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Volumn 192, Issue 1, 2013, Pages 131-143

Genome-wide InDel marker system for application in rice breeding and mapping studies

Author keywords

Agarose gel electrophoresis; Breeding friendly system; Deletion; InDel; Insertion; Marker development; Oryza sativa

Indexed keywords

JAPONICA; ORYZA SATIVA;

EID: 84878900742     PISSN: 00142336     EISSN: 15735060     Source Type: Journal    
DOI: 10.1007/s10681-013-0925-z     Document Type: Article
Times cited : (41)

References (44)
  • 1
    • 79951567068 scopus 로고    scopus 로고
    • Discovery of genome-wide DNA polymorphisms in a Landrace Cultivar of Japonica rice by whole-genome sequencing
    • Arai-Kichise Y, Shiwa Y, Nagasaki H, Ebana K, Yoshikawa H, Yano M, Wakasa K (2011) Discovery of genome-wide DNA polymorphisms in a Landrace Cultivar of Japonica rice by whole-genome sequencing. Plant Cell Physiol 52: 274-282.
    • (2011) Plant Cell Physiol , vol.52 , pp. 274-282
    • Arai-Kichise, Y.1    Shiwa, Y.2    Nagasaki, H.3    Ebana, K.4    Yoshikawa, H.5    Yano, M.6    Wakasa, K.7
  • 3
    • 84862076106 scopus 로고    scopus 로고
    • Yield-related QTLs and their applications in rice genetic improvement
    • Bai X, Wu B, Xing Y (2012) Yield-related QTLs and their applications in rice genetic improvement. J Integr Plant Biol 54: 300-311.
    • (2012) J Integr Plant Biol , vol.54 , pp. 300-311
    • Bai, X.1    Wu, B.2    Xing, Y.3
  • 4
    • 54949113665 scopus 로고    scopus 로고
    • Molecular markers and selection for complex traits in plants: learning from the last 20 years
    • Bernardo R (2008) Molecular markers and selection for complex traits in plants: learning from the last 20 years. Crop Sci 48: 1649-1664.
    • (2008) Crop Sci , vol.48 , pp. 1649-1664
    • Bernardo, R.1
  • 6
    • 54849439072 scopus 로고    scopus 로고
    • Waxy gene haplotypes: associations with pasting properties in an international rice germplasm collection
    • Chen MH, Bergman CJ, Pinson SRM, Fjellstrom RG (2008) Waxy gene haplotypes: associations with pasting properties in an international rice germplasm collection. J Cereal Sci 48: 781-788.
    • (2008) J Cereal Sci , vol.48 , pp. 781-788
    • Chen, M.H.1    Bergman, C.J.2    Pinson, S.R.M.3    Fjellstrom, R.G.4
  • 8
    • 79958720120 scopus 로고    scopus 로고
    • Genetic analysis and molecular mapping of a novel recessive gene xa34(t) for resistance against Xanthomonas oryzae pv. oryzae
    • Chen S, Liu XQ, Zeng LX, Ouyang DM, Yang JY, Zhu XY (2011b) Genetic analysis and molecular mapping of a novel recessive gene xa34(t) for resistance against Xanthomonas oryzae pv. oryzae. Theor Appl Genet 122: 1331-1338.
    • (2011) Theor Appl Genet , vol.122 , pp. 1331-1338
    • Chen, S.1    Liu, X.Q.2    Zeng, L.X.3    Ouyang, D.M.4    Yang, J.Y.5    Zhu, X.Y.6
  • 9
    • 40949130394 scopus 로고    scopus 로고
    • Marker-assisted selection: an approach for precision plant breeding in the twenty-first century
    • Collard BCY, Mackill DJ (2008) Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Philos Trans R Soc B Biol Sci 363: 557-572.
    • (2008) Philos Trans R Soc B Biol Sci , vol.363 , pp. 557-572
    • Collard, B.C.Y.1    Mackill, D.J.2
  • 10
    • 0000485878 scopus 로고
    • Template mixing-a method of enhancing detection and interpretation of codominant Rapd markers
    • Davis TM, Yu H, Haigis KM, Mcgowan PJ (1995) Template mixing-a method of enhancing detection and interpretation of codominant Rapd markers. Theor Appl Genet 91: 582-588.
    • (1995) Theor Appl Genet , vol.91 , pp. 582-588
    • Davis, T.M.1    Yu, H.2    Haigis, K.M.3    McGowan, P.J.4
  • 11
    • 0000479431 scopus 로고
    • Isolation of plant DNA from fresh tissue
    • Doyle JJ, Doyle JL (1990) Isolation of plant DNA from fresh tissue. Focus 12: 13-15.
    • (1990) Focus , vol.12 , pp. 13-15
    • Doyle, J.J.1    Doyle, J.L.2
  • 12
    • 4644353880 scopus 로고    scopus 로고
    • An SNP resource for rice genetics and breeding based on subspecies Indica and Japonica genome alignments
    • Feltus FA, Wan J, Schulze SR, Estill JC, Jiang N, Paterson AH (2004) An SNP resource for rice genetics and breeding based on subspecies Indica and Japonica genome alignments. Genome Res 14: 1812-1819.
    • (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
  • 13
    • 84857029435 scopus 로고    scopus 로고
    • Comparative use of InDel and SSR markers in deciphering the interspecific structure of cultivated citrus genetic diversity: a perspective for genetic association studies
    • Garcia-Lor A, Luro F, Navarro L, Ollitrault P (2012) Comparative use of InDel and SSR markers in deciphering the interspecific structure of cultivated citrus genetic diversity: a perspective for genetic association studies. Mol Genet Genomics 287: 77-94.
    • (2012) Mol Genet Genomics , vol.287 , pp. 77-94
    • Garcia-Lor, A.1    Luro, F.2    Navarro, L.3    Ollitrault, P.4
  • 14
    • 78650059479 scopus 로고    scopus 로고
    • Application of single nucleotide polymorphisms to non-model species: a technical review
    • Garvin MR, Saitoh K, Gharrett AJ (2010) Application of single nucleotide polymorphisms to non-model species: a technical review. Mol Ecol Res 10: 915-934.
    • (2010) Mol Ecol Res , vol.10 , pp. 915-934
    • Garvin, M.R.1    Saitoh, K.2    Gharrett, A.J.3
  • 15
    • 0034094869 scopus 로고    scopus 로고
    • The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat
    • Gupta PK, Varshney RK (2000) The development and use of microsatellite markers for genetic analysis and plant breeding with emphasis on bread wheat. Euphytica 113: 163-185.
    • (2000) Euphytica , vol.113 , pp. 163-185
    • Gupta, P.K.1    Varshney, R.K.2
  • 17
    • 33745508915 scopus 로고    scopus 로고
    • Development of PCR-based allele-specific and InDel marker sets for nine rice blast resistance genes
    • Hayashi K, Yoshida H, Ashikawa I (2006) Development of PCR-based allele-specific and InDel marker sets for nine rice blast resistance genes. Theor Appl Genet 113: 251-260.
    • (2006) Theor Appl Genet , vol.113 , pp. 251-260
    • Hayashi, K.1    Yoshida, H.2    Ashikawa, I.3
  • 22
    • 80053073214 scopus 로고    scopus 로고
    • Marker-assisted-selection (MAS): a fast track to increase genetic gain in horticultural crop breeding
    • Ibitoye DO, Akin-Idowu PE (2011) Marker-assisted-selection (MAS): a fast track to increase genetic gain in horticultural crop breeding. Afr J Biotechnol 10: 11333-11339.
    • (2011) Afr J Biotechnol , vol.10 , pp. 11333-11339
    • Ibitoye, D.O.1    Akin-Idowu, P.E.2
  • 23
    • 84907150192 scopus 로고    scopus 로고
    • The map-based sequence of the rice genome
    • IRGSP IRGSP
    • IRGSP IRGSP (2005) The map-based sequence of the rice genome. Nature 436: 793-800.
    • (2005) Nature , vol.436 , pp. 793-800
  • 24
    • 76549088573 scopus 로고    scopus 로고
    • Two sequence alterations, a 136 bp InDel and an A/C polymorphic site, in the S5 locus are associated with spikelet fertility of indica-japonica hybrid in rice
    • Ji Q, Lu JF, Chao Q, Zhang Y, Zhang MJ, Gu MH, Xu ML (2010) Two sequence alterations, a 136 bp InDel and an A/C polymorphic site, in the S5 locus are associated with spikelet fertility of indica-japonica hybrid in rice. J Genet Genomics 37: 57-68.
    • (2010) J Genet Genomics , vol.37 , pp. 57-68
    • Ji, Q.1    Lu, J.F.2    Chao, Q.3    Zhang, Y.4    Zhang, M.J.5    Gu, M.H.6    Xu, M.L.7
  • 25
    • 84858615845 scopus 로고    scopus 로고
    • Rapid identification of oral isolates of Aggregatibacter actinomycetemcomitans obtained from humans and primates by an ultrafast super convection based polymerase chain reaction
    • Karched M, Furgang D, Sawalha N, Fine DH (2012) Rapid identification of oral isolates of Aggregatibacter actinomycetemcomitans obtained from humans and primates by an ultrafast super convection based polymerase chain reaction. J Microbiol Method 89: 71-75.
    • (2012) J Microbiol Method , vol.89 , pp. 71-75
    • Karched, M.1    Furgang, D.2    Sawalha, N.3    Fine, D.H.4
  • 26
    • 35348847064 scopus 로고    scopus 로고
    • SNP genotyping: technologies and biomedical applications
    • Kim S, Misra A (2007) SNP genotyping: technologies and biomedical applications. Annu Rev Biomed Eng 9: 289-320.
    • (2007) Annu Rev Biomed Eng , vol.9 , pp. 289-320
    • Kim, S.1    Misra, A.2
  • 27
    • 6844263345 scopus 로고
    • Genetic analysis of fertility restoration in male sterile lines of rice
    • Manila, Philippines, IRRI, 1985
    • Li YC, Yuan LP (1986) Genetic analysis of fertility restoration in male sterile lines of rice. In: Rice genetics. Proc. Internatl. Symp. May 27-31, 1985. Manila, Philippines, IRRI, pp 617-632.
    • (1986) In: Rice genetics. Proc. Internatl. Symp. May 27-31 , pp. 617-632
    • Li, Y.C.1    Yuan, L.P.2
  • 28
    • 84859801730 scopus 로고    scopus 로고
    • Single-seeded InDel fingerprints in rice: an effective tool for indica-japonica rice classification and evolutionary studies
    • Liu P, Cai XX, Lu BR (2012) Single-seeded InDel fingerprints in rice: an effective tool for indica-japonica rice classification and evolutionary studies. J Syst Evol 50: 1-11.
    • (2012) J Syst Evol , vol.50 , pp. 1-11
    • Liu, P.1    Cai, X.X.2    Lu, B.R.3
  • 29
    • 70350618917 scopus 로고    scopus 로고
    • Efficient indica and japonica rice identification based on the InDel molecular method: its implication in rice breeding and evolutionary research
    • Lu BR, Cai XX, Jin X (2009) Efficient indica and japonica rice identification based on the InDel molecular method: its implication in rice breeding and evolutionary research. Prog Nat Sci 19: 1241-1252.
    • (2009) Prog Nat Sci , vol.19 , pp. 1241-1252
    • Lu, B.R.1    Cai, X.X.2    Jin, X.3
  • 33
    • 33748447484 scopus 로고    scopus 로고
    • Repetitive indel markers within the ALMT1 gene conditioning aluminium tolerance in wheat (Triticum aestivum L.)
    • Raman H, Raman R, Wood R, Martin P (2006) Repetitive indel markers within the ALMT1 gene conditioning aluminium tolerance in wheat (Triticum aestivum L.). Mol Breed 18: 171-183.
    • (2006) Mol Breed , vol.18 , pp. 171-183
    • Raman, H.1    Raman, R.2    Wood, R.3    Martin, P.4
  • 35
    • 43049140496 scopus 로고    scopus 로고
    • InDel markers distinguish Basmatis from other fragrant rice varieties
    • Steele KA, Ogden R, McEwing R, Briggs H, Gorham J (2008) InDel markers distinguish Basmatis from other fragrant rice varieties. Field Crops Res 105: 81-87.
    • (2008) Field Crops Res , vol.105 , pp. 81-87
    • Steele, K.A.1    Ogden, R.2    McEwing, R.3    Briggs, H.4    Gorham, J.5
  • 37
    • 0036566806 scopus 로고    scopus 로고
    • Heteroduplexes in mixed-template amplifications: formation, consequence and elimination by 'reconditioning PCR
    • Thompson JR, Marcelino LA, Polz MF (2002) Heteroduplexes in mixed-template amplifications: formation, consequence and elimination by 'reconditioning PCR'. Nucleic Acids Res 30: 2083-2088.
    • (2002) Nucleic Acids Res , vol.30 , pp. 2083-2088
    • Thompson, J.R.1    Marcelino, L.A.2    Polz, M.F.3
  • 38
    • 40949091938 scopus 로고    scopus 로고
    • Insertion-deletion polymorphisms (indels) as genetic markers in natural populations
    • Vali U, Brandstrom M, Johansson M, Ellegren H (2008) Insertion-deletion polymorphisms (indels) as genetic markers in natural populations. Bmc Genetics 9: 8.
    • (2008) Bmc Genetics , vol.9 , pp. 8
    • Vali, U.1    Brandstrom, M.2    Johansson, M.3    Ellegren, H.4
  • 39
    • 0036325076 scopus 로고    scopus 로고
    • Co-dominant RAPD markers closely linked with two morphological genes in rice (Oryza sativa L.)
    • Wu JY, Wu HK, Chung MC (2002) Co-dominant RAPD markers closely linked with two morphological genes in rice (Oryza sativa L.). Bot Bull Acad Sinica 43: 171-180.
    • (2002) Bot Bull Acad Sinica , vol.43 , pp. 171-180
    • Wu, J.Y.1    Wu, H.K.2    Chung, M.C.3
  • 40
    • 78651517565 scopus 로고    scopus 로고
    • Comparative analyses of linkage maps and segregation distortion of two F-2 populations derived from japonica crossed with indica rice
    • Wu Y-P, Ko P-Y, Lee W-C, Wei F-J, Kuo S-C, Ho S-W, Hour A-L, Hsing Y-I, Lin Y-R (2010) Comparative analyses of linkage maps and segregation distortion of two F-2 populations derived from japonica crossed with indica rice. Hereditas 147: 225-236.
    • (2010) Hereditas , vol.147 , pp. 225-236
    • Wu, Y.-P.1    Ko, P.-Y.2    Lee, W.-C.3    Wei, F.-J.4    Kuo, S.-C.5    Ho, S.-W.6    Hour, A.-L.7    Hsing, Y.-I.8    Lin, Y.-R.9
  • 41
    • 77954533063 scopus 로고    scopus 로고
    • Differentiation and distribution of indica and japonica rice varieties along the altitude gradients in Yunnan Province of China as revealed by InDel molecular markers
    • Xiong ZY, Zhang SJ, Wang YY, Ford-Lloyd BV, Tu M, Jin X, Wu Y, Yan HX, Yang XA, Liu P, Lu BR (2010) Differentiation and distribution of indica and japonica rice varieties along the altitude gradients in Yunnan Province of China as revealed by InDel molecular markers. Genet Resour Crop Evol 57: 891-902.
    • (2010) Genet Resour Crop Evol , vol.57 , pp. 891-902
    • Xiong, Z.Y.1    Zhang, S.J.2    Wang, Y.Y.3    Ford-Lloyd, B.V.4    Tu, M.5    Jin, X.6    Wu, Y.7    Yan, H.X.8    Yang, X.A.9    Liu, P.10    Lu, B.R.11
  • 42
    • 79952260743 scopus 로고    scopus 로고
    • Fine mapping and candidate gene analysis of ptgms2-1, the photoperiod-thermo-sensitive genic male sterile gene in rice (Oryza sativa L.)
    • Xu JJ, Wang BH, Wu YH, Du PN, Wang J, Wang M, Yi CD, Gu MH, Liang GH (2011) Fine mapping and candidate gene analysis of ptgms2-1, the photoperiod-thermo-sensitive genic male sterile gene in rice (Oryza sativa L.). Theor Appl Genet 122: 365-372.
    • (2011) Theor Appl Genet , vol.122 , pp. 365-372
    • Xu, J.J.1    Wang, B.H.2    Wu, Y.H.3    Du, P.N.4    Wang, J.5    Wang, M.6    Yi, C.D.7    Gu, M.H.8    Liang, G.H.9
  • 43
    • 77951217695 scopus 로고    scopus 로고
    • Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms
    • Yamamoto T, Nagasaki H, Yonemaru J-i, Ebana K, Nakajima M, Shibaya T, Yano M (2010) Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms. Bmc Genomics 11: 267.
    • (2010) Bmc Genomics , vol.11 , pp. 267
    • Yamamoto, T.1    Nagasaki, H.2    Yonemaru, J.-I.3    Ebana, K.4    Nakajima, M.5    Shibaya, T.6    Yano, M.7
  • 44
    • 0037976417 scopus 로고    scopus 로고
    • An efficient procedure for genotyping single nucleotide polymorphisms
    • art. no.-arte88
    • Ye S, Dhillon S, Ke XY, Collins AR, Day INM (2001) An efficient procedure for genotyping single nucleotide polymorphisms. Nucleic Acids Res 29: art. no.-e88.
    • (2001) Nucleic Acids Res , vol.29
    • Ye, S.1    Dhillon, S.2    Ke, X.Y.3    Collins, A.R.4    Day, I.N.M.5


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