Gene targeting by homologous recombination as a biotechnological tool for rice functional genomics

Plant Physiology

Volumn 144, Issue 2, 2007, Pages 846-856

  Terada, Rie ^a   Johzuka Hisatomi, Yasuyo ^a   Saitoh, Miho ^a   Asao, Hisayo ^a   Iida, Shigeru ^a  

^a NATIONAL INSTITUTE FOR BASIC BIOLOGY   (Japan)

Author keywords

[No Author keywords available]

Indexed keywords

ENZYME ACTIVITY; GENES; PLANTS (BOTANY);

ENDOGENOUS GENES; GENE SPECIFIC SELECTION; GENE TARGETING; GENOMICS;

GENETIC ENGINEERING;

BIOTECHNOLOGY; CHROMOSOMES; GENETIC ENGINEERING; PLANTS; RICE;

EMBRYOPHYTA; ORYZA SATIVA;

EID: 34250620130     PISSN: 00320889     EISSN: 15322548     Source Type: Journal    
DOI: 10.1104/pp.107.095992     Document Type: Article

References (52)

1. Britt AB, May GD (2003) Re-engineering plant gene targeting. Trends Plant Sci 8: 90-95
2. Brunaud V, Balzergue S, Dubreucq B, Aubourg S, Samson F, Chauvin S, Bechtold N, Cruaud C, DeRose R, Pelletier G, et al (2002) T-DNA integration into the Arabidopsis genome depends on sequences of preinsertion sites. EMBO Rep 3: 1152-1157
3. Clough SJ, Bent AF (1998) Floral dip: a simplified method for Agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J 16: 735-743
4. Cove D (2005) The moss Physcomitrella patens. Annu Rev Genet 39: 339-358
5. Dolferus R, Osterman JC, Peacock WJ, Dennis ES (1997) Cloning of the Arabidopsis and rice formaldehyde dehydrogenase genes: implications for the origin of plant ADH enzymes. Genetics 146: 1131-1141
6. Emmanuel E, Yehuda E, Melamed-Bessudo C, Avivi-Ragolsky N, Levy AA (2006) The role of AtMSH2 in homologous recombination in Arabidopsis thaliana. EMBO Rep 7: 100-105
7. Endo M, Ishikawa Y, Osakabe K, Nakayama S, Kaya H, Araki T, Shibahara K, Abe K, Ichikawa H, Valentine L, et al (2006a) Increased frequency of homologous recombination and T-DNA integration in Arabidopsis CAF-1 mutants. EMBO J 25: 5579-5590
8. Endo M, Osakabe K, Ichikawa H, Toki S (2006b) Molecular characterization of true and ectopic gene targeting events at the acetolactate synthase gene in Arabidopsis. Plant Cell Physiol 47: 372-379
9. Evans MJ, Smithies O, Capecchi MR (2001) Mouse gene targeting. Nat Med 7: 1081-1090
10. Girke T, Schmidt H, Zähringer U, Reski R, Heinz E (1998) Identification of a novel Δ6-acyl-group desaturase by targeted gene disruption in Physcomitrella patens. Plant J 15: 39-48
11. Hanin M, Paszkowski J (2003) Plant genome modification by homologous recombination. Curr Opin Plant Biol 6: 157-162
12. Hanin M, Volrath S, Bogucki A, Briker M, Ward E, Paszkowski J (2001) Gene targeting in Arabidopsis. Plant J 28: 671-677
13. Hohe A, Reski R (2003) A tool for understanding homologous recombination in plants. Plant Cell Rep 21: 1135-1142
14. Hohn B, Puchta H (2003) Some like it sticky: targeting of the rice gene Waxy. Trends Plant Sci 8: 51-53
15. Iida S, Terada R (2004) A tale of two integrations, transgene and T-DNA: gene targeting by homologous recombination in rice. Curr Opin Biotechnol 15: 132-138
16. Iida S, Terada R (2005) Modification of endogenous natural genes by gene targeting in rice and other higher plants. Plant Mol Biol 59: 205-219
17. International Rice Genome Sequencing Project (2005) The map-based sequence of the rice genome. Nature 436: 793-800
18. Jasin M, Moynahan ME, Richardson C (1996) Targeted transgenesis. Proc Natl Acad Sci USA 93: 8804-8808
19. Jeddeloh JA, Stokes TL, Richards EJ (1999) Maintenance of genomic methylation requires a SWI2/SNF2-like protein. Nat Genet 22: 94-97
20. Kaeppler SM, Kaeppler HF, Rhee Y (2000) Epigenetic aspects of somaclonal variation in plants. Plant Mol Biol 43: 179-188
21. Kamisugi Y, Cuming AC, Cove DJ (2005) Parameters determining the efficiency of gene targeting in the moss Physcomitrella patens. Nucleic Acids Res 33: e173
22. Kamisugi Y, Schlink K, Rensing SA, Schween G, von Stackelberg M, Cuming AC, Reski R, Cove DJ (2006) The mechanism of gene targeting in Physcomitrella patens: homologous recombination, concatenation and multiple integration. Nucleic Acids Res 34: 6205-6214
23. Kempin SA, Liljegren SJ, Block LM, Rounsley SD, Yanofsky MF, Lam E (1997) Targeted disruption in Arabidopsis. Nature 389: 802-803
24. Kirik A, Pecinka A, Wendeler E, Reiss B (2006) The chromatin assembly factor subunit FASCIATA1 is involved in homologous recombination in plants. Plant Cell 18: 2431-2442
25. Larkin PJ, Scowcroft WR (1981) Somaclonal variation: a novel source of variability from cell cultures for plant improvement. Theor Appl Genet 60: 197-214
26. Matsumoto S, Ito Y, Hosoi T, Takahashi Y, Machida Y (1990) Integration of Agrobacterium T-DNA into a tobacco chromosome: possible involvement of DNA homology between T-DNA and plant DNA. Mol Gen Genet 224: 309-316
27. Matsumura H, Takano T, Takeda G, Uchimiya H (1998) Adh1 is transcriptionally active but its translational product is reduced in a rad mutant of rice (Oryza sativa L.), which is vulnerable to submergence stress. Theor Appl Genet 97: 1197-1203
28. Morita Y, Hoshino A, Kikuchi Y, Okuhara H, Ono E, Tanaka Y, Fukui Y, Saito N, Nitasaka E, Noguchi H, et al (2005) Japanese morning glory dusky mutants displaying reddish-brown or purplish-gray flowers are deficient in a novel glycosylation enzyme for anthocyanin biosynthesis, UDP-glucose:anthocyanidin 3-O-glucoside-2″-O- glucosyltransferase, due to 4-bp insertions in the gene. Plant J 42: 353-363
29. Morton R, Hooykaas PJJ (1995) Gene replacement. Mol Breed 1: 123-132
30. Murashige T, Skoog F (1962) A revised medium for rapid growth and bioassays with tobacco tissue cultures. Physiol Plant 15: 473-497
31. Puchta H (1998) Towards targeted transformation in plants. Trends Plant Sci 3: 77-78
32. Puchta H (2002) Gene replacement by homologous recombination in plants. Plant Mol Biol 48: 173-182
33. Reiss B (2003) Homologous recombination and gene targeting in plant cells. Int Rev Cytol 228: 85-139
34. Reski R (1998) Physcomitrella and Arabidopsis: the David and Goliath of reverse genetics. Trends Plant Sci 3: 209-210
35. Sachs MM, Subbaiah CC, Saab IN (1996) Anaerobic gene expression and flooding tolerance in maize. J Exp Bot 47: 1-15
36. Saika H, Matsumura H, Takano T, Tsutsumi N, Nakazono M (2006) A point mutation of Adh1 gene is involved in the repression of coleoptile elongation under submergence in rice. Breed Sci 56: 69-74
37. Sallaud C, Meynard D, van Boxtel J, Gay C, Bes M, Brizard JP, Larmande P, Ortega D, Raynal M, Portefaix M, et al (2003) Highly efficient production and characterization of T-DNA plants for rice (Oryza sativa L.) functional genomics. Theor Appl Genet 106: 1396-1408
38. Schaefer DG (2002) A new moss genetics: targeted mutagenesis in Physcomitrella patens. Annu Rev Plant Biol 53: 477-501
39. Schaefer DG, Zryd J-P (1997) Efficient gene targeting in the moss Physcomitrella patens. Plant J 11: 1195-1206
40. Schuermann D, Molinier J, Fritsch O, Hohn B (2005) The dual nature of homologous recombination in plants. Trends Genet 21: 172-181
41. Shaked H, Melamed-Bessudo C, Levy AA (2005) High-frequency gene targeting in Arabidopsis plants expressing the yeast RAD54 gene. Proc Natl Acad Sci USA 102: 12265-12269
42. Somers DA, Makarevitch I (2004) Transgene integration in plants: poking or patching holes in promiscuous genomes? Curr Opin Biotechnol 15: 126-131
43. Strepp R, Scholz S, Kruse S, Speth V, Reski R (1998) Plant nuclear gene knockout reveals a role in plastid division for the homolog of the bacterial cell division protein FtsZ, an ancestral tubulin. Proc Natl Acad Sci USA 95: 4368-4373
44. Tarchini R, Biddle P, Wineland R, Tingey S, Rafalski A (2000) The complete sequence of 340 kb of DNA around the rice Adh1-Adh2 region reveals interrupted colinearity with maize chromosome 4. Plant Cell 12: 381-391
45. Terada R, Asao H, Iida S (2004) A large-scale Agrobacterium-mediated transformation procedure with a strong positive-negative selection for gene targeting in rice (Oryza sativa L.). Plant Cell Rep 22: 653-659
46. Terada R, Urawa H, Inagaki Y, Tsugane K, Iida S (2002) Efficient gene targeting by homologous recombination in rice. Nat Biotechnol 20: 1030-1034
47. Tinland B, Hohn B (1995) Recombination between prokaryotic and eukaryotic DNA: integration of Agrobacterium tumefaciens T-DNA into the plant genome. Genet Eng 17: 209-229
48. Tzfira T, Citovsky V (2006) Agrobacterium-mediated genetic transformation of plants: biology and biotechnology. Curr Opin Biotechnol 17: 147-154
49. Tzfira T, Li J, Lacroix B, Citovsky V (2004) Agrobacterium T-DNA integration: molecules and models. Trends Genet 20: 375-383
50. Tzfira T, White C (2005) Towards targeted mutagenesis and gene replacement in plants. Trends Biotechnol 23: 567-569
51. Xie Y, Wu R (1989) Rice alcohol dehydrogenase genes: anaerobic induction, organ specific expression and characterization of cDNA clones. Plant Mol Biol 13: 53-68
52. Zhu Q-H, Ramm K, Eamens AL, Dennis ES, Upadhyaya NM (2006) Transgene structures suggest that multiple mechanisms are involved in T-DNA integration in plants. Plant Sci 171: 308-322