Protocol: a simple gel-free method for SNP genotyping using allele-specific primers in rice and other plant species
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- 作者：Naoki Hirotsu (1) (2)
Naomi Murakami (1)
Takayuki Kashiwagi (1) (3)
Kazuhiro Ujiie (1)
Ken Ishimaru (1) - 刊名：Plant Methods
- 出版年：2010
- 出版时间：December 2010
- 年：2010
- 卷：6
- 期：1
- 全文大小：1323KB
- 参考文献：1. Konieczny K, Ausubel FM: A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers. / Plant J 1993, 4:403鈥?10. CrossRef
2. Harushima Y, Yano M, Shomura A, Sato M, Shimano T, Kuboki Y, Yamamoto T, Lin SY, Antonio BA, Parco A, Kajiya H, Huang N, Yamamoto K, Nagamura Y, Kurata N, Khush GS, Sasaki T: A high-density rice genetic linkage map with 2275 markers using a single F 2 population. / Genetics 1988, 148:479鈥?94.
3. McCouch SR, Teytelman L, Xu Y, Lobos KB, Clare K, Walton M, Fu B, Maghirang R, Li Z, Xing Y, Zhang Q, Kono I, Yano M, Fjellstrom R, DeClerck G, Schneider D, Cartinhour S, Ware D, Stein L: Development and mapping of 2240 new SSR markers for rice ( Oryza sativa L.). / DNA Res 2002, 9:199鈥?07. CrossRef
4. Shen YJ, Jiang H, Jin JP, Zhang ZB, Xi B, He YY, Wang G, Wang C, Qian L, Li X, Yu QB, Liu HJ, Chen DH, Gao JH, Huang H, Shi TL, Yang ZN: Development of genome-wide DNA polymorphism database for map-based cloning of rice genes. / Plant Physiol 2004, 135:1198鈥?205. CrossRef
5. Jander G, Norris S, Rounsley S, Bush D, Levin I, Last R: Arabidopsis map-based cloning in the post-genome era. / Plant Physiol 2002, 129:440鈥?50. CrossRef
6. Zhu YL, Song QJ, Hyten DL, Van Tassell CP, Matukumalli LK, Grimm DR, Hyatt SM, Fickus EW, Young ND, Cregan PB: Single-nucleotide polymorphisms in soybean. / Genetics 2003, 163:1123鈥?134.
7. Batley J, Barker G, O'Sullivan H, Edwards KJ, Edwards D: Mining for single nucleotide polymorphisms and insertions/deletions in maize expressed sequence tag data. / Plant Physiol 2003, 132:84鈥?1. CrossRef
8. International Rice Genome Sequencing Project: The map-based sequence of the rice genome. / Nature 2005, 436:793鈥?00. CrossRef
9. Yu J, Hu S, Wang J, Wong GK, Li S, Liu B, Deng Y, Dai L, Zhou Y, Zhang X, Cao M, Liu J, Sun J, Tang J, Chen Y, Huang X, Lin W, Ye C, Tong W, Cong L, Geng J, Han Y, Li L, Li W, Hu G, Huang X, Li W, Li J, Liu Z, Li L, Liu J, Qi Q, Liu J, Li L, Li T, Wang X, Lu H, Wu T, Zhu M, Ni P, Han H, Dong W, Ren X, Feng X, Cui P, Li X, Wang H, Xu X, Zhai W, Xu Z, Zhang J, He S, Zhang J, Xu J, Zhang K, Zheng X, Dong J, Zeng W, Tao L, Ye J, Tan J, Ren X, Chen X, He J, Liu D, Tian W, Tian C, Xia H, Bao Q, Li G, Gao H, Cao T, Wang J, Zhao W, Li P, Chen W, Wang X, Zhang Y, Hu J, Wang J, Liu S, Yang J, Zhang G, Xiong Y, Li Z, Mao L, Zhou C, Zhu Z, Chen R, Hao B, Zheng W, Chen S, Guo W, Li G, Liu S, Tao M, Wang J, Zhu L, Yuan L, Yang H: A draft sequence of the rice genome ( Oryza sativa L. ssp indica ). / Science 2002, 296:79鈥?2. CrossRef
10. Nasu S, Suzuki J, Ohta R, Hasegawa K, Yui R, Kitazawa N, Monna L, Minobe Y: Search for and analysis of single nucleotide polymorphisms (SNPs) in rice ( Oryza sativa , Oryza rufipogon ) and establishment of SNP markers. / DNA Res 2002, 9:163鈥?71. CrossRef
11. Feltus FA, Wan J, Schulze SR, Estill JC, Jiang N, Paterson AH: An SNP resource for rice genetics and breeding based on subspecies indica and japonica genome alignments. / Genome Res 2004, 14:1812鈥?819. CrossRef
12. Monna L, Ohta R, Masuda H, Koike A, Minobe Y: Genome-wide searching of single-nucleotide polymorphisms among eight distantly and closely related rice cultivars ( Oryza sativa L.) and a wild accession ( Oryza rufipogon Griff.). / DNA Res 2006, 13:43鈥?1. CrossRef
13. Cho RJ, Mindrinos M, Richards DR, Sapolsky RJ, Anderson M, Drenkard E, Dewdney J, Reuber TL, Stammers M, Federspiel N, Theologis A, Yang WH, Hubbell E, Au M, Chung EY, Lashkari D, Lemieux B, Dean C, Lipshutz RJ, Ausubel FM, Davis RW, Oefner PJ: Genome-wide mapping with biallelic markers in Arabidopsis thaliana. / Nat Genet 1999, 23:203鈥?07. CrossRef
14. Newton CR, Graham A, Heptinstall LE, Powell SJ, Summers C, Kalsheker N, Smith JC, Markham AF: Analysis of any point mutation in DNA. The amplification refractory mutation system (ARMS). / Nucleic Acids Res 1989, 17:2503鈥?516. CrossRef
15. Cha RS, Zarbl H, Keohavong P, Thilly WG: Mismatch amplification mutation assay (MAMA): amplification to the c-H- ras gene. / PCR Method Appl 1992, 2:14鈥?0.
16. Kwok S, Kellog DE, McKinney N, Spasic D, Goda L, Levenson C, Sninsky JJ: Effects of primer-template mismatches on the polymerase chain reaction: Human immunodeficiency virus type q model studies. / Nucleic Acids Res 1990, 18:999鈥?005. CrossRef
17. Hayashi K, Hashimoto N, Daigen M, Ashikawa I: Development of PCR-based SNP markers for rice blast resistance genes at the Piz locus. / Theor Appl Genet 2004, 108:1212鈥?220. CrossRef
18. Drenkard E, Richter BG, Rozen S, Stutius LM, Angell NA, Mindrinos M, Cho RJ, Oefner PJ, Davis RW, Ausubel FM: A simple procedure for the analysis of single nicleotide polymorphisms facilitates map-based cloning in Arabidopsis. / Plant Physiol 2000, 124:1483鈥?492. CrossRef
19. Wei B, Jing R, Wang C, Chen J, Mao X, Chang X, Jia J: Dreb1 genes in wheat ( Triticum aestivum L.): development of functional markers and gene mapping based on SNPs. / Mol Breeding 2009, 23:13鈥?2. CrossRef
20. Shirasawa K, Monna L, Kishitani S, Nishio T: Single nucleotide polymorphisms in randomly selected genes among japonica Rice ( Oryza sativa L.) varieties identified by PCR-RF-SSCP. / DNA Res 2004, 11:275鈥?83. CrossRef
21. Murray MG, Thompson WF: Rapid isolation of high molecular weight plant DNA. / Nucleic Acids Res 1980, 8:4321鈥?325. CrossRef
22. Zipper H, Brunner H, Bernhagen J, Vitzthum F: Investigation on DNA intercalation and surface binding by SYBR Green I, its structure determination and methodological implications. / Nucleic Acids Res 2004, 32:e103. CrossRef
23. Vitzthum F, Geiger G, Bisswanger H, Brunner H, Bernhagen J: A quantitative fluorescence-based microplate assay for the detection of double-strand DNA using SYBR Green I and a standard ultraviolet transilluminator gel imaging system. / Anal Biochem 1999, 276:59鈥?4. CrossRef
24. Ishimaru K, Togawa E, Ookawa T, Kashiwagi T, Madoka Y, Hirotsu N: New target for rice lodging resistance and its effect in a typhoon. / Planta 2008, 227:601鈥?09. CrossRef
25. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG: The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. / Nucleic Acids Res 1997, 24:4876鈥?882. CrossRef
26. Perri猫re G, Gouy M: WWW-Query: An on-line retrieval system for biological sequence banks. / Biochimie 1996, 78:364鈥?69. CrossRef
27. Ishimaru K, Yano M, Aoki N, Ono K, Hirose T, Lin SY, Monna L, Sasaki T, Ohsugi R: Toward the mapping of physiological and agronomic characters on a rice function map: QTL analysis and comparison between QTLs and expressed sequence tags. / Theor Appl Genet 2001, 102:793鈥?00. CrossRef
28. Madoka Y, Kashiwagi T, Hirotsu N, Ishimaru K: Indian rice "Kasalath" contains genes that improve traits of Japanese premium rice "Koshihikari". / Theor Appl Genet 2008, 116:603鈥?12. CrossRef
29. Londo JP, Chiang YC, Hung KH, Chiang TY, Shaal BA: Phylogeography of asian wild rice, Oryza rufipogon , reveals multiple independent domestications of cultivated rice, Oryza sativa . / Proc Natl Acad Sci USA 2006, 103:9578鈥?583. CrossRef
30. Kurata N, Yamazaki Y: Oryzabase. An integrated biological and genome information database for rice. / Plant Physiol 2006, 140:12鈥?7. CrossRef
31. Kojima Y, Ebana K, Fukuoka S, Nagamine T, Kawase M: Development of an RFLP-based rice diversity research set of germplasm. / Breed Sci 2005, 55:431鈥?40. CrossRef
32. Shi MM: Enabling large-scale pharmacogenetic studies by high-throughput mutation detection and genotyping technologies. / Cli Chem 2001, 47:164鈥?72.
33. Syv盲nen AC: Accessing genetic variation: Genotyping single nucleotide polymorphism. / Nat Rev Genet 2001, 2:930鈥?42. CrossRef
34. Livak KJ, Flood SJA, Marmaro J, Giusti W, Deetz K: Oligonucleotides with fluorescent dyes at opposite ends provide a quenched probe system useful for detecting PCR product and nucleic acid hybridization. / PCR Method Appl 1995, 4:357鈥?62.
35. Hacia JG, Sun B, Hunt N, Edgemon K, Mosbrook D, Robbins C, Fodor SPA, Tagle DA, Collins FS: Strategies for mutational analysis of the large multiexon ATM gene using high-density oligonucleotide arrays. / Genone Res 1998, 8:1245鈥?258.
36. Chen X, Levine L, Kwok PY: Fluorescence polarization in homogeneous nucleic acid analysis. / Genome Res 1999, 9:492鈥?98.
37. Alderson A, Kristofferson A, Hammerling U: Determination of single-nucleotide polymorphisms by real-time pyrophosphate DNA sequencing. / Genome Res 2000, 10:1249鈥?258. CrossRef
38. Jurinke C, Boom D, Cantor CR, Koster H: Automated genotyping using the DNA MassArray technology. / Method Mol Biol 2001, 170:103鈥?16.
39. Zhou GH, Kamahori M, Okano K, Chuan G, Harada K, Kambara H: Quantitative detection of single nucleotide polymorphisms for a pooled sample by a bioluminometric assay coupled with modified primer extension reactions (BAMPER). / Nucleic Acids Res 2001, 29:e93. CrossRef - 作者单位：Naoki Hirotsu (1) (2)
Naomi Murakami (1)
Takayuki Kashiwagi (1) (3)
Kazuhiro Ujiie (1)
Ken Ishimaru (1)
1. Division of Plant Sciences, National Institute of Agrobiological Sciences, Kannondai 2-1-2, Tsukuba, Ibaraki, 305-8602, Japan
2. Department of Life Sciences, Faculty of Life Sciences, Toyo University, 1-1-1 Izumino, Itakura, Gunma, 374-0193, Japan
3. Department of Bioproductive Science, Faculty of Agriculture, Utsunomiya University, 350 Mine, Utsunomiya, Tochigi, 321-8505, Japan
文摘
Background Genotype analysis using multiple single nucleotide polymorphisms (SNPs) is a useful but labor-intensive or high-cost procedure in plant research. Here we describe an alternative genotyping method that is suited to multi-sample or multi-locus SNP genotyping and does not require electrophoresis or specialized equipment. Results We have developed a simple method for multi-sample or multi-locus SNP genotyping using allele-specific primers (ASP). More specifically, we (1) improved the design of allele-specific primers, (2) established a method to detect PCR products optically without electrophoresis, and (3) standardized PCR conditions for parallel genomic assay using various allele-specific primers. As an illustration of multi-sample SNP genotyping using ASP, we mapped the locus for lodging resistance in a typhoon (lrt5). Additionally, we successfully tested multi-locus ASP-PCR analysis using 96 SNPs located throughout the genomes of rice (Oryza sativa) cultivars 'Koshihikari' and 'Kasalath', and demonstrated its applicability to other diverse cultivars/subspecies, including wild rice (O. rufipogon). Conclusion Our ASP methodology allows characterization of SNPs genotypes without electrophoresis, expensive probes or specialized equipment, and is highly versatile due to the flexibility in the design of primers. The method could be established easily in any molecular biology laboratory, and is applicable to diverse organisms.