메뉴 건너뛰기




Volumn 6, Issue 1, 2010, Pages

Protocol: A simple gel-free method for SNP genotyping using allele-specific primers in rice and other plant species

Author keywords

[No Author keywords available]

Indexed keywords

ORYZA SATIVA; ZIZANIA;

EID: 77951051005     PISSN: None     EISSN: 17464811     Source Type: Journal    
DOI: 10.1186/1746-4811-6-12     Document Type: Article
Times cited : (28)

References (39)
  • 1
    • 0027650566 scopus 로고
    • A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers
    • 10.1046/j.1365-313X.1993.04020403.x, 8106085
    • Konieczny K, Ausubel FM. A procedure for mapping Arabidopsis mutations using co-dominant ecotype-specific PCR-based markers. Plant J 1993, 4:403-410. 10.1046/j.1365-313X.1993.04020403.x, 8106085.
    • (1993) Plant J , vol.4 , pp. 403-410
    • Konieczny, K.1    Ausubel, F.M.2
  • 5
    • 0035983615 scopus 로고    scopus 로고
    • Arabidopsis map-based cloning in the post-genome era
    • 10.1104/pp.003533, 1540230, 12068090
    • Jander G, Norris S, Rounsley S, Bush D, Levin I, Last R. Arabidopsis map-based cloning in the post-genome era. Plant Physiol 2002, 129:440-450. 10.1104/pp.003533, 1540230, 12068090.
    • (2002) Plant Physiol , vol.129 , pp. 440-450
    • Jander, G.1    Norris, S.2    Rounsley, S.3    Bush, D.4    Levin, I.5    Last, R.6
  • 7
    • 0037986743 scopus 로고    scopus 로고
    • Mining for single nucleotide polymorphisms and insertions/deletions in maize expressed sequence tag data
    • 10.1104/pp.102.019422, 166954, 12746514
    • 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, 132:84-91. 10.1104/pp.102.019422, 166954, 12746514.
    • (2003) Plant Physiol , vol.132 , pp. 84-91
    • Batley, J.1    Barker, G.2    O'Sullivan, H.3    Edwards, K.J.4    Edwards, D.5
  • 8
    • 84907150192 scopus 로고    scopus 로고
    • The map-based sequence of the rice genome
    • 10.1038/nature03895, 16100779, International Rice Genome Sequencing Project
    • International Rice Genome Sequencing Project The map-based sequence of the rice genome. Nature 2005, 436:793-800. 10.1038/nature03895, 16100779, International Rice Genome Sequencing Project.
    • (2005) Nature , vol.436 , pp. 793-800
  • 10
    • 0036928794 scopus 로고    scopus 로고
    • Search for and analysis of single nucleotide polymorphisms (SNPs) in rice (Oryza sativa, Oryza rufipogon) and establishment of SNP markers
    • 10.1093/dnares/9.5.163, 12465716
    • 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, 9:163-171. 10.1093/dnares/9.5.163, 12465716.
    • (2002) DNA Res , vol.9 , pp. 163-171
    • Nasu, S.1    Suzuki, J.2    Ohta, R.3    Hasegawa, K.4    Yui, R.5    Kitazawa, N.6    Monna, L.7    Minobe, Y.8
  • 11
    • 4644353880 scopus 로고    scopus 로고
    • An SNP resource for rice genetics and breeding based on subspecies indica and japonica genome alignments
    • 10.1101/gr.2479404, 515328, 15342564
    • 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, 14:1812-1819. 10.1101/gr.2479404, 515328, 15342564.
    • (2004) Genome Res , vol.14 , pp. 1812-1819
    • Feltus, F.A.1    Wan, J.2    Schulze, S.R.3    Estill, J.C.4    Jiang, N.5    Paterson, A.H.6
  • 12
    • 33744902325 scopus 로고    scopus 로고
    • 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.)
    • 10.1093/dnares/dsi030, 16766512
    • 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, 13:43-51. 10.1093/dnares/dsi030, 16766512.
    • (2006) DNA Res , vol.13 , pp. 43-51
    • Monna, L.1    Ohta, R.2    Masuda, H.3    Koike, A.4    Minobe, Y.5
  • 15
    • 85045497108 scopus 로고
    • Mismatch amplification mutation assay (MAMA): amplification to the c-H-ras gene
    • Cha RS, Zarbl H, Keohavong P, Thilly WG. Mismatch amplification mutation assay (MAMA): amplification to the c-H-ras gene. PCR Method Appl 1992, 2:14-20.
    • (1992) PCR Method Appl , vol.2 , pp. 14-20
    • Cha, R.S.1    Zarbl, H.2    Keohavong, P.3    Thilly, W.G.4
  • 16
    • 0025305576 scopus 로고
    • Effects of primer-template mismatches on the polymerase chain reaction: Human immunodeficiency virus type q model studies
    • 10.1093/nar/18.4.999, 330356, 2179874
    • 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, 18:999-1005. 10.1093/nar/18.4.999, 330356, 2179874.
    • (1990) Nucleic Acids Res , vol.18 , pp. 999-1005
    • Kwok, S.1    Kellog, D.E.2    McKinney, N.3    Spasic, D.4    Goda, L.5    Levenson, C.6    Sninsky, J.J.7
  • 17
    • 2442557312 scopus 로고    scopus 로고
    • Development of PCR-based SNP markers for rice blast resistance genes at the Piz locus
    • 10.1007/s00122-003-1553-0, 14740086
    • 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, 108:1212-1220. 10.1007/s00122-003-1553-0, 14740086.
    • (2004) Theor Appl Genet , vol.108 , pp. 1212-1220
    • Hayashi, K.1    Hashimoto, N.2    Daigen, M.3    Ashikawa, I.4
  • 19
    • 56649086745 scopus 로고    scopus 로고
    • Dreb1 genes in wheat (Triticum aestivum L.): development of functional markers and gene mapping based on SNPs
    • 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, 23:13-22.
    • (2009) Mol Breeding , vol.23 , pp. 13-22
    • Wei, B.1    Jing, R.2    Wang, C.3    Chen, J.4    Mao, X.5    Chang, X.6    Jia, J.7
  • 20
    • 11144325580 scopus 로고    scopus 로고
    • Single nucleotide polymorphisms in randomly selected genes among japonica Rice (Oryza sativa L.) varieties identified by PCR-RF-SSCP
    • 10.1093/dnares/11.4.275, 15500252
    • 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, 11:275-283. 10.1093/dnares/11.4.275, 15500252.
    • (2004) DNA Res , vol.11 , pp. 275-283
    • Shirasawa, K.1    Monna, L.2    Kishitani, S.3    Nishio, T.4
  • 21
    • 0019321718 scopus 로고
    • Rapid isolation of high molecular weight plant DNA
    • 10.1093/nar/8.19.4321, 324241, 7433111
    • Murray MG, Thompson WF. Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 1980, 8:4321-4325. 10.1093/nar/8.19.4321, 324241, 7433111.
    • (1980) Nucleic Acids Res , vol.8 , pp. 4321-4325
    • Murray, M.G.1    Thompson, W.F.2
  • 22
    • 3142708522 scopus 로고    scopus 로고
    • Investigation on DNA intercalation and surface binding by SYBR Green I, its structure determination and methodological implications
    • 10.1093/nar/gnh101, 484200, 15249599
    • 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. 10.1093/nar/gnh101, 484200, 15249599.
    • (2004) Nucleic Acids Res , vol.32
    • Zipper, H.1    Brunner, H.2    Bernhagen, J.3    Vitzthum, F.4
  • 23
    • 0032805947 scopus 로고    scopus 로고
    • 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
    • 10.1006/abio.1999.4298, 10585744
    • 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, 276:59-64. 10.1006/abio.1999.4298, 10585744.
    • (1999) Anal Biochem , vol.276 , pp. 59-64
    • Vitzthum, F.1    Geiger, G.2    Bisswanger, H.3    Brunner, H.4    Bernhagen, J.5
  • 24
    • 38049174950 scopus 로고    scopus 로고
    • New target for rice lodging resistance and its effect in a typhoon
    • 10.1007/s00425-007-0642-8, 17960419
    • 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, 227:601-609. 10.1007/s00425-007-0642-8, 17960419.
    • (2008) Planta , vol.227 , pp. 601-609
    • Ishimaru, K.1    Togawa, E.2    Ookawa, T.3    Kashiwagi, T.4    Madoka, Y.5    Hirotsu, N.6
  • 25
    • 0031574072 scopus 로고    scopus 로고
    • The ClustalX windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools
    • 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, 24:4876-4882.
    • (1997) Nucleic Acids Res , vol.24 , pp. 4876-4882
    • Thompson, J.D.1    Gibson, T.J.2    Plewniak, F.3    Jeanmougin, F.4    Higgins, D.G.5
  • 26
    • 0029853148 scopus 로고    scopus 로고
    • WWW-Query: An on-line retrieval system for biological sequence banks
    • 10.1016/0300-9084(96)84768-7, 8905155
    • Perrière G, Gouy M. WWW-Query: An on-line retrieval system for biological sequence banks. Biochimie 1996, 78:364-369. 10.1016/0300-9084(96)84768-7, 8905155.
    • (1996) Biochimie , vol.78 , pp. 364-369
    • Perrière, G.1    Gouy, M.2
  • 27
    • 0034977257 scopus 로고    scopus 로고
    • Toward the mapping of physiological and agronomic characters on a rice function map: QTL analysis and comparison between QTLs and expressed sequence tags
    • 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, 102:793-800.
    • (2001) Theor Appl Genet , vol.102 , pp. 793-800
    • Ishimaru, K.1    Yano, M.2    Aoki, N.3    Ono, K.4    Hirose, T.5    Lin, S.Y.6    Monna, L.7    Sasaki, T.8    Ohsugi, R.9
  • 28
    • 40049106350 scopus 로고    scopus 로고
    • Indian rice "Kasalath" contains genes that improve traits of Japanese premium rice "Koshihikari"
    • 10.1007/s00122-007-0693-z, 18097643
    • 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, 116:603-612. 10.1007/s00122-007-0693-z, 18097643.
    • (2008) Theor Appl Genet , vol.116 , pp. 603-612
    • Madoka, Y.1    Kashiwagi, T.2    Hirotsu, N.3    Ishimaru, K.4
  • 29
    • 33745439823 scopus 로고    scopus 로고
    • Phylogeography of asian wild rice, Oryza rufipogon, reveals multiple independent domestications of cultivated rice, Oryza sativa
    • 10.1073/pnas.0603152103, 1480449, 16766658
    • 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, 103:9578-9583. 10.1073/pnas.0603152103, 1480449, 16766658.
    • (2006) Proc Natl Acad Sci USA , vol.103 , pp. 9578-9583
    • Londo, J.P.1    Chiang, Y.C.2    Hung, K.H.3    Chiang, T.Y.4    Shaal, B.A.5
  • 30
    • 33645805022 scopus 로고    scopus 로고
    • Oryzabase. An integrated biological and genome information database for rice
    • 10.1104/pp.105.063008, 1326027, 16403737
    • Kurata N, Yamazaki Y. Oryzabase. An integrated biological and genome information database for rice. Plant Physiol 2006, 140:12-17. 10.1104/pp.105.063008, 1326027, 16403737.
    • (2006) Plant Physiol , vol.140 , pp. 12-17
    • Kurata, N.1    Yamazaki, Y.2
  • 31
    • 29144473038 scopus 로고    scopus 로고
    • Development of an RFLP-based rice diversity research set of germplasm
    • Kojima Y, Ebana K, Fukuoka S, Nagamine T, Kawase M. Development of an RFLP-based rice diversity research set of germplasm. Breed Sci 2005, 55:431-440.
    • (2005) Breed Sci , vol.55 , pp. 431-440
    • Kojima, Y.1    Ebana, K.2    Fukuoka, S.3    Nagamine, T.4    Kawase, M.5
  • 32
    • 0035134454 scopus 로고    scopus 로고
    • Enabling large-scale pharmacogenetic studies by high-throughput mutation detection and genotyping technologies
    • Shi MM. Enabling large-scale pharmacogenetic studies by high-throughput mutation detection and genotyping technologies. Cli Chem 2001, 47:164-172.
    • (2001) Cli Chem , vol.47 , pp. 164-172
    • Shi, M.M.1
  • 33
    • 0035654137 scopus 로고    scopus 로고
    • Accessing genetic variation: Genotyping single nucleotide polymorphism
    • 10.1038/35103535, 11733746
    • Syvänen AC. Accessing genetic variation: Genotyping single nucleotide polymorphism. Nat Rev Genet 2001, 2:930-942. 10.1038/35103535, 11733746.
    • (2001) Nat Rev Genet , vol.2 , pp. 930-942
    • Syvänen, A.C.1
  • 34
    • 0028834086 scopus 로고
    • Oligonucleotides with fluorescent dyes at opposite ends provide a quenched probe system useful for detecting PCR product and nucleic acid hybridization
    • 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, 4:357-362.
    • (1995) PCR Method Appl , vol.4 , pp. 357-362
    • Livak, K.J.1    Flood, S.J.A.2    Marmaro, J.3    Giusti, W.4    Deetz, K.5
  • 36
    • 0033058730 scopus 로고    scopus 로고
    • Fluorescence polarization in homogeneous nucleic acid analysis
    • 310763, 10330129
    • Chen X, Levine L, Kwok PY. Fluorescence polarization in homogeneous nucleic acid analysis. Genome Res 1999, 9:492-498. 310763, 10330129.
    • (1999) Genome Res , vol.9 , pp. 492-498
    • Chen, X.1    Levine, L.2    Kwok, P.Y.3
  • 37
    • 0033824460 scopus 로고    scopus 로고
    • Determination of single-nucleotide polymorphisms by real-time pyrophosphate DNA sequencing
    • 10.1101/gr.10.8.1249, 310924, 10958643
    • Alderson A, Kristofferson A, Hammerling U. Determination of single-nucleotide polymorphisms by real-time pyrophosphate DNA sequencing. Genome Res 2000, 10:1249-1258. 10.1101/gr.10.8.1249, 310924, 10958643.
    • (2000) Genome Res , vol.10 , pp. 1249-1258
    • Alderson, A.1    Kristofferson, A.2    Hammerling, U.3
  • 38
    • 0035221755 scopus 로고    scopus 로고
    • Automated genotyping using the DNA MassArray technology
    • Jurinke C, Boom D, Cantor CR, Koster H. Automated genotyping using the DNA MassArray technology. Method Mol Biol 2001, 170:103-116.
    • (2001) Method Mol Biol , vol.170 , pp. 103-116
    • Jurinke, C.1    Boom, D.2    Cantor, C.R.3    Koster, H.4
  • 39
    • 0035487816 scopus 로고    scopus 로고
    • Quantitative detection of single nucleotide polymorphisms for a pooled sample by a bioluminometric assay coupled with modified primer extension reactions (BAMPER)
    • 10.1093/nar/29.10.2003, 60253, 11574695
    • 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. 10.1093/nar/29.10.2003, 60253, 11574695.
    • (2001) Nucleic Acids Res , vol.29
    • Zhou, G.H.1    Kamahori, M.2    Okano, K.3    Chuan, G.4    Harada, K.5    Kambara, H.6


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.