR Information Analysis and Markers Development in Fusarium oxysporum[J].Scientia Agricultura Sinica, 2014, 47(20): 3982-3991.

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References

[1] Lunt D H, Whipple L E, Hyman B C. Mitochondrial DNA variable number tandem repeats (VNTRs): utility and problems in molecular ecology. Molecular Ecology, 1998, 7(11): 1441-1455.

[2] Suga H, Gale L R, Kistler H C. Development of VNTR markers for two Fusarium graminearum clade species. Molecular Ecology Notes, 2004, 4(3): 468-470.

[3] Naef A, Senatore M, Defago G. A microsatellite based method for quantification of fungi in decomposing plant material elucidates the role of Fusarium graminearum DON production in the saprophytic competition with Trichoderma atroviride in maize tissue microcosms. FEMS Microbiology Ecology, 2006, 55: 211-220.

[4] Saharana M S, Naef A. Detection of genetic variation among Indian wheat head scab pathogens (Fusarium spp. /isolates) with microsatellite markers. Crop Protection, 2008, 27(7): 1148-1154.

[5] Scott J B, Chakraborty S.Identification of 11 polymorphic simple sequence repeat loci in the phytopathogenic fungus Fusarium pseudograminearum as a tool for genetic studies. Molecular Ecology Resources, 2008, 8(3): 628-630.

[6] 任旭, 朱振东, 李洪杰, 段灿星, 王晓鸣. 轮枝镰孢SSR标记开发及在玉米分离群体遗传多样性分析中的应用. 中国农业科学, 2012, 45(1): 52-66.

Ren X, Zhu Z D, Li H J, Duan C X, Wang X M. SSR marker development and analysis of genetic diversity of Fusarium verticillioides isolated from maize in China. Scientia Agricultura Sinica, 2012, 45(1): 52-66. (in Chinese)

[7] Giraud T, Fournier E, Vautrin D, Solignac M, Vercken E, Bakan B, Brygoo Y. Isolation of eight polymorphic microsatellite loci, using an enrichment protocol, in the phytopathogenic fungus Fusarium culmorum. Molecular Ecology Notes, 2002, 2(2): 121-123.

[8] Vogelgsang S, Enkerli J, Jenny E, Roffler S, Widmer F. Characterization of Fusarium poae microsatellite markers on strains from Switzerland and other countries. Journal of Phytopathology, 2011, 159: 197-200.

[9] Naef A, Defago G. Population structure of plant pathogenic Fusarium species in overwintered stalk residues from Bt-transformed and non-transformed maize crops. European Journal of Plant Pathology, 2006, 116: 129-143.

[10] Bogale M, Wingfield B D, Wingfiele M J, Steenkamp E T. Simple sequence repeat markers for species in the Fusarium oxysporum complex. Molecular Ecology Notes, 2005, 5: 622-624.

[11] Britz H, Wingfield B D, Coutinho T A, Wingfield M J. Sequence characterized amplified polymorphic markers for the pitch canker pathogen, Fusarium circinatum. Molecular Ecology Notes, 2002, 2: 577-580.

[12] Booth C (陈其煐译). 镰刀菌属. 北京: 中国农业出版社, 1988.

Booth C (Chen Qi-ying translated). The Genus Fusarium. Beijing: China Agriculture Press, 1988. (in Chinese)

[13] Leslie J F, Summerell B A. The Fusarium Laboratory Manual. Iowa: Blackwell Publishing Professional, 2006.

[14] Lodhi M A, Ye G N, Weeden N F, Reisch B I. A simple and efficient method for DNA extraction from grapevine cultivars and Vitis species. Plant Molecular Biology Reporter, 1994, 12(1): 6-13.

[15] Bassam B J, Caetano-Anolles G. Silver staining of DNA in polyacrylamide gels. Applied Biochemistry and Biotechnology, 1993, 42: 181-188.

[16] 蔺宇, 徐静静, 王晓鸣, 武小菲, 李彦舫, 朱振东. 适用于大豆疫霉菌遗传分析的新EST-SSR标记. 中国农业科学, 2008, 41(8): 2294-2301.

Lin Y, Xu J J, Wang X M, Wu X F, Li Y F, Zhu Z D. Novel EST-SSR markers for genetic analysis of Phytophthora sojae. Scientia Agricultura Sinica, 2008, 41(8): 2294-2301. (in Chinese)

[17] Kantety R V, Rota M L, Matthews D E, Sorrels M E. Data mining for simple sequence repeats in expressed sequence tags from barley, maize, rice, sorghum and wheat. Plant Molecular Biology, 2002, 48: 501-510.

[18] Singh R, Sheoran S, Sharma P, Chatrath R. Analysis of simple repeats (SSRs) dynamics in fungus Fusarium graminearum. Bioinformation, 2011, 5(10): 402-404.

[19] 徐静静, 蔺宇, 朱振东. 植物病原菌SSR标记开发与利用. 植物保护, 2008, 34(1): 14-21.

Xu J J, Lin Y, Zhu Z D. Development and applications of SSR markers in plant pathogens. Plant Protection, 2008, 34(1): 14-21. (in Chinese)

[20] Dubey S C, Tripathi A, Singh S R. ITS-RFLP fingerprinting and molecular marker for detection of Fusarium oxysporum f. sp. ciceris. Folia Microbiology, 2010, 55(6): 629-634.

[21] Mishra R K, Pandey B K, Singh V, Mathew A J, Pathak N, Zeeshan M. Molecular detection and genotyping of Fusarium oxysporum f. sp. psidii isolates from different agro-ecological regions of India. Journal of Microbiology, 2013, 51(4): 405-412.

[22] Durai M, Dubey S C, Tripathi A. Genetic diversity analysis and development of SCAR marker for detection of Indian populations of Fusarium oxysporum f. sp. ciceris causing chickpea wilt. Folia Microbiology, 2012, 57: 229-235.

[23] Cabanás C G L, Valverde-Corredor A, Pérez-Artés E. Molecular analysis of Spanish populations of Fusarium oxysporum f. sp. dianthi demonstrates a high genetic diversity and identifies virulence groups in races 1 and 2 of the pathogen. European Journal of Plant Pathology, 2012, 132: 561-576.

[24] Rodríguez-Molina M C, Morales-Rodríguez M C, Palo C, Osuna M D, Iglesias M J, García J A. Pathogenicity, vegetative compatibility and RAPD analysis of Fusarium oxysporum isolates from tobacco fields in Extremadura. European Journal of Plant Pathology, 2013, 136: 639-650.

[25] Thangavelu R, Kumar K M, Devi P G, Mustaffa M M. Genetic diversity of Fusarium oxysporum f. sp. cubense isolates (Foc) of India by inter simple sequence repeats (ISSR) analysis. Molecular Biotechnology, 2012, 51: 203-211.

[26] 王建明, 李蕊倩, 畅引东, 何瑞, 李新凤, 徐玉梅, 高俊明. 尖孢镰刀菌及芬芳镰刀菌遗传多样性的ISSR分析. 植物病理学报, 2011, 41(4): 337-344.

Wang J M, Li R Q, Chang Y D, He R, Li X F, Xu Y M, Gao J M. ISSR analysis of genetic diversity of Fusarium oxysporum and F. redolens. Acta Phytopathologica Sinica, 2011, 41(4): 337-344. (in Chinese)

[27] 张述义, 李新凤, 韦晓艳, 王建明. 33株尖孢镰刀菌遗传多样性的ISSR分析. 生态学杂志, 2013, 32(5): 1195-1202.
Zhang S Y, Li X F, Wei X Y, Wang J M. ISSR analysis of genetic diversity of 33 Fusarium oxysporum strains. Chinese Journal of Ecology, 2013, 32(5): 1195-1202. (in Chinese)

[28] Yuan L, Mi N, Liu S S, Zhang H, Li Z Q. Genetic diversity and structure of the Fusarium oxysporum f. sp. lini populations on linseed (Linum usitatissimum) in China. Phytoparasitica, 2013, 41: 391-401.

[29] Poli A, Gilardi G, Spadaro D, Gullino M L, Garibaldi A. Molecular characterization of Fusarium oxysporum f. sp. cichorii pathogenic on chicory (Cichorium intybus). Phytoparasitica, 2012, 40: 383-391.

[30] Mirtalebi M, Banihashemi Z, Linde C C. Phylogenetic relationships of Fusarium oxysporum f. sp. melonis in Iran. European Journal of Plant Pathology, 2013, 136: 749-762.

[31] Dubey S C, Priyanka K, Singh V. Phylogenetic relationship between different race representative populations of Fusarium oxysporum f. sp. ciceris in respect of translation elongation factor-1α, β-tubulin, and internal transcribed spacer region genes. Archives of Microbiology, 2014, 196(6): 445-452.

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EST-SSR Information Analysis and Markers Development in Fusarium oxysporum

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