Tnt1 retrotransposon mutagenesis: A tool for soybean functional genomics

Plant Physiology

Volumn 161, Issue 1, 2013, Pages 36-47

  Cui, Yaya ^a   Barampuram, Shyam ^a   Stacey, Minviluz G ^a   Nathan Hancock, C ^b   Findley, Seth ^a   Mathieu, Melanie ^a   Zhang, Zhanyuan ^a   Parrott, Wayne A ^c   Stacey, Gary ^a  

^a UNIVERSITY OF MISSOURI   (United States)

^b UNIVERSITY OF SOUTH CAROLINA AIKEN   (United States)

^c UNIVERSITY OF GEORGIA   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

AGROBACTERIUM TUMEFACIENS; GLYCINE MAX; NICOTIANA TABACUM;

EID: 84871758486     PISSN: 00320889     EISSN: 15322548     Source Type: Journal    
DOI: 10.1104/pp.112.205369     Document Type: Article

References (55)

1. Alonso JM, Stepanova AN, Leisse TJ, Kim CJ, Chen H, Shinn P, Stevenson DK, Zimmerman J, Barajas P, Cheuk R, et al (2003) Genome-wide insertional mutagenesis of Arabidopsis thaliana. Science 301: 653-657
2. An G, Ebert PR, Mitra A, Ha SB (1988) Binary vectors. In SB Gelvin, RA Schilperoot, eds, Plant Molecular Biology Manual, Vol 3. Martinus Nijhoff, Dordrecht, The Netherlands, pp 1-19
3. An S, Park S, Jeong D-H, Lee D-Y, Kang H-G, Yu J-H, Hur J, Kim S-R, Kim Y-H, Lee M, et al (2003) Generation and analysis of end sequence database for T-DNA tagging lines in rice. Plant Physiol 133: 2040-2047
4. Bolon YT, Haun WJ, Xu WW, Grant D, Stacey MG, Nelson RT, Gerhardt DJ, Jeddeloh JA, Stacey G, Muehlbauer GJ, et al (2011) Phenotypic and genomic analyses of a fast neutron mutant population resource in soybean. Plant Physiol 156: 240-253
5. Cheng X, Wen J, Tadege M, Ratet P, Mysore KS (2011) Reverse genetics in Medicago truncatula using Tnt1 insertion mutants. Methods Mol Biol 678: 179-190
6. Cooper JL, Till BJ, Laport RG, Darlow MC, Kleffner JM, Jamai A, El-Mellouki T, Liu S, Ritchie R, Nielsen N, et al (2008) TILLING to detect induced mutations in soybean. BMC Plant Biol 8: 8-9
7. Courtial B, Feuerbach F, Eberhard S, Rohmer L, Chiapello H, Camilleri C, Lucas H (2001) Tnt1 transposition events are induced by in vitro transformation of Arabidopsis thaliana, and transposed copies integrate into genes. Mol Genet Genomics 265: 32-42
8. Cowperthwaite M, Park W, Xu Z, Yan X, Maurais SC, Dooner HK (2002) Use of the transposon Ac as a gene-searching engine in the maize genome. Plant Cell 14: 713-726
9. Dellaporta SL, Wood J, Hicks JB (1983) A plant DNA minipreparation: version II. Plant Mol Biol 1: 19-21
10. d'Erfurth I, Cosson V, Eschstruth A, Lucas H, Kondorosi A, Ratet P (2003) Efficient transposition of the Tnt1 tobacco retrotransposon in the model legume Medicago truncatula. Plant J 34: 95-106
11. Fladung M, Deutsch F, Hönicka H, Kumar S (2004) T-DNA and transposon tagging in aspen. Plant Biol (Stuttg) 6: 5-11
12. Fukai E, Soyano T, Umehara Y, Nakayama S, Hirakawa H, Tabata S, Sato S, Hayashi M (2012) Establishment of a Lotus japonicus gene tagging population using the exon-targeting endogenous retrotransposon LORE1. Plant J 69: 720-730
13. Gamborg OL, Miller RA, Ojima K (1968) Nutrient requirements of suspension cultures of soybean root cells. Exp Cell Res 50: 151-158
14. Gepts P, Beavis WD, Brummer EC, Shoemaker RC, Stalker HT, Weeden NF, Young ND (2005) Legumes as a model plant family: genomics for food and feed report of the cross-legume advances through genomics conference. Plant Physiol 137: 1228-1235
15. Gill N, Findley S, Walling JG, Hans C, Ma J, Doyle J, Stacey G, Jackson SA (2009) Molecular and chromosomal evidence for allopolyploidy in soybean. Plant Physiol 151: 1167-1174
16. Hancock CN, Zhang F, Floyd K, Richardson AO, Lafayette P, Tucker D, Wessler SR, Parrott WA (2011) The rice miniature inverted repeat transposable element mPing is an effective insertional mutagen in soybean. Plant Physiol 157: 552-562
17. Hirochika H (1993) Activation of tobacco retrotransposons during tissue culture. EMBO J 12: 2521-2528
18. Hirochika H, Otsuki H, Yoshikawa M, Otsuki Y, Sugimoto K, Takeda S (1996) Autonomous transposition of the tobacco retrotransposon Tto1 in rice. Plant Cell 8: 725-734
19. Iantcheva A, Chabaud M, Cosson V, Barascud M, Schutz B, Primard-Brisset C, Durand P, Barker DG, Vlahova M, Ratet P (2009) Osmotic shock improves Tnt1 transposition frequency in Medicago truncatula cv Jemalong during in vitro regeneration. Plant Cell Rep 28: 1563-1572
20. Ishizaki T, Kato A (2005) Introduction of the tobacco retrotransposon Tto1 into diploid potato. Plant Cell Rep 24: 52-58
21. Ito T, Seki M, Hayashida N, Shibata D, Shinozaki K (1999) Regional insertional mutagenesis of genes on Arabidopsis thaliana chromosome V using the Ac/Ds transposon in combination with a cDNA scanning method. Plant J 17: 433-444
22. Jiang N, Bao ZR, Zhang XY, Hirochika H, Eddy SR, McCouch SR, Wessler SR (2003) An active DNA transposon family in rice. Nature 421: 163-167
23. Jones JD, Carland F, Lim E, Ralston E, Dooner HK (1990) Preferential transposition of the maize element Activator to linked chromosomal locations in tobacco. Plant Cell 2: 701-707
24. Kikuchi K, Terauchi K, Wada M, Hirano HY (2003) The plant MITE mPing is mobilized in anther culture. Nature 421: 167-170
25. Klein-Lankhorst RM, Rietveld P, Machiels B, Verkerk R, Weide R, Gebhardt C, Koornneef M, Zabel P (1991) RFLP markers linked to the root knot nematode resistance gene Mi in tomato. Theor Appl Genet 81: 661-667
26. Kumar A, Bennetzen JL (1999) Plant retrotransposons. Annu Rev Genet 33: 479-532
27. Kumar A, Hirochika H (2001) Applications of retrotransposons as genetic tools in plant biology. Trends Plant Sci 6: 127-134
28. Libault M, Farmer A, Joshi T, Takahashi K, Langley RJ, Franklin LD, He J, Xu D, May G, Stacey G (2010) An integrated transcriptome atlas of the crop model Glycine max, and its use in comparative analyses in plants. Plant J 63: 86-99
29. Lucas H, Feuerbach F, Kunert K, Grandbastien MA, Caboche M (1995) RNA-mediated transposition of the tobacco retrotransposon Tnt1 in Arabidopsis thaliana. EMBO J 14: 2364-2373
30. Mathieu M, Winters EK, Kong F, Wan J, Wang S, Eckert H, Luth D, Paz M, Donovan C, Zhang Z, et al (2009) Establishment of a soybean (Glycine max Merr. L) transposon-based mutagenesis repository. Planta 229: 279-289
31. Mazier M, Botton E, Flamain F, Bouchet J-P, Courtial B, Chupeau M-C, Chupeau Y, Maisonneuve B, Lucas H (2007) Successful gene tagging in lettuce using the Tnt1 retrotransposon from tobacco. Plant Physiol 144: 18-31
32. Murashige T, Skoog F (1962) A revised medium for rapid growth and bioassays with tobacco tissue cultures. Physiol Plant 15: 473-497
33. Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8: 4321-4325
34. Naito K, Cho E, Yang GJ, Campbell MA, Yano K, Okumoto Y, Tanisaka T, Wessler SR (2006) Dramatic amplification of a rice transposable element during recent domestication. Proc Natl Acad Sci USA 103: 17620-17625
35. Nakazaki T, Okumoto Y, Horibata A, Yamahira S, Teraishi M, Nishida H, Inoue H, Tanisaka T (2003) Mobilization of a transposon in the rice genome. Nature 421: 170-172
36. O'Brian MR, Vance CP (2007) Legume biology: sequence to seeds. Plant Physiol 144: 537
37. Okamoto H, Hirochika H (2000) Efficient insertion mutagenesis of Arabidopsis by tissue culture-induced activation of the tobacco retrotransposon Tto1. Plant J 23: 291-304
38. Olhoft PM, Flagel LE, Donovan CM, Somers DA (2003) Efficient soybean transformation using hygromycin B selection in the cotyledonary-node method. Planta 216: 723-735
39. Parinov S, Sundaresan V (2000) Functional genomics in Arabidopsis: largescale insertional mutagenesis complements the genome sequencing project. Curr Opin Biotechnol 11: 157-161
40. Parrott WA, Clemente TE (2004) Transgenic soybean. In JE Specht, HR Boerma, eds, Soybeans: Improvement, Production, and Uses. ASA-CSASSSA, Madison, WI, pp 265-302
41. Piffanelli P, Droc G, Mieulet D, Lanau N, Bès M, Bourgeois E, Rouvière C, Gavory F, Cruaud C, Ghesquière A, et al (2007) Large-scale characterization of Tos17 insertion sites in a rice T-DNA mutant library. Plant Mol Biol 65: 587-601
42. Ratet P, Porcedu A, Tadege M, Mysore KS (2006) Insertional mutagenesis in Medicago truncatula using Tnt1 retrotransposon. In U Mathesius, EP Journet, LWSumner, eds, The Medicago truncatula handbook. http://www.noble.org/MedicagoHandbook/(December 3, 2012)
43. Sambrook J, Fritsch EF, Maniatis T (1989) Molecular Cloning: A Laboratory Manual. Cold Spring Harbor Laboratory Press, Cold Spring Harbor, NY
44. Schmutz J, Cannon SB, Schlueter J, Ma J, Mitros T, Nelson W, Hyten DL, Song Q, Thelen JJ, Cheng J, et al (2010) Genome sequence of the palaeopolyploid soybean. Nature 463: 178-183
45. Scholte M, d'Erfurth I, Ripa S (2002) T-DNA tagging in the model legume Medicago truncatula allows efficient gene discovery. Mol Breed 10: 203-215
46. Stacey MG, Osawa H, Patel A, Gassmann W, Stacey G (2006) Expression analyses of Arabidopsis oligopeptide transporters during seed germination, vegetative growth and reproduction. Planta 223: 291-305
47. Tadege M, Ratet P, Mysore KS (2005) Insertional mutagenesis: a Swiss Army knife for functional genomics of Medicago truncatula. Trends Plant Sci 10: 229-235
48. Tadege M, Wen J, He J, Tu H, Kwak Y, Eschstruth A, Cayrel A, Endre G, Zhao PX, Chabaud M, et al (2008) Large-scale insertional mutagenesis using the Tnt1 retrotransposon in the model legume Medicago truncatula. Plant J 54: 335-347
49. Trick HN, Dinkins RD, Santarem ER, Di R, Samoylov V, Meurer C, Walker D, Parrott WA, Finer JJ, Collins GB (1997) Recent advances in soybean transformation. Plant Tissue Cult Biotechnol 3: 9-26
50. Urbański DF, Małolepszy A, Stougaard J, Andersen SU (2012) Genomewide LORE1 retrotransposon mutagenesis and high-throughput insertion detection in Lotus japonicus. Plant J 69: 731-741
51. Van den Broeck D, Maes T, Sauer M, Zethof J, De Keukeleire P, D'hauw M, Van Montagu M, Gerats T (1998) Transposon display identifies individual transposable elements in high copy number lines. Plant J 13: 121-129
52. Vega JM, Yu W, Kennon AR, Chen X, Zhang ZJ (2008) Improvement of Agrobacterium-mediated transformation in Hi-II maize (Zea mays) using standard binary vectors. Plant Cell Rep 27: 297-305
53. Wessler SR (2006) Transposable elements and the evolution of eukaryotic genomes. Proc Natl Acad Sci USA 103: 17600-17601
54. Williams-Carrier R, Stiffler N, Belcher S, Kroeger T, Stern DB, Monde RA, Coalter R, Barkan A (2010) Use of Illumina sequencing to identify transposon insertions underlying mutant phenotypes in high-copy Mutator lines of maize. Plant J 63: 167-177
55. Zeng P, Vadnais DA, Zhang Z, Polacco JC (2004) Refined glufosinate selection in Agrobacterium-mediated transformation of soybean [Glycine max (L.) Merrill]. Plant Cell Rep 22: 478-482