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Volumn 10, Issue 6, 2012, Pages 623-634

Genome-wide DNA polymorphisms in elite indica rice inbreds discovered by whole-genome sequencing

Author keywords

Deletions; Genome wide variations; Insertions; Next generation sequencing; Rice (Oryza sativa L.); Single nucleotide polymorphism

Indexed keywords

ARTICLE; DNA SEQUENCE; GENETICS; HETEROSIS; INDEL MUTATION; PLANT GENOME; RICE; SINGLE NUCLEOTIDE POLYMORPHISM;

EID: 84863565805     PISSN: 14677644     EISSN: 14677652     Source Type: Journal    
DOI: 10.1111/j.1467-7652.2011.00676.x     Document Type: Article
Times cited : (135)

References (47)
  • 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. and 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
  • 2
    • 0037986743 scopus 로고    scopus 로고
    • Mining for single nucleotide polymorphisms and insertions/deletions in maize expressed sequence tag data
    • Batley, J., Barker, G., O'Sullivan, H., Edwards, K.J. and Edwards, D. (2003) Mining for single nucleotide polymorphisms and insertions/deletions in maize expressed sequence tag data. Plant Physiol. 132, 84-91.
    • (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
  • 3
    • 33750953227 scopus 로고    scopus 로고
    • Whole-genome re-sequencing
    • Bentley, D.R. (2006) Whole-genome re-sequencing. Curr. Opin. Genet. Dev. 16, 545-552.
    • (2006) Curr. Opin. Genet. Dev. , vol.16 , pp. 545-552
    • Bentley, D.R.1
  • 4
    • 64749112341 scopus 로고    scopus 로고
    • Targeted single nucleotide polymorphism (SNP) discovery in a highly polyploid plant species using 454 sequencing
    • Bundock, P.C., Eliott, F.G., Ablett, G., Benson, A.D., Casu, R.E., Aitken, K.S. and Henry, R.J. (2010) Targeted single nucleotide polymorphism (SNP) discovery in a highly polyploid plant species using 454 sequencing. Plant Biotechnol. J. 7, 347-354.
    • (2010) Plant Biotechnol. J. , vol.7 , pp. 347-354
    • Bundock, P.C.1    Eliott, F.G.2    Ablett, G.3    Benson, A.D.4    Casu, R.E.5    Aitken, K.S.6    Henry, R.J.7
  • 6
    • 75949117260 scopus 로고    scopus 로고
    • Molecular mechanisms of polyploidy and hybrid vigour
    • Chen, Z.J. (2010) Molecular mechanisms of polyploidy and hybrid vigour. Trends Plant Sci. 15, 57-71.
    • (2010) Trends Plant Sci. , vol.15 , pp. 57-71
    • Chen, Z.J.1
  • 7
    • 0018185292 scopus 로고
    • Molecular basis of base substitution hot spots in Escherichia coli
    • Coulondre, C., Miller, J.H., Farabaugh, P.J. and Gilbert, W. (1978) Molecular basis of base substitution hot spots in Escherichia coli. Nature, 274, 775-780.
    • (1978) Nature , vol.274 , pp. 775-780
    • Coulondre, C.1    Miller, J.H.2    Farabaugh, P.J.3    Gilbert, W.4
  • 8
    • 4644353880 scopus 로고    scopus 로고
    • An SNP resource for rice genetics and breeding based on subspecies indica and japonica genome alignments
    • Feltus, A., Wan, J., Schulze, S.R., Estill, J.C., Jiang, N. and Paterson, A.H. (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, A.1    Wan, J.2    Schulze, S.R.3    Estill, J.C.4    Jiang, N.5    Paterson, A.H.6
  • 9
    • 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. and Ashikawa, I. (2006) Development of PCR-based allele-specific and InDel marker sets for nine rice blast resistance genes. Theor. Appl. Genet. 113, 251-266.
    • (2006) Theor. Appl. Genet. , vol.113 , pp. 251-266
    • Hayashi, K.1    Yoshida, H.2    Ashikawa, I.3
  • 10
    • 64749083993 scopus 로고    scopus 로고
    • New tools for single nucleotide polymorphism (SNP) discovery and analysis accelerating plant biotechnology
    • Henry, R.J. and Edwards, K. (2009) New tools for single nucleotide polymorphism (SNP) discovery and analysis accelerating plant biotechnology. Plant Biotechnol. J. 7, 311.
    • (2009) Plant Biotechnol. J. , vol.7 , pp. 311
    • Henry, R.J.1    Edwards, K.2
  • 11
    • 34548395815 scopus 로고    scopus 로고
    • Towards the molecular basis of heterosis
    • Hochholdinger, F. and Hoecker, N. (2007) Towards the molecular basis of heterosis. Trends Plant Sci. 12, 427-432.
    • (2007) Trends Plant Sci. , vol.12 , pp. 427-432
    • Hochholdinger, F.1    Hoecker, N.2
  • 12
    • 0036963688 scopus 로고    scopus 로고
    • Genetic dissection of an elite rice hybrid revealed that heterozygotes are not always advantageous for performance
    • Hua, J., Xing, Y., Xu, C., Sun, X., Yu, S. and Zhang, Q. (2002) Genetic dissection of an elite rice hybrid revealed that heterozygotes are not always advantageous for performance. Genetics, 162, 1885-1895.
    • (2002) Genetics , vol.162 , pp. 1885-1895
    • Hua, J.1    Xing, Y.2    Xu, C.3    Sun, X.4    Yu, S.5    Zhang, Q.6
  • 13
    • 0037418206 scopus 로고    scopus 로고
    • Single-locus heterotic effects and dominance by dominance interactions can adequately explain the genetic basis of heterosis in an elite rice hybrid
    • Hua, J., Xing, Y., Wu, W., Xu, C., Sun, X., Yu, S. and Zhang, Q. (2003) Single-locus heterotic effects and dominance by dominance interactions can adequately explain the genetic basis of heterosis in an elite rice hybrid. Proc. Natl Acad. Sci. USA, 100, 2574-2579.
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 2574-2579
    • Hua, J.1    Xing, Y.2    Wu, W.3    Xu, C.4    Sun, X.5    Yu, S.6    Zhang, Q.7
  • 14
    • 33750488136 scopus 로고    scopus 로고
    • Heterosis and polymorphisms of gene expression in an elite rice hybrid as revealed by a microarray analysis of 9198 unique ESTs
    • Huang, Y., Zhang, L., Zhang, J., Yuan, D., Xu, C., Li, X., Zhou, D., Wang, S. and Zhang, Q. (2006) Heterosis and polymorphisms of gene expression in an elite rice hybrid as revealed by a microarray analysis of 9198 unique ESTs. Plant Mol. Biol. 62, 579-591.
    • (2006) Plant Mol. Biol. , vol.62 , pp. 579-591
    • Huang, Y.1    Zhang, L.2    Zhang, J.3    Yuan, D.4    Xu, C.5    Li, X.6    Zhou, D.7    Wang, S.8    Zhang, Q.9
  • 15
    • 64749113018 scopus 로고    scopus 로고
    • Discovering genetic polymorphisms in next-generation sequence data
    • Imelfort, M., Duran, C., Batley, J. and Edwards, D. (2010) Discovering genetic polymorphisms in next-generation sequence data. Plant Biotechnol. J. 7, 312-317.
    • (2010) Plant Biotechnol. J. , vol.7 , pp. 312-317
    • Imelfort, M.1    Duran, C.2    Batley, J.3    Edwards, D.4
  • 16
    • 84907150192 scopus 로고    scopus 로고
    • The map based sequence of the rice genome
    • IRGSP (International Rice Genome Sequencing Project)
    • IRGSP (International Rice Genome Sequencing Project) (2005) The map based sequence of the rice genome. Nature, 436, 793-800.
    • (2005) Nature , vol.436 , pp. 793-800
  • 17
    • 68749104735 scopus 로고    scopus 로고
    • Markers and mapping revisited: finding your gene
    • Jones, N., Ougham, H., Thomas, H. and Pašakinskiene, I. (2009) Markers and mapping revisited: finding your gene. New Phytol. 183, 935-966.
    • (2009) New Phytol. , vol.183 , pp. 935-966
    • Jones, N.1    Ougham, H.2    Thomas, H.3    Pašakinskiene, I.4
  • 18
    • 0034851443 scopus 로고    scopus 로고
    • Overdominant epistatic loci are the primary genetic basis of inbreeding depression and heterosis in rice. I. Biomass and grain yield
    • Li, Z.K., Luo, L.J., Mei, H.W., Wang, D.L., Shu, Q.Y., Tabien, R., Zhong, D.B., Ying, C.S., Stansel, J.W., Khush, G.S. and Paterson, A.H. (2001) Overdominant epistatic loci are the primary genetic basis of inbreeding depression and heterosis in rice. I. Biomass and grain yield. Genetics, 158, 1737-1753.
    • (2001) Genetics , vol.158 , pp. 1737-1753
    • Li, Z.K.1    Luo, L.J.2    Mei, H.W.3    Wang, D.L.4    Shu, Q.Y.5    Tabien, R.6    Zhong, D.B.7    Ying, C.S.8    Stansel, J.W.9    Khush, G.S.10    Paterson, A.H.11
  • 19
    • 79953037834 scopus 로고    scopus 로고
    • Genetic analysis and fine mapping of a novel semidominant dwarfing gene LB4D in rice
    • Liang, F., Xin, X., Hu, Z., Xu, J., Wei, G., Qian, X., Yang, J., He, H. and Luo, X. (2011) Genetic analysis and fine mapping of a novel semidominant dwarfing gene LB4D in rice. J. Integr. Plant Biol. 53, 312-323.
    • (2011) J. Integr. Plant Biol. , vol.53 , pp. 312-323
    • Liang, F.1    Xin, X.2    Hu, Z.3    Xu, J.4    Wei, G.5    Qian, X.6    Yang, J.7    He, H.8    Luo, X.9
  • 20
    • 38549148784 scopus 로고    scopus 로고
    • High throughput SNP discovery and genotyping in grapevine (Vitis vinifera L.) by combining a resequencing approach and SNPlex technology
    • Lijavetzky, D., Cabezas, J.A., Ibáñez, A., Rodríguez, V. and Zapater, J.M. (2007) High throughput SNP discovery and genotyping in grapevine (Vitis vinifera L.) by combining a resequencing approach and SNPlex technology. BMC Genomics, 8, 424.
    • (2007) BMC Genomics , vol.8 , pp. 424
    • Lijavetzky, D.1    Cabezas, J.A.2    Ibáñez, A.3    Rodríguez, V.4    Zapater, J.M.5
  • 21
    • 0034845083 scopus 로고    scopus 로고
    • Overdominant epistatic loci are the primary genetic basis of inbreeding depression and heterosis in rice. II. Grain yield components
    • Luo, L.J., Li, Z.K., Mei, H.W., Shu, Q.Y., Tabien, R., Zhong, D.B., Ying, C.S., Stansel, J.W., Khush, G.S. and Paterson, A.H. (2001) Overdominant epistatic loci are the primary genetic basis of inbreeding depression and heterosis in rice. II. Grain yield components. Genetics, 158, 1755-1771.
    • (2001) Genetics , vol.158 , pp. 1755-1771
    • Luo, L.J.1    Li, Z.K.2    Mei, H.W.3    Shu, Q.Y.4    Tabien, R.5    Zhong, D.B.6    Ying, C.S.7    Stansel, J.W.8    Khush, G.S.9    Paterson, A.H.10
  • 24
    • 0028865532 scopus 로고
    • Neighboring base composition and transversion/transition bias in a comparison of rice and maize chloroplast noncoding regions
    • Morton, B.R. (1995) Neighboring base composition and transversion/transition bias in a comparison of rice and maize chloroplast noncoding regions. Proc. Natl Acad. Sci. USA, 92, 9717-9721.
    • (1995) Proc. Natl Acad. Sci. USA , vol.92 , pp. 9717-9721
    • Morton, B.R.1
  • 25
    • 78751503447 scopus 로고    scopus 로고
    • Core single-nucleotide polymorphisms-a tool for genetic analysis of the Japanese rice population
    • Nagasaki, H., Ebana, K., Shibaya, T., Yonemaru, J. and Yano, M. (2010) Core single-nucleotide polymorphisms-a tool for genetic analysis of the Japanese rice population. Breed. Sci. 60, 648-655.
    • (2010) Breed. Sci. , vol.60 , pp. 648-655
    • Nagasaki, H.1    Ebana, K.2    Shibaya, T.3    Yonemaru, J.4    Yano, M.5
  • 26
    • 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
    • Nasu, S., Suzuki, J., Ohta, R., Hasegawa, K., Yui, R., Kitazawa, N., Monna, L. and Minobe, Y. (2002) Search for and analysis of single nucleotide polymorphisms (SNPs) in rice (Oryza sativa, Oryza rufipogon) and establishment of SNP markers. DNA Res. 9, 163-171.
    • (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
  • 29
    • 0036008761 scopus 로고    scopus 로고
    • Applications of single nucleotide polymorphisms in crop genetics
    • Rafalski, A. (2002) Applications of single nucleotide polymorphisms in crop genetics. Curr. Opin. Plant Biol. 5, 94-100.
    • (2002) Curr. Opin. Plant Biol. , vol.5 , pp. 94-100
    • Rafalski, A.1
  • 33
    • 0036606953 scopus 로고    scopus 로고
    • Regional similarities in polymorphism in the human genome extend over many megabases
    • Smith, N.G.C. and Lercher, M.J. (2002) Regional similarities in polymorphism in the human genome extend over many megabases. Trends Genet. 18, 281-283.
    • (2002) Trends Genet. , vol.18 , pp. 281-283
    • Smith, N.G.C.1    Lercher, M.J.2
  • 34
    • 43049140496 scopus 로고    scopus 로고
    • InDel markers distinguish Basmatis from other fragrant rice varieties
    • Steele, K.A., Ogden, R., McEwing, R., Briggs, H. and 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
  • 35
    • 33751367186 scopus 로고    scopus 로고
    • Genomic variation in rice: genesis of highly polymorphic linkage blocks during domestication
    • Tang, T., Lu, J., Huang, J., McCouch, S.R., Shen, Y., Kai, Z., Purugganan, M.D., Shi, S. and Wu, C. (2006) Genomic variation in rice: genesis of highly polymorphic linkage blocks during domestication. PLoS Genet. 2, 1824-1833.
    • (2006) PLoS Genet. , vol.2 , pp. 1824-1833
    • Tang, T.1    Lu, J.2    Huang, J.3    McCouch, S.R.4    Shen, Y.5    Kai, Z.6    Purugganan, M.D.7    Shi, S.8    Wu, C.9
  • 37
    • 53349173110 scopus 로고    scopus 로고
    • Development of genomic resources for Citrus clementina: characterization of three deep-coverage BAC libraries and analysis of 46000 BAC end sequences
    • Terol, J., Naranjo, M.A., Ollitrault, P. and Talon, M. (2008) Development of genomic resources for Citrus clementina: characterization of three deep-coverage BAC libraries and analysis of 46000 BAC end sequences. BMC Genomics, 9, 423.
    • (2008) BMC Genomics , vol.9 , pp. 423
    • Terol, J.1    Naranjo, M.A.2    Ollitrault, P.3    Talon, M.4
  • 39
    • 77950466040 scopus 로고    scopus 로고
    • Discovery and application of insertion-deletion (INDEL) polymorphisms for QTL mapping of early life-history traits in Atlantic salmon
    • Vasemagi, A., Gross, R., Palm, D., Paaver, T. and Primmer, C.R. (2010) Discovery and application of insertion-deletion (INDEL) polymorphisms for QTL mapping of early life-history traits in Atlantic salmon. BMC Genomics, 11, 156.
    • (2010) BMC Genomics , vol.11 , pp. 156
    • Vasemagi, A.1    Gross, R.2    Palm, D.3    Paaver, T.4    Primmer, C.R.5
  • 40
    • 0035983148 scopus 로고    scopus 로고
    • A review on SNP and other types of molecular markers and their use in animal genetics
    • Vignal, A., Milan, D., Cristobal, M.S. and Eggen, A. (2002) A review on SNP and other types of molecular markers and their use in animal genetics. Genet. Sel. Evol. 34, 275-305.
    • (2002) Genet. Sel. Evol. , vol.34 , pp. 275-305
    • Vignal, A.1    Milan, D.2    Cristobal, M.S.3    Eggen, A.4
  • 41
    • 0001062055 scopus 로고    scopus 로고
    • The excess of transitions among nucleotide substitutions: new methods of estimating transition bias underscore it s significance
    • Wakeley, J. (1996) The excess of transitions among nucleotide substitutions: new methods of estimating transition bias underscore it s significance. Tree, 11, 158-162.
    • (1996) Tree , vol.11 , pp. 158-162
    • Wakeley, J.1
  • 42
    • 62449183461 scopus 로고    scopus 로고
    • SNP deserts of Asian cultivated rice: genomic regions under domestication
    • Wang, L., Hao, L., Li, X., Hu, S., Ge., S. and Yu, J. (2009) SNP deserts of Asian cultivated rice: genomic regions under domestication. J. Evol. Biol. 22, 751-761.
    • (2009) J. Evol. Biol. , vol.22 , pp. 751-761
    • Wang, L.1    Hao, L.2    Li, X.3    Hu, S.4    Ge, S.5    Yu, J.6
  • 44
    • 0029035408 scopus 로고
    • Dominance is the major genetic basis of heterosis in rice as revealed by QTL analysis using molecular markers
    • Xiao, J., Li, J., Yuan, L. and Tanksley, S.D. (1995) Dominance is the major genetic basis of heterosis in rice as revealed by QTL analysis using molecular markers. Genetics, 140, 745-754.
    • (1995) Genetics , vol.140 , pp. 745-754
    • Xiao, J.1    Li, J.2    Yuan, L.3    Tanksley, S.D.4
  • 45
    • 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., Ebana, K., Nakajima, M., Shibaya, T. and 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.3    Ebana, K.4    Nakajima, M.5    Shibaya, T.6    Yano, M.7
  • 47
    • 66049146171 scopus 로고    scopus 로고
    • A genome-wide transcription analysis reveals a close correlation of promoter INDEL polymorphism and heterotic gene expression in rice hybrids
    • Zhang, H., He, H., Chen, L., Li, L., Liang, M., Wang, X., Liu, X., He, G., Chen, R., Ma, L. and Deng, X. (2008) A genome-wide transcription analysis reveals a close correlation of promoter INDEL polymorphism and heterotic gene expression in rice hybrids. Mol. Plant, 1, 720-731.
    • (2008) Mol. Plant , vol.1 , pp. 720-731
    • Zhang, H.1    He, H.2    Chen, L.3    Li, L.4    Liang, M.5    Wang, X.6    Liu, X.7    He, G.8    Chen, R.9    Ma, L.10    Deng, X.11


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