Comparison of DNA walking methods for isolation of transgene-flanking regions in GM potato

Molecular Biotechnology

Volumn 49, Issue 1, 2011, Pages 19-31

  Cullen, Danny ^a   Harwood, Wendy ^b   Smedley, Mark ^b   Davies, Howard ^a   Taylor, Mark ^a  

^a SCOTTISH CROP RESEARCH INSTITUTE   (United Kingdom)

^b JOHN INNES CENTRE   (United Kingdom)

Author keywords

DNA rearrangements; DNA walking methods; Transgenic flanking regions; Transgenic potato; Vector backbone

Indexed keywords

COPY NUMBER; DEGREES OF COMPLEXITY; DNA REARRANGEMENTS; DNA WALKING; DNA WALKING METHODS; FLANKING SEQUENCE; GENOME-WALKING; INSERTION SITE; KEY CONFIRMATION; PCR TECHNIQUES; SAFETY ASSESSMENTS; STANDARD OPERATING PROCEDURES; TRANSGENE; TRANSGENIC LINES; TRANSGENIC PLANTS; TRANSGENIC POTATO; TRANSGENICS;

DNA; GENES; RHENIUM COMPOUNDS; SELF ASSEMBLY;

POLYMERASE CHAIN REACTION;

PLANT DNA;

ARTICLE; CONTROLLED STUDY; COPY NUMBER VARIATION; DNA DETERMINATION; DNA EXTRACTION; DNA FLANKING REGION; GENE SEQUENCE; GENETICALLY MODIFIED FOOD; INTERMETHOD COMPARISON; NONHUMAN; PLANT LEAF; POLYMERASE CHAIN REACTION; POTATO; TRANSGENE; TRANSGENIC CROP;

BASE SEQUENCE; CHROMOSOME WALKING; DATABASES, GENETIC; DNA, PLANT; GENE DOSAGE; GENE REARRANGEMENT; GENOME, PLANT; MOLECULAR SEQUENCE DATA; PLANTS, GENETICALLY MODIFIED; REAL-TIME POLYMERASE CHAIN REACTION; SEQUENCE ANALYSIS, DNA; SOLANUM TUBEROSUM; TERMINAL REPEAT SEQUENCES; TRANSGENES;

SOLANUM TUBEROSUM;

EID: 79960968886     PISSN: 10736085     EISSN: 15590305     Source Type: Journal    
DOI: 10.1007/s12033-010-9371-5     Document Type: Article

References (25)

1. C Halpin 2005 Gene stacking in transgenic plants-the challenge for 21st century plant biotechnology Plant Biotechnology Journal 3 141 155 10.1111/j.1467-7652.2004.00113.x 1:CAS:528:DC%2BD2MXivVyhurg%3D (Pubitemid 41615419)
2. CM Rommens MA Haring K Swords HV Davies WR Belknap 2007 The intragenic approach as a new extension to traditional plant breeding Trends in Plant Science 12 397 403 10.1016/j.tplants.2007.08.001 1:CAS:528:DC%2BD2sXhtVWmur7N (Pubitemid 47371213)
3. S Travella SM Ross J Harden C Everett JW Snape WAA Harwood 2005 Comparison of transgenic barley lines produced by particle bombardment and Agrobacterium-mediated techniques Plant Cell Reporter 23 780 789 10.1007/s00299-004-0892-x 1:CAS:528:DC%2BD2MXitFCgt74%3D (Pubitemid 40473777)
4. C Grevelding V Fantes E Kemper J Schell R Masterson 1993 Single-copy T-DNA insertions in Arabidopsis are the pre-dominant form of integration in root-derived transgenics, whereas multiple insertions are found in leaf discs Plant Molecular Biology 23 847 860 10.1007/BF00021539 1:CAS:528: DyaK2cXht1KktL4%3D (Pubitemid 2021246)
5. EK Hui PC Wang SJ Lo 1998 Strategies for cloning unknown cellular flanking DNA sequences from foreign integrants Cellular and Molecular Life Sciences 54 1403 1411 10.1007/s000180050262 1:CAS:528:DyaK1MXitlGlug%3D%3D (Pubitemid 29015299)
6. C Sallaud C Gay P Larmande M Bes P Piffanelli B Piégu, et al. 2004 High throughput T-DNA insertion mutagenesis in rice: A first step towards in silico reverse genetics Plant Journal 39 450 464 10.1111/j.1365-313X.2004.02145. x 1:CAS:528:DC%2BD2cXnsVSqu7g%3D (Pubitemid 39040149)
7. S An S Park DH Jeong DY Lee HG Kang JH Yu, et al. 2003 Generation and analysis of end sequence database for T-DNA tagging lines in rice Plant Physiology 133 2040 2047 10.1104/pp.103.030478 1:CAS:528:DC%2BD2cXhvFOg (Pubitemid 38047330)
8. Y Sha S Li Z Pei L Luo Y Tian C He 2004 Generation and flanking sequence analysis of a rice T-DNA tagged population Theoretical and Applied Genetics 108 306 314 10.1007/s00122-003-1423-9 1:CAS:528:DC%2BD2cXjtFCguw%3D%3D (Pubitemid 38162213)
9. LJ Ducreux WL Morris PE Hedley T Shepherd HV Davies S Millam MA Taylor 2005 Metabolic engineering of high carotenoid potato tubers containing enhanced levels of beta-carotene and lutein Journal of Experimental Botany 56 81 89 1:CAS:528:DC%2BD2MXkt1Wmtg%3D%3D (Pubitemid 40078394)
10. WL Morris LJM Ducreux P Hedden S Millam MA Taylor 2006 Over-expression of a bacterial 1-deoxy-d-xylulose 5-phosphate synthase gene in potato tubers perturbs the isoprenoid metabolic network: Implications for the control of the tuber life-cycle Journal of Experimental Botany 57 3007 3018 10.1093/jxb/erl061 1:CAS:528:DC%2BD28Xps1ygsb4%3D (Pubitemid 44453514)
11. D Spertini C Béliveau G Bellemare 1999 Screening of transgenic plants by amplification of unknown genomic DNA flanking T-DNA BioTechniques 27 308 314 1:CAS:528:DyaK1MXltFWlu74%3D (Pubitemid 29382395)
12. H Salvo-Garrido S Travella LJ Bilham WA Harwood JW Snape 2004 The distribution of transgene insertion sites in barley determined by physical and genetic mapping Genetics 167 1371 1379 10.1534/genetics.103.023747 1:CAS:528:DC%2BD2cXnt1Gju7g%3D (Pubitemid 39045643)
13. DS Smith PW Maxwell SH De Boer 2005 Comparison of several methods for the extraction of DNA from potatoes and potato-derived products Journal of Agriculture and Food Chemistry 53 9848 9859 10.1021/jf051201v 1:CAS:528:DC%2BD2MXht1KktrnL (Pubitemid 43081189)
14. H Wu CA Sparks HD Jones 2006 Characterisation of T-DNA loci and vector backbone sequences in transgenic wheat produced by Agrobacterium-mediated transformation Molecular Breeding 18 195 208 10.1007/s11032-006-9027-0
15. A Kovřík MA Matzke AJM Matzke B Koukalová 2001 Transposition of IS10 from the host Escherichia coli genome to a plasmid may lead to cloning artefacts Molecular Genetics and Genomics 266 216 222 10.1007/s004380100542 (Pubitemid 32938415)
16. G Bogosian K Bilyeu JP O'Neil 1993 Genome rearrangements by residual IS10 elements in strains of Escherichia coli K-12 which have undergone Tn10 mutagenesis and fusaric acid selection Molecular Genetics and Genomics 233 17 22
17. C Petti T Wendt C Meade E Mullins 2009 Evidence of genotype dependency within Agrobacterium tumefaciens in relation to the integration of vector backbone sequence in transgenic Phytophthora infestans-tolerant potato Journal of Bioscience and Bioengineering 107 301 306 10.1016/j.jbiosc.2008.11.012 1:CAS:528:DC%2BD1MXlvVGjsb8%3D
18. ME Kononov B Bassuner SB Gelvin 1997 Integration of T-DNA binary vector backbone sequences into the tobacco genome: Evidence for multiple complex pattern of integration Plant Journal 11 945 957 10.1046/j.1365-313X.1997. 11050945.x 1:CAS:528:DyaK2sXkt1els7c%3D (Pubitemid 27236421)
19. AS Afolabi B Worland JW Snape P Vain 2004 A large-scale study of rice plants transformed with different T-DNAs provides new insights into locus composition and T-DNA linkage configurations Theoretical and Applied Genetics 109 815 826 10.1007/s00122-004-1692-y 1:CAS:528:DC%2BD2cXntFGnsro%3D (Pubitemid 39211091)
20. TJ Meza B Strageland IS Mercy M Skarn DA Nymoen A Berg MA Butenko A-M Hakelien C Haslekas LA Meza-Zepeda RA Aalen 2002 Analyses of single-copy Arabidopsis T-DNA-transformed lines show that the presence of vector backbone sequences, short inverted repeats and DNA methylation is not sufficient or necessary for the induction of transgene silencing Nucleic Acids Research 30 4556 4566 10.1093/nar/gkf568 1:CAS:528:DC%2BD38Xot1Cju7o%3D (Pubitemid 35277266)
21. SA Abdal-Aziz F Pliego-Alfaro MA Quesada JA Mercado 2006 Evidence of frequent integration of non-T-DNA vector backbone sequences in transgenic strawberry plant Journal of Bioscience and Bioengineering 101 508 510 10.1263/jbb.101.508 1:CAS:528:DC%2BD28Xotlakt74%3D (Pubitemid 44354434)
22. M Lange E Vincze MJ Moller PB Holm 2006 Molecular analysis of transgene and vector backbone integration into the barley genome following Agrobacterium-mediated transformation Plant Cell Reporter 25 815 820 10.1007/s00299-006-0140-7 1:CAS:528:DC%2BD28XmvFars7k%3D (Pubitemid 44078575)
23. A-M Wolters LM Trindale E Jacobsen RGV Visser 1998 Fluorescence in situ hybridization on extended DNA fibres as a tool to analyse complex T-DNA loci in potato Plant Journal 13 837 847 10.1046/j.1365-313X.1998.00079.x 1:CAS:528:DyaK1cXislejsLk%3D (Pubitemid 28178645)
24. AJM Matzke MA Matzke 1998 Position effects and epigenetic silencing of plant transgenes Current Opinion in Plant Biology 1 142 148 10.1016/S1369- 5266(98)80016-2 1:CAS:528:DyaK1cXivVynsLc%3D (Pubitemid 128653967)
25. MA Matzke MF Mette AJM Matzke 2000 Transgene silencing by the host genome defense: Implications for the evolution of epigenetic control mechanisms in plants and vertebrates Plant Molecular Biology 43 401 415 10.1023/A: 1006484806925 1:CAS:528:DC%2BD3cXmsF2js70%3D