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Volumn 8, Issue 1, 2015, Pages

Southern-by-sequencing: A robust screening approach for molecular characterization of genetically modified crops

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EID: 84925955341     PISSN: None     EISSN: 19403372     Source Type: Journal    
DOI: 10.3835/plantgenome2014.08.0037     Document Type: Article
Times cited : (62)

References (35)
  • 1
    • 35748951614 scopus 로고    scopus 로고
    • Direct selection of human genomic loci by microarray hybridization. Nat
    • Albert, T.J., M.N. Molla, D.M. Muzny, L. Nazareth, D. Wheeler, X. Song, et al. 2007. Direct selection of human genomic loci by microarray hybridization. Nat. Methods 11:903–905. doi:10.1038/nmeth1111
    • (2007) Methods , vol.11 , pp. 903-905
    • Albert, T.J.1    Molla, M.N.2    Muzny, D.M.3    Nazareth, L.4    Wheeler, D.5    Song, X.6
  • 2
    • 81855178276 scopus 로고    scopus 로고
    • Somatic retrotransposition alters the genetic landscape of the human brain
    • Baillie, J.K., M.W. Barnett, K.R. Upton, D.J. Gerhardt, T.A. Richmond, F. De Sapio, et al. 2011. Somatic retrotransposition alters the genetic landscape of the human brain. Nature 479:534–537. doi:10.1038/nature10531
    • (2011) Nature , vol.479 , pp. 534-537
    • Baillie, J.K.1    Barnett, M.W.2    Upton, K.R.3    Gerhardt, D.J.4    Richmond, T.A.5    De Sapio, F.6
  • 3
    • 0036806428 scopus 로고    scopus 로고
    • Molecular and genetic analyses of transgenic plants: Considerations and approaches
    • Bhat, S.R., and S. Srinivasan. 2002. Molecular and genetic analyses of transgenic plants: Considerations and approaches. Plant Sci. 163(4):673–681. doi:10.1016/S0168-9452(02)00152-8
    • (2002) Plant Sci , vol.163 , Issue.4 , pp. 673-681
    • Bhat, S.R.1    Srinivasan, S.2
  • 4
    • 79956046982 scopus 로고    scopus 로고
    • Phenotypic and genomic analyses of a fast neutron mutant population resource in soybean
    • Bolon, Y.T., W.J. Haun, W.W. Xu, D. Grant, M.G. Stacey, R.T. Nelson, et al. 2011. Phenotypic and genomic analyses of a fast neutron mutant population resource in soybean. Plant Physiol. 156:240–253. doi:10.1104/pp.110.170811
    • (2011) Plant Physiol , vol.156 , pp. 240-253
    • Bolon, Y.T.1    Haun, W.J.2    Xu, W.W.3    Grant, D.4    Stacey, M.G.5    Nelson, R.T.6
  • 5
    • 69249208477 scopus 로고    scopus 로고
    • Mutation discovery in the mouse using genetically guided array capture and resequencing. Mamm
    • D’Ascenzo, M., C. Meacham, J. Kitzman, C. Middle, J. Knight, R. Winer, et al. 2009. Mutation discovery in the mouse using genetically guided array capture and resequencing. Mamm. Genome 20:424–436. doi:10.1007/s00335-009-9200-y
    • (2009) Genome , vol.20 , pp. 424-436
    • D’Ascenzo, M.1    Meacham, C.2    Kitzman, J.3    Middle, C.4    Knight, J.5    Winer, R.6
  • 7
    • 0031955518 scopus 로고    scopus 로고
    • Base-calling of automated sequencer traces using phred. I. Accuracy assessment
    • Ewing, B., L. Hillier, M.C. Wendl, and P. Green. 1998. Base-calling of automated sequencer traces using phred. I. Accuracy assessment. Genome Res. 8:175–185. doi:10.1101/gr.8.3.175
    • (1998) Genome Res , vol.8 , pp. 175-185
    • Ewing, B.1    Hillier, L.2    Wendl, M.C.3    Green, P.4
  • 8
    • 0031978181 scopus 로고    scopus 로고
    • Base-calling of automated sequencer traces using phred. II. Error probabilities
    • Ewing, B., and P. Green. 1998. Base-calling of automated sequencer traces using phred. II. Error probabilities. Genome Res. 8:186–194. doi:10.1101/gr.8.3.175
    • (1998) Genome Res , vol.8 , pp. 186-194
    • Ewing, B.1    Green, P.2
  • 9
    • 77952865614 scopus 로고    scopus 로고
    • Repeat subtraction-mediated sequence capture from a complex genome
    • Fu, Y., N.M. Springer, D.J. Gerhardt, K. Ying, C.T. Yeh, W. Wu, et al. 2010. Repeat subtraction-mediated sequence capture from a complex genome. Plant J. 62:898–909. doi:10.1111/j.1365-313X.2010.04196.x
    • (2010) Plant J , vol.62 , pp. 898-909
    • Fu, Y.1    Springer, N.M.2    Gerhardt, D.J.3    Ying, K.4    Yeh, C.T.5    Wu, W.6
  • 12
    • 84925951125 scopus 로고    scopus 로고
    • Green, D., J. Wendt, C. Kashuk, M. Brockman, and D. Burgess. 2012. Double capture: An alternative protocol for sequence capture of difficult targets. SeqCap EZ Library: Technical note. Roche NimbleGen, Inc. http://www.nimblegen.com/products/lit/06870406001_NG_Seq-CapEZ_DoubleCaptureSR_20Aug2012.pdf (accessed 5 Dec. 2014).
    • Green, D.1    Wendt, J.2    Kashuk, C.3    Brockman, M.4    Burgess, D.5
  • 13
    • 0036226603 scopus 로고    scopus 로고
    • BLAT—the BLAST-like alignment tool
    • Kent, W.J. 2002. BLAT—the BLAST-like alignment tool. Genome Res. 12:656–664. doi:10.1101/gr.229202
    • (2002) Genome Res , vol.12 , pp. 656-664
    • Kent, W.J.1
  • 14
    • 70350448623 scopus 로고    scopus 로고
    • The development of herbicide-resistant maize: Stable
    • Kim, H.A., S.D. Utomo, S.Y. Kwon, S.R. Min, J.S. Kim, H.S. Yoo, and P.S. Choi. 2009. The development of herbicide-resistant maize: Stable Agrobacteriummediated transformation of maize using explants of type II embryogenic calli. Plant Biotechnol. Rep. 3:277–283. doi:10.1007/s11816-009-0099-2
    • (2009) Rep , vol.3 , pp. 277-283
    • Kim, H.A.1    Utomo, S.D.2    Kwon, S.Y.3    Min, S.R.4    Kim, J.S.5    Yoo, H.S.6    Choi, P.S.7
  • 15
    • 0001601321 scopus 로고
    • Genetic transformation of maize cells by particle bombardment
    • Klein, T.M., L. Kornstein, J.C. Sanford, and M.E. Fromm. 1989. Genetic transformation of maize cells by particle bombardment. Plant Physiol. 91:440–444. doi:10.1104/pp.91.1.440
    • (1989) Plant Physiol , vol.91 , pp. 440-444
    • Klein, T.M.1    Kornstein, L.2    Sanford, J.C.3    Fromm, M.E.4
  • 16
    • 84882455681 scopus 로고    scopus 로고
    • The use of next generation sequencing and junction sequence analysis bioinformatics to achieve molecular characterization of crops improved through modern biotechnology
    • Kovalic, D., C. Garnaat, L. Guo, Y. Yan, J. Groat, A. Silvanovich, et al. 2012. The use of next generation sequencing and junction sequence analysis bioinformatics to achieve molecular characterization of crops improved through modern biotechnology. Plant Gen. 5(3):149–163 doi:10.3835/plantgenome2012.10.0026
    • (2012) Plant Gen , vol.5 , Issue.3 , pp. 149-163
    • Kovalic, D.1    Garnaat, C.2    Guo, L.3    Yan, Y.4    Groat, J.5    Silvanovich, A.6
  • 17
    • 62349130698 scopus 로고    scopus 로고
    • Ultrafast and memory-efficient alignment of short DNA sequences to the human genome
    • Langmead, B., C. Trapnell, M. Pop, and S.L. Salzberg. 2009. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 10:R25. doi:10.1186/gb-2009-10-3-r25
    • (2009) Genome Biol , vol.10 , pp. R25
    • Langmead, B.1    Trapnell, C.2    Pop, M.3    Salzberg, S.L.4
  • 18
    • 84881497686 scopus 로고    scopus 로고
    • Time- and cost-efficient identification of T-DNA insertions sites through targeted genomic sequencing
    • Lapage, É., É. Zampini, B. Boyle, and N. Brisson. 2013. Time- and cost-efficient identification of T-DNA insertions sites through targeted genomic sequencing. PLoS ONE 8(8):e70912. doi:10.1371/journal.pone.0070912
    • (2013) Plos ONE , vol.8 , Issue.8
    • Lapage, É.1    Zampini, É.2    Boyle, B.3    Brisson, N.4
  • 19
    • 77949587649 scopus 로고    scopus 로고
    • Fast and accurate long-read alignment with Burrows–Wheeler transform
    • Li, H., and R. Durbin. 2010. Fast and accurate long-read alignment with Burrows–Wheeler transform. Bioinformatics 26(5):589–595. doi:10.1093/bioinformatics/btp698
    • (2010) Bioinformatics , vol.26 , Issue.5 , pp. 589-595
    • Li, H.1    Durbin, R.2
  • 20
    • 75149155568 scopus 로고    scopus 로고
    • The sequence and
    • Li, R., W. Fan, G. Tian, H. Zhu, L. He, J. Cai, et al. 2010. The sequence and de novo assembly of the giant panda genome. Nature 463:311–317. doi:10.1038/nature08696
    • (2010) Nature , vol.463 , pp. 311-317
    • Li, R.1    Fan, W.2    Tian, G.3    Zhu, H.4    He, L.5    Cai, J.6
  • 21
    • 79952592810 scopus 로고    scopus 로고
    • A fast, lock-free approach for efficient parallel counting of occurrences of
    • Marcais, G., and C. Kinsford. 2011. A fast, lock-free approach for efficient parallel counting of occurrences of k-mers. Bioinformatics 27:764–770. doi:10.1093/bioinformatics/btr011
    • (2011) Bioinformatics , vol.27 , pp. 764-770
    • Marcais, G.1    Kinsford, C.2
  • 22
    • 42949157236 scopus 로고    scopus 로고
    • The draft genome of the transgenic tropical fruit tree papaya (
    • Ming, R., S. Hou, Y. Feng, Q. Yu, A. Dionne-Laporte, J.H. Saw, et al. 2008. The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 452:991–996. doi:10.1038/nature06856
    • (2008) Nature , vol.452 , pp. 991-996
    • Ming, R.1    Hou, S.2    Feng, Y.3    Yu, Q.4    Dionne-Laporte, A.5    Saw, J.H.6
  • 23
    • 84867660741 scopus 로고    scopus 로고
    • Development of an agricultural biotechnology crop product: Testing from discovery to commercialization
    • Privalle, L.S., J. Chen, G. Clapper, P. Hunst, F. Spiegelhalter, and C.X. Zhong. 2012. Development of an agricultural biotechnology crop product: Testing from discovery to commercialization. J. Agric. Food Chem. 60(41):10179–10187. doi:10.1021/jf302706e
    • (2012) J. Agric. Food Chem , vol.60 , Issue.41 , pp. 10179-10187
    • Privalle, L.S.1    Chen, J.2    Clapper, G.3    Hunst, P.4    Spiegelhalter, F.5    Zhong, C.X.6
  • 24
    • 0002788379 scopus 로고
    • Extraction of DNA from milligram amounts of fresh, herbarium and mummified plant tissues. Plant Mol
    • Rogers, S.O., and A.J. Bendich. 1985. Extraction of DNA from milligram amounts of fresh, herbarium and mummified plant tissues. Plant Mol. Biol. 5(2):69–76. doi:10.1007/BF00020088
    • (1985) Biol , vol.5 , Issue.2 , pp. 69-76
    • Rogers, S.O.1    Bendich, A.J.2
  • 25
    • 70450202132 scopus 로고    scopus 로고
    • The B73 maize genome: Complexity, diversity, and dynamics
    • Schnable, P.S., D. Ware, R.S. Fulton, J.C. Stein, F. Wei, S. Pasternak, et al. 2009. The B73 maize genome: Complexity, diversity, and dynamics. Science 325:1112–1115. doi:10.1126/science.1178534
    • (2009) Science , vol.325 , pp. 1112-1115
    • Schnable, P.S.1    Ware, D.2    Fulton, R.S.3    Stein, J.C.4    Wei, F.5    Pasternak, S.6
  • 28
    • 0016700864 scopus 로고
    • Detection of specific sequences among DNA fragments separated by gel electrophoresis
    • Southern, E.M. 1975. Detection of specific sequences among DNA fragments separated by gel electrophoresis. J. Mol. Biol. 98:503–517. doi:10.1016/S0022-2836(75)80083-0
    • (1975) J. Mol. Biol , vol.98 , pp. 503-517
    • Southern, E.M.1
  • 29
    • 34249831354 scopus 로고
    • Osmotic treatment enhances particle bombardment-mediated transient and stable transformation of maize
    • Vain, P., M.D. McMullen, and J.J. Finer. 1993. Osmotic treatment enhances particle bombardment-mediated transient and stable transformation of maize. Plant Cell Rep. 12:84–88. doi:10.1007/BF00241940
    • (1993) Plant Cell Rep , vol.12 , pp. 84-88
    • Vain, P.1    McMullen, M.D.2    Finer, J.J.3
  • 30
    • 84862956715 scopus 로고    scopus 로고
    • Draft genome sequence of pigeonpea (
    • Varshney, R.K., W. Chen, Y. Li, A.K. Bharti, R.K. Saxena, J.A. Schueter, et al. 2011. Draft genome sequence of pigeonpea (Cajanus cajan), an orphan legume crop of resource-poor farmers. Nat. Biotechnol. 30:83–89. doi:10.1038/nbt.2022
    • (2011) Biotechnol , vol.30 , pp. 83-89
    • Varshney, R.K.1    Chen, W.2    Li, Y.3    Bharti, A.K.4    Saxena, R.K.5    Schueter, J.A.6
  • 31
    • 33847307402 scopus 로고    scopus 로고
    • Assembling millions of short DNA sequences using SSAKE
    • Warren, R.L., G.G. Sutton, S.J. Jones, and R.A. Holt. 2007. Assembling millions of short DNA sequences using SSAKE. Bioinformatics 23:500–501. doi:10.1093/bioinformatics/btl629
    • (2007) Bioinformatics , vol.23 , pp. 500-501
    • Warren, R.L.1    Sutton, G.G.2    Jones, S.J.3    Holt, R.A.4
  • 33
    • 84885165844 scopus 로고    scopus 로고
    • Development and characterization of simple sequence repeat markers providing genomewide coverage and high resolution in maize
    • Xu, J., L. Liu, Y. Xu, C. Chen, T. Rong, F. Ali, et al. 2013. Development and characterization of simple sequence repeat markers providing genomewide coverage and high resolution in maize. DNA Res. 20:497–509. doi:10.1093/dnares/dst026
    • (2013) DNA Res , vol.20 , pp. 497-509
    • Xu, J.1    Liu, L.2    Xu, Y.3    Chen, C.4    Rong, T.5    Ali, F.6
  • 34
    • 59949102336 scopus 로고    scopus 로고
    • Characterization and event-specific quantitative detection of DAS-59122-7 maize insert with the application of plasmidic reference material
    • Xu, W., Z. Liang, Y. Rong, Y. Luo, F. Zhang, Y. Yuan, and K. Huang. 2008. Characterization and event-specific quantitative detection of DAS-59122-7 maize insert with the application of plasmidic reference material. J. Sci. Food Agric. 89:494–503. doi:10.1002/jsfa.3479
    • (2008) J. Sci. Food Agric , vol.89 , pp. 494-503
    • Xu, W.1    Liang, Z.2    Rong, Y.3    Luo, Y.4    Zhang, F.5    Yuan, Y.6    Huang, K.7
  • 35
    • 0035561248 scopus 로고    scopus 로고
    • High throughput genetic transformation mediated by
    • Zhao, Z., W. Gu, T. Cai, L. Tagliani, D. Hondred, D. Bond, et al. 2001. High throughput genetic transformation mediated by Agrobacterium tumefaciens in maize. Mol. Breed. 8:323–333 10.1023/A:1015243600325
    • (2001) Mol. Breed , vol.8 , pp. 323-333
    • Zhao, Z.1    Gu, W.2    Cai, T.3    Tagliani, L.4    Hondred, D.5    Bond, D.6


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