title: Reasons for lower transformation efficiency in indica rice using Agrobacterium tumefaciens-mediated transformation: lessons from transformation assays and genome-wide expression profiling.
abstract: Agrobacterium tumefaciens-mediated genetic transformation has been routinely used in rice for more than a decade. However, the transformation efficiency of the indica rice variety is still unsatisfactory and much lower than that of japonica cultivars. Further improvement on the transformation efficiency lies in the genetic manipulation of the plant itself, which requires a better understanding of the underlying process accounting for the susceptibility of plant cells to Agrobacterium infection as well as the identification of plant genes involved in the transformation process. In this study, transient and stable transformation assays using different japonica and indica cultivars showed that the lower transformation efficiency in indica rice was mainly due to the low efficiency in T-DNA integration into the plant genome. Analyses of the global gene expression patterns across the transformation process in different varieties revealed major differences in the expression of genes responding to Agrobacterium within the first 6 h after infection and more differentially expressed genes were observed in the indica cultivar Zhenshan 97 (ZS), with a number of genes repressed early during infection. Microarray analysis revealed an important effect of plant defense response on Agrobacterium-mediated transformation. It has been shown that some genes which may be necessary for the transformation process were down-regulated in the indica cultivar ZS. This dataset provided a versatile resource for plant genomic research to understand the regulatory network of transformation process, and showed great promise for improving indica rice transformation using genetic manipulation of the rice genome.
authors.affiliation: National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China.
authors.forename: Weiwei
authors.initials: W
authors.lastname: Tie
authors.forename: Fei
authors.initials: F
authors.lastname: Zhou
authors.forename: Lei
authors.initials: L
authors.lastname: Wang
authors.forename: Weibo
authors.initials: W
authors.lastname: Xie
authors.forename: Hao
authors.initials: H
authors.lastname: Chen
authors.forename: Xianghua
authors.initials: X
authors.lastname: Li
authors.forename: Yongjun
authors.initials: Y
authors.lastname: Lin
mesh_terms: D016960:Agrobacterium tumefaciens / Q000235:genetics* / Q000502:physiology; D004269:DNA, Bacterial / Q000235:genetics; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant / Q000235:genetics; D018745:Genome, Plant / Q000235:genetics*; D054884:Host-Pathogen Interactions / Q000235:genetics; D020411:Oligonucleotide Array Sequence Analysis; D012275:Oryza / Q000145:classification / Q000235:genetics* / Q000382:microbiology; D030821:Plants, Genetically Modified; D011995:Recombination, Genetic; D020133:Reverse Transcriptase Polymerase Chain Reaction; D013045:Species Specificity; D046509:Tissue Culture Techniques; D059467:Transcriptome; D014170:Transformation, Genetic
chemical_list: D004269:DNA, Bacterial; C036483:T-DNA
references.citation: Mol Plant Microbe Interact. 2008 Dec;21(12):1528-38
references.pmid: 18986249
references.citation: Bioinformatics. 2006 Feb 15;22(4):507-8
references.pmid: 16357033
references.citation: Annu Rev Cell Dev Biol. 2006;22:101-27
references.pmid: 16709150
references.citation: Mol Gen Genet. 1999 Apr;261(3):429-38
references.pmid: 10323222
references.citation: Annu Rev Phytopathol. 2007;45:399-436
references.pmid: 17506648
references.citation: Plant Mol Biol. 1997 Sep;35(1-2):205-18
references.pmid: 9291974
references.citation: Plant Mol Biol. 1992 Dec;20(6):1071-87
references.pmid: 1463842
references.citation: Annu Rev Phytopathol. 2010;48:45-68
references.pmid: 20337518
references.citation: Mol Plant Microbe Interact. 2006 Jun;19(6):665-81
references.pmid: 16776300
references.citation: Chem Biol. 2000 Aug;7(8):611-21
references.pmid: 11048952
references.citation: Plant Physiol. 2003 Jun;132(2):494-505
references.pmid: 12805582
references.citation: Trends Plant Sci. 2000 Aug;5(8):354-7
references.pmid: 10908881
references.citation: Plant Cell Rep. 2005 Jan;23(8):540-7
references.pmid: 15309499
references.citation: EMBO J. 2001 Nov 15;20(22):6550-8
references.pmid: 11707425
references.citation: Plant Mol Biol. 2009 Mar;69(4):473-88
references.pmid: 19083153
references.citation: Plant Mol Biol. 1998 Jun;37(3):549-59
references.pmid: 9617821
references.citation: Nature. 2004 Sep 2;431(7004):87-92
references.pmid: 15343337
references.citation: Biostatistics. 2003 Apr;4(2):249-64
references.pmid: 12925520
references.citation: Bioinformatics. 2004 Feb 12;20(3):307-15
references.pmid: 14960456
references.citation: Plant Physiol. 1986 Oct;82(2):622-4
references.pmid: 16665082
references.citation: Plant J. 1994 Aug;6(2):271-82
references.pmid: 7920717
references.citation: Proc Natl Acad Sci U S A. 1994 Aug 2;91(16):7603-7
references.pmid: 8052627
references.citation: Cell Microbiol. 2007 Jan;9(1):9-20
references.pmid: 17222189
references.citation: Mol Plant Microbe Interact. 2007 Jan;20(1):41-52
references.pmid: 17249421
references.citation: Trends Biotechnol. 2006 Jun;24(6):267-73
references.pmid: 16650909
references.citation: Plant Physiol. 2008 Feb;146(2):703-15
references.pmid: 18156296
references.citation: ACS Chem Biol. 2006 Apr 25;1(3):165-75
references.pmid: 17163664
references.citation: Genome Biol. 2004;5(10):R80
references.pmid: 15461798
references.citation: Plant Cell. 1996 May;8(5):873-86
references.pmid: 8672885
references.citation: Plant Cell. 2009 Sep;21(9):2948-62
references.pmid: 19794116
references.citation: Proc Natl Acad Sci U S A. 2000 Jan 18;97(2):948-53
references.pmid: 10639185
references.citation: Mol Plant Microbe Interact. 2007 Sep;20(9):1048-54
references.pmid: 17849707
references.citation: Plant Physiol. 1991 May;96(1):121-9
references.pmid: 16668140
references.citation: FEMS Microbiol Lett. 2005 Jun 15;247(2):207-13
references.pmid: 15936896
references.citation: Cell. 2006 May 19;125(4):749-60
references.pmid: 16713565
references.citation: Mol Plant. 2009 Jul;2(4):832-837
references.pmid: 19825658
references.citation: EMBO J. 1987 Dec 20;6(13):3901-7
references.pmid: 3327686
references.citation: Bioinformatics. 2006 Nov 15;22(22):2825-7
references.pmid: 16982708
references.citation: BMC Bioinformatics. 2006 Apr 05;7:191
references.pmid: 16597342
references.citation: Plant J. 2003 Jul;35(2):219-36
references.pmid: 12848827
references.citation: Plant Cell. 1997 Mar;9(3):317-33
references.pmid: 9090878
references.citation: Curr Opin Biotechnol. 2002 Apr;13(2):173-80
references.pmid: 11950572
references.citation: Biophys J. 2005 Sep;89(3):2134-45
references.pmid: 16040740
references.citation: Nature. 2006 Nov 16;444(7117):323-9
references.pmid: 17108957
references.citation: Proc Natl Acad Sci U S A. 2006 Mar 21;103(12):4658-62
references.pmid: 16537403
references.citation: Proc Natl Acad Sci U S A. 2005 Dec 27;102(52):19231-6
references.pmid: 16380432
references.citation: BMC Genomics. 2007 Oct 01;8:344
references.pmid: 17908303
references.citation: Plant Cell. 2009 Oct;21(10):3350-67
references.pmid: 19820187
references.citation: Plant Physiol. 2009 Aug;150(4):1665-76
references.pmid: 19439569
references.citation: Stat Appl Genet Mol Biol. 2004;3:Article3
references.pmid: 16646809
references.citation: Nucleic Acids Res. 2003 Feb 1;31(3):826-32
references.pmid: 12560477
references.citation: Plant Mol Biol. 1992 Dec;20(6):1037-48
references.pmid: 1463839
references.citation: EMBO J. 2001 Jul 2;20(13):3596-607
references.pmid: 11432846
references.citation: Proc Natl Acad Sci U S A. 2005 Aug 23;102(34):12265-9
references.pmid: 16093317
references.citation: Nucleic Acids Res. 2008 Jul 1;36(Web Server issue):W358-63
references.pmid: 18487275
references.citation: Annu Rev Plant Biol. 2008;59:191-223
references.pmid: 18257708