메뉴 건너뛰기




Volumn 51, Issue 5, 2007, Pages 910-918

SNP discovery via 454 transcriptome sequencing

Author keywords

454 sequencing; ESTs; Maize; Markers; SNPs

Indexed keywords

COMPUTATION THEORY; GENES; POLYMORPHISM;

EID: 34548128406     PISSN: 09607412     EISSN: 1365313X     Source Type: Journal    
DOI: 10.1111/j.1365-313X.2007.03193.x     Document Type: Article
Times cited : (331)

References (44)
  • 1
    • 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. 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
  • 2
    • 0030246842 scopus 로고    scopus 로고
    • The contributions of retroelements to plant genome organization, function and evolution
    • Bennetzen, J.L. (1996) The contributions of retroelements to plant genome organization, function and evolution. Trends Microbiol. 4, 347 353.
    • (1996) Trends Microbiol. , vol.4 , pp. 347-353
    • Bennetzen, J.L.1
  • 3
    • 0037623912 scopus 로고    scopus 로고
    • Cis-acting variation in the expression of a high proportion of genes in human brain
    • Bray, N.J., Buckland, P.R., Owen, M.J. O'Donovan, M.C. (2003) Cis-acting variation in the expression of a high proportion of genes in human brain. Hum. Genet. 113, 149 153.
    • (2003) Hum. Genet. , vol.113 , pp. 149-153
    • Bray, N.J.1    Buckland, P.R.2    Owen, M.J.3    O'Donovan, M.C.4
  • 6
    • 4043108373 scopus 로고    scopus 로고
    • Automated SNP detection in expressed sequence tags: Statistical considerations and application to maritime pine sequences
    • Dantec, L.L., Chagne, D., Pot, D. et al. (2004) Automated SNP detection in expressed sequence tags: statistical considerations and application to maritime pine sequences. Plant Mol. Biol. 54, 461 470.
    • (2004) Plant Mol. Biol. , vol.54 , pp. 461-470
    • Dantec, L.L.1    Chagne, D.2    Pot, D.3
  • 8
    • 33845984917 scopus 로고    scopus 로고
    • Gene discovery and annotation using LCM-454 transcriptome sequencing
    • Emrich, S.J., Barbazuk, W.B., Li, L. Schnable, P.S. (2007a) Gene discovery and annotation using LCM-454 transcriptome sequencing. Genome Res. 17, 69 73.
    • (2007) Genome Res. , vol.17 , pp. 69-73
    • Emrich, S.J.1    Barbazuk, W.B.2    Li, L.3    Schnable, P.S.4
  • 10
    • 4644353880 scopus 로고    scopus 로고
    • An SNP resource for rice genetics and breeding based on subspecies indica and japonica genome alignments
    • Feltus, F.A., Wan, J., Schulze, S.R., Estill, J.C., Jiang, N. 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, F.A.1    Wan, J.2    Schulze, S.R.3    Estill, J.C.4    Jiang, N.5    Paterson, A.H.6
  • 12
    • 24744442994 scopus 로고    scopus 로고
    • Quality assessment of maize assembled genomic islands (MAGIs) and large-scale experimental verification of predicted genes
    • Fu, Y., Emrich, S.J., Guo, L., Wen, T.-J., Ashlock, D.A., Aluru, S. Schnable, P.S. (2005) Quality assessment of maize assembled genomic islands (MAGIs) and large-scale experimental verification of predicted genes. Proc. Natl Acad. Sci. USA, 102, 12282 12287.
    • (2005) Proc. Natl Acad. Sci. USA , vol.102 , pp. 12282-12287
    • Fu, Y.1    Emrich, S.J.2    Guo, L.3    Wen, T.-J.4    Ashlock, D.A.5    Aluru, S.6    Schnable, P.S.7
  • 13
    • 34548116605 scopus 로고    scopus 로고
    • Genetic dissection of intermated recombinant inbred lines using a new genetic map of maize
    • Fu, Y., Wen, T.J., Ronin, Y.I. et al. (2006) Genetic dissection of intermated recombinant inbred lines using a new genetic map of maize. Genetics, 175, 429 439.
    • (2006) Genetics , vol.175 , pp. 429-439
    • Fu, Y.1    Wen, T.J.2    Ronin, Y.I.3
  • 14
    • 0141872967 scopus 로고    scopus 로고
    • Genome-wide mRNA profiling reveals heterochronic allelic variation and a new imprinted gene in hybrid maize endosperm
    • Guo, M., Rupe, M.A., Danilevskaya, O.N., Yang, X. Hu, Z. (2003) Genome-wide mRNA profiling reveals heterochronic allelic variation and a new imprinted gene in hybrid maize endosperm. Plant J. 36, 30 44.
    • (2003) Plant J. , vol.36 , pp. 30-44
    • Guo, M.1    Rupe, M.A.2    Danilevskaya, O.N.3    Yang, X.4    Hu, Z.5
  • 15
    • 0035010640 scopus 로고    scopus 로고
    • Automation in genotyping of single nucleotide polymorphisms
    • Gut, I.G. (2001) Automation in genotyping of single nucleotide polymorphisms. Hum. Mutat. 17, 475 492.
    • (2001) Hum. Mutat. , vol.17 , pp. 475-492
    • Gut, I.G.1
  • 17
    • 0036306905 scopus 로고    scopus 로고
    • Generation and comparison of EST-derived SSRs and SNPs in barley (Hordeum vulgare L.)
    • Kota, R., Varshney, R.K., Thiel, T., Dehmer, K.J. Graner, A. (2001) Generation and comparison of EST-derived SSRs and SNPs in barley (Hordeum vulgare L.). Hereditas, 135, 145 151.
    • (2001) Hereditas , vol.135 , pp. 145-151
    • Kota, R.1    Varshney, R.K.2    Thiel, T.3    Dehmer, K.J.4    Graner, A.5
  • 19
    • 0035776497 scopus 로고    scopus 로고
    • Methods for genotyping single nucleotide polymorphisms
    • Kwok, P.Y. (2001) Methods for genotyping single nucleotide polymorphisms. Annu. Rev. Genomics Hum. Genet., 2, 235 258.
    • (2001) Annu. Rev. Genomics Hum. Genet. , vol.2 , pp. 235-258
    • Kwok, P.Y.1
  • 20
    • 16244399810 scopus 로고    scopus 로고
    • Using cDNA and genomic sequences as tools to develop SNP strategies in cassava (Manihot esculenta Crantz)
    • Lopez, C., Piegu, B., Cooke, R., Delseny, M., Tohme, J. Verdier, V. (2005) Using cDNA and genomic sequences as tools to develop SNP strategies in cassava (Manihot esculenta Crantz). Theor. Appl. Genet. 110, 425 431.
    • (2005) Theor. Appl. Genet. , vol.110 , pp. 425-431
    • Lopez, C.1    Piegu, B.2    Cooke, R.3    Delseny, M.4    Tohme, J.5    Verdier, V.6
  • 22
    • 24044455869 scopus 로고    scopus 로고
    • Genome sequencing in microfabricated high-density picolitre reactors
    • Margulies, M., Egholm, M., Altman, W.E. et al. (2005) Genome sequencing in microfabricated high-density picolitre reactors. Nature, 437, 376 380.
    • (2005) Nature , vol.437 , pp. 376-380
    • Margulies, M.1    Egholm, M.2    Altman, W.E.3
  • 24
    • 0034755894 scopus 로고    scopus 로고
    • Abundance, distribution, and transcriptional activity of repetitive elements in the maize genome
    • Meyers, B.C., Tingey, S.V. Morgante, M. (2001) Abundance, distribution, and transcriptional activity of repetitive elements in the maize genome. Genome Res. 11, 1660 1676.
    • (2001) Genome Res. , vol.11 , pp. 1660-1676
    • Meyers, B.C.1    Tingey, S.V.2    Morgante, M.3
  • 25
    • 0030872838 scopus 로고    scopus 로고
    • PolyPhred: Automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing
    • Nickerson, D.A., Tobe, V.O. Taylor, S.L. (1997) PolyPhred: automating the detection and genotyping of single nucleotide substitutions using fluorescence-based resequencing. Nucleic Acids Res. 25, 2745 2751.
    • (1997) Nucleic Acids Res. , vol.25 , pp. 2745-2751
    • Nickerson, D.A.1    Tobe, V.O.2    Taylor, S.L.3
  • 26
    • 33748126341 scopus 로고    scopus 로고
    • Automated SNP detection from a large collection of white spruce expressed sequences: Contributing factors and approaches for the categorization of SNPs
    • Pavy, N., Parsons, L., Paule, C., Mackay, J. Bousquet, J. (2006) Automated SNP detection from a large collection of white spruce expressed sequences: contributing factors and approaches for the categorization of SNPs. BMC Genomics, 7.
    • (2006) BMC Genomics , vol.7
    • Pavy, N.1    Parsons, L.2    Paule, C.3    MacKay, J.4    Bousquet, J.5
  • 27
    • 0036186213 scopus 로고    scopus 로고
    • Novel genetic mapping tools in plants: SNPs and LD-based approaches
    • Rafalski, J.A. (2002) Novel genetic mapping tools in plants: SNPs and LD-based approaches. Plant Sci. 162, 329 333.
    • (2002) Plant Sci. , vol.162 , pp. 329-333
    • Rafalski, J.A.1
  • 28
    • 0035865322 scopus 로고    scopus 로고
    • A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms
    • Sachidanandam, R., Weissman, D., Schmidt, S.C. et al. (2001) A map of human genome sequence variation containing 1.42 million single nucleotide polymorphisms. Nature, 409, 928 933.
    • (2001) Nature , vol.409 , pp. 928-933
    • Sachidanandam, R.1    Weissman, D.2    Schmidt, S.C.3
  • 29
    • 0013630297 scopus 로고    scopus 로고
    • Nested retrotransposons in the intergenic regions of the maize genome
    • SanMiguel, P., Tikhonov, A., Jin, Y.K. et al. (1996) Nested retrotransposons in the intergenic regions of the maize genome. Science, 274, 765 768.
    • (1996) Science , vol.274 , pp. 765-768
    • Sanmiguel, P.1    Tikhonov, A.2    Jin, Y.K.3
  • 31
    • 33747866029 scopus 로고    scopus 로고
    • Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression patterns in the F1 hybrid
    • Stupar, R.M. Springer, N.M. (2006) Cis-transcriptional variation in maize inbred lines B73 and Mo17 leads to additive expression patterns in the F1 hybrid. Genetics, 173, 2199 2210.
    • (2006) Genetics , vol.173 , pp. 2199-2210
    • Stupar, R.M.1    Springer, N.M.2
  • 33
    • 3042595170 scopus 로고    scopus 로고
    • Selection versus demography: A multilocus investigation of the domestication process in maize
    • Tenaillon, M.I., U'Ren, J., Tenaillon, O. Gaut, B.S. (2004) Selection versus demography: a multilocus investigation of the domestication process in maize. Mol. Biol. Evol. 21, 1214 1225.
    • (2004) Mol. Biol. Evol. , vol.21 , pp. 1214-1225
    • Tenaillon, M.I.1    U'Ren, J.2    Tenaillon, O.3    Gaut, B.S.4
  • 34
    • 0035756174 scopus 로고    scopus 로고
    • High-throughput identification, database storage and analysis of SNPs in EST sequences
    • Useche, F.J., Gao, G., Harafey, M. Rafalski, A. (2001) High-throughput identification, database storage and analysis of SNPs in EST sequences. Genome Inform. 12, 194 203.
    • (2001) Genome Inform. , vol.12 , pp. 194-203
    • Useche, F.J.1    Gao, G.2    Harafey, M.3    Rafalski, A.4
  • 35
    • 0034129194 scopus 로고    scopus 로고
    • Optimal spliced alignment of homologous cDNA to a genomic DNA template
    • Usuka, J., Zhu, W. Brendel, V. (2000) Optimal spliced alignment of homologous cDNA to a genomic DNA template. Bioinformatics, 16, 203 211.
    • (2000) Bioinformatics , vol.16 , pp. 203-211
    • Usuka, J.1    Zhu, W.2    Brendel, V.3
  • 36
    • 25444532272 scopus 로고    scopus 로고
    • A method for finding single-nucleotide polymorphisms with allele frequencies in sequences of deep coverage
    • Wang, J. Huang, X. (2005) A method for finding single-nucleotide polymorphisms with allele frequencies in sequences of deep coverage. BMC Bioinformatics, 6.
    • (2005) BMC Bioinformatics , vol.6
    • Wang, J.1    Huang, X.2
  • 37
    • 0033580401 scopus 로고    scopus 로고
    • The limits of selection during maize domestication
    • Wang, R.L., Stec, A., Hey, J., Lukens, L. Doebley, J. (1999) The limits of selection during maize domestication. Nature, 398, 236 239.
    • (1999) Nature , vol.398 , pp. 236-239
    • Wang, R.L.1    Stec, A.2    Hey, J.3    Lukens, L.4    Doebley, J.5
  • 39
    • 0345731466 scopus 로고    scopus 로고
    • Enrichment of gene-coding sequences in maize by genome filtration
    • Whitelaw, C.A., Barbazuk, W.B., Pertea, G. et al. (2003) Enrichment of gene-coding sequences in maize by genome filtration. Science, 302, 2118 2120.
    • (2003) Science , vol.302 , pp. 2118-2120
    • Whitelaw, C.A.1    Barbazuk, W.B.2    Pertea, G.3
  • 41
    • 0037452982 scopus 로고    scopus 로고
    • Genome-wide single-nucleotide polymorphism analysis defines haplotype patterns in mouse
    • Wiltshire, T., Pletcher, M.T., Batalov, S. et al. (2003) Genome-wide single-nucleotide polymorphism analysis defines haplotype patterns in mouse. Proc. Natl Acad. Sci. USA, 100, 3380 3385.
    • (2003) Proc. Natl Acad. Sci. USA , vol.100 , pp. 3380-3385
    • Wiltshire, T.1    Pletcher, M.T.2    Batalov, S.3
  • 43
    • 33344469072 scopus 로고    scopus 로고
    • A large-scale screen for artificial selection in maize identifies candidate agronomic loci for domestication and crop improvement
    • Yamasaki, M., Tenaillon, M.I., Bi, I.V., Schroeder, S.G., Sanchez-Villeda, H., Doebley, J.F., Gaut, B.S. McMullen, M.D. (2005) A large-scale screen for artificial selection in maize identifies candidate agronomic loci for domestication and crop improvement. Plant Cell, 17, 2859 2872.
    • (2005) Plant Cell , vol.17 , pp. 2859-2872
    • Yamasaki, M.1    Tenaillon, M.I.2    Bi, I.V.3    Schroeder, S.G.4    Sanchez-Villeda, H.5    Doebley, J.F.6    Gaut, B.S.7    McMullen, M.D.8


* 이 정보는 Elsevier사의 SCOPUS DB에서 KISTI가 분석하여 추출한 것입니다.