Do transgenesis and marker-assisted backcross breeding produce substantially equivalent plants? - A comparative study of transgenic and backcross rice carrying bacterial blight resistant gene Xa21

BMC Genomics

Volumn 14, Issue 1, 2013, Pages

  Gao, Lifen ^a,b   Cao, Yinghao ^a,c   Xia, Zhihui ^a   Jiang, Guanghuai ^a   Liu, Guozhen ^c   Zhang, Weixiong ^b,d   Zhai, Wenxue ^a  

^a INSTITUTE OF GENETICS AND DEVELOPMENTAL BIOLOGY   (China)

^b JIANGHAN UNIVERSITY   (China)

^c AGRICULTURAL UNIVERSITY OF HEBEI   (China)

^d WASHINGTON UNIVERSITY IN ST LOUIS   (United States)

Author keywords

Marker assisted backcrossing; Substantial equivalence; Transcriptome profile; Transgenesis; Xa21

Indexed keywords

TRANSCRIPTOME; PROTEIN SERINE THREONINE KINASE; VEGETABLE PROTEIN; XA21 PROTEIN, ORYZA SATIVA;

ARTICLE; BACTERIAL LEAF BLIGHT; COMPARATIVE STUDY; CONTROLLED STUDY; DISEASE RESISTANCE; FOOD SAFETY; GENE EXPRESSION; GENE SEQUENCE; MARKER ASSISTED BACKCROSS BREEDING; NONHUMAN; PLANT BREEDING; PLANT DISEASE; PLANT GENE; PLANT STRESS; RICE; SIGNAL TRANSDUCTION; STRAIN DIFFERENCE; TRANSGENIC CROP; TRANSGENIC PLANT; TRANSGENICS; WORLD HEALTH ORGANIZATION; XA21 GENE; DNA SEQUENCE; GENETICS; HIGH THROUGHPUT SEQUENCING; INBREEDING; METABOLISM; MICROBIOLOGY; PHENOTYPE; PLANT CELL;

BACTERIA (MICROORGANISMS);

HIGH-THROUGHPUT NUCLEOTIDE SEQUENCING; INBREEDING; ORYZA SATIVA; PHENOTYPE; PLANT CELLS; PLANT DISEASES; PLANT PROTEINS; PLANTS, GENETICALLY MODIFIED; PROTEIN-SERINE-THREONINE KINASES; SEQUENCE ANALYSIS, DNA; TRANSCRIPTOME;

EID: 84886392985     PISSN: None     EISSN: 14712164     Source Type: Journal    
DOI: 10.1186/1471-2164-14-738     Document Type: Article

References (53)

1. Han F, Romagosa I, Ullrich S, Jones B, Hayes P, Wesenberg D. Molecular marker-assisted selection for malting quality traits in barley. Mol Breeding 1997, 3(6):427-437.
2. Ribaut JM, Ragot M. Marker-assisted selection to improve drought adaptation in maize: the backcross approach, perspectives, limitations, and alternatives. J Exp Bot 2007, 58(2):351-360.
3. Neeraja C, Maghirang-Rodriguez R, Pamplona A, Heuer S, Collard BCY, Septiningsih E, Vergara G, Sanchez D, Xu K, Ismail A. A marker-assisted backcross approach for developing submergence-tolerant rice cultivars. Theor Appl Genet 2007, 115(6):767-776.
4. Visscher PM, Haley CS, Thompson R. Marker-assisted introgression in backcross breeding programs. Genetics 1996, 144(4):1923-1932.
5. Collard BCY, Mackill DJ. Marker-assisted selection: an approach for precision plant breeding in the twenty-first century. Phil Trans R Soc B 2008, 363(1491):557-572.
6. Regierer B, Fernie AR, Springer F, Perez-Melis A, Leisse A, Koehl K, Willmitzer L, Geigenberger P, Kossmann J. Starch content and yield increase as a result of altering adenylate pools in transgenic plants. Nat Biotechnol 2002, 20(12):1256-1260.
7. Xue G, Patel M, Johnson J, Smyth D, Vickers C. Selectable marker-free transgenic barley producing a high level of cellulase (1, 4-β-glucanase) in developing grains. Plant Cell Rep 2003, 21(11):1088-1094.
8. Paine JA, Shipton CA, Chaggar S, Howells RM, Kennedy MJ, Vernon G, Wright SY, Hinchliffe E, Adams JL, Silverstone AL. Improving the nutritional value of Golden Rice through increased pro-vitamin A content. Nat Biotechnol 2005, 23(4):482-487.
9. Zhai W, Li X, Tian W, Zhou Y, Pan X, Cao S, Zhao X, Zhao B, Zhang Q, Zhu L. Introduction of a rice blight resistance gene, Xa21, into five Chinese rice varieties through an Agrobacterium-mediated system. Sci China C Life Sci 2000, 43(4):361-368.
10. Baudo MM, Lyons R, Powers S, Pastori GM, Edwards KJ, Holdsworth MJ, Shewry PR. Transgenesis has less impact on the transcriptome of wheat grain than conventional breeding. Plant Biotechnol J 2006, 4(4):369-380.
11. OECD Safety evaluation of foods derived by modern biotechnology: Concepts and principles 1993, Paris, France: Organization for Economic Cooperation and Development, OECD.
12. Hoekenga OA. Using metabolomics to estimate unintended effects in transgenic crop plants: problems, promises, and opportunities. J Biomol Tech 2008, 19(3):159-166.
13. Millstone E, Brunner E, Mayer S. Beyond substantial equivalence. Nature 1999, 401(6753):525-526.
14. FAO/WHO Biotechnology and food safety. Report of a joint FAO/WHO consultation 1996, ROME: FAO, FAO/WHO.
15. Ogawa T. Methods and strategy for monitoring race distribution and identification of resistance genes to bacterial leaf blight (Xanthomonas campestris pv. oryzae)in rice. Jpn Agric Res Q 1993, 27:71-80.
16. Song WY, Wang GL, Chen LL, Kim HS, Pi LY, Holsten T, Gardner J, Wang B, Zhai WX, Zhu LH, et al. A receptor kinase-like protein encoded by the rice disease resistance gene, Xa21. Science 1995, 270(5243):1804-1806.
17. Bharani M, Nagarajan P, Rabindran R, Saraswathi R, Balasubramanian P, Ramalingam J. Bacterial leaf blight resistance genes (Xa21, xa13 and xa5) pyramiding through molecular marker assisted selection into rice cultivars. Arch Phytopathol Plant Protect 2010, 43(10):1032-1043.
18. Afroz A, Chaudhry Z, Rashid U, Ali GM, Nazir F, Iqbal J, Khan MR. Enhanced resistance against bacterial wilt in transgenic tomato (Lycopersicon esculentum) lines expressing the Xa21 gene. Plant Cell Tissue Organ Cult 2011, 104(2):227-237.
19. Xia ZH, Li XB, Chen CY, Fan HK, Jiang GH, Zhu LH, Zhai WX. Generation of selectable marker-free and vector backbone sequence-free Xa21 transgenic rice. Chin J biotech 2006, 22(2):204-210.
20. Perez LM, Redoña ED, Mendioro MS, Vera Cruz CM, Leung H. Introgression of Xa4, Xa7 and Xa21 for resistance to bacterial blight in thermosensitive genetic male sterile rice (Oryza sativa L.) for the development of two-line hybrids. Euphytica 2008, 164(3):627-636.
21. Zhang J, Li X, Jiang G, Xu Y, He Y. Pyramiding of Xa7 and Xa21 for the improvement of disease resistance to bacterial blight in hybrid rice. Plant Breed 2006, 125(6):600-605.
22. Gao LF, Xia ZH, Jiang GH, Peng H, Zhao XF, Zhai WX. Generation of marker-free, bacterial blight-resistant transgenic sterile line and hybrid rice with Xa21. Plant Breed 2011, 130(4):438-443.
23. Ikeda R, Khush G, Tabien R. A new resistance gene to bacterial blight derived from O. longistaminata. Jpn J Breed 1990, 40(Suppl 1):280-281.
24. Git A, Dvinge H, Salmon-Divon M, Osborne M, Kutter C, Hadfield J, Bertone P, Caldas C. Systematic comparison of microarray profiling, real-time PCR, and next-generation sequencing technologies for measuring differential microRNA expression. RNA 2010, 16(5):991-1006.
25. Zhang W, Gao S, Zhou X, Chellappan P, Chen Z, Zhang X, Fromuth N, Coutino G, Coffey M. Bacteria-responsive microRNAs regulate plant innate immunity by modulating plant hormone networks. Plant Mol Biol 2011, 75(1):93-105.
26. Hirochika H, Sugimoto K, Otsuki Y, Tsugawa H, Kanda M. Retrotransposons of rice involved in mutations induced by tissue culture. Proc Natl Acad Sci 1996, 93(15):7783-7788.
27. Wang GL, Ruan DL, Song WY, Sideris S, Chen LL, Pi LY, Zhang S, Zhang Z, Fauquet C, Gaut BS. Xa21D encodes a receptor-like molecule with a leucine-rich repeat domain that determines race-specific recognition and is subject to adaptive evolution. The Plant Cell Online 1998, 10(5):765-780.
28. Park CJ, Peng Y, Chen X, Dardick C, Ruan DL, Bart R, Canlas PE, Ronald PC. Rice XB15, a protein phosphatase 2C, negatively regulates cell death and XA21-mediated innate immunity. PLoS Biol 2008, 6(9):e231.
29. Wang YS, Pi LY, Chen X, Chakrabarty PK, Jiang J, De Leon AL, Liu GZ, Li L, Benny U, Oard J. Rice XA21 binding protein 3 is a ubiquitin ligase required for full Xa21-mediated disease resistance. The Plant Cell Online 2006, 18(12):3635-3646.
30. Peng Y, Bartley LE, Chen X, Dardick C, Chern M, Ruan R, Canlas PE, Ronald PC. OsWRKY62 is a negative regulator of basal and Xa21-mediated defense against Xanthomonas oryzae pv. oryzae in rice. Mol plant 2008, 1(3):446-458.
31. Chen X, Ronald PC. Innate immunity in rice. Trends Plant Sci 2011, 16(8):451-460.
32. Chen X, Chern M, Canlas PE, Ruan D, Jiang C, Ronald PC. An ATPase promotes autophosphorylation of the pattern recognition receptor XA21 and inhibits XA21-mediated immunity. Sci STKE 2010, 107(17):8029-8034.
33. Feuillet C, Travella S, Stein N, Albar L, Nublat A, Keller B. Map-based isolation of the leaf rust disease resistance gene Lr10 from the hexaploid wheat (Triticum aestivum L.) genome. Proc Natl Acad Sci 2003, 100(25):15253-15258.
34. Boyes DC, Nam J, Dangl JL. The Arabidopsis thaliana RPM1 disease resistance gene product is a peripheral plasma membrane protein that is degraded coincident with the hypersensitive response. Proc Natl Acad Sci 1998, 95(26):15849-15854.
35. Sara M, Walter S, Paola C, Luigi M, Luigi F, Raffalella EM. Solanaceae evolutionary dynamics of the I2-NBS domain. American J Plant Sci 2012, 3(2):283-294.
36. Sha A, Lin X, Huang J, Zhang D. Analysis of DNA methylation related to rice adult plant resistance to bacterial blight based on methylation-sensitive AFLP (MSAP) analysis. Mol Genet Genomics 2005, 273(6):484-490.
37. Akimoto K, Katakami H, Kim HJ, Ogawa E, Sano CM, Wada Y, Sano H. Epigenetic inheritance in rice plants. Ann Bot-London 2007, 100(2):205-217.
38. Li Y, Xia Q, Kou H, Wang D, Lin X, Wu Y, Xu C, Xing S, Liu B. Induced Pib Expression and resistance to magnaporthe grisea are compromised by cytosine demethylation at critical promoter regions in rice. J Integr Plant Biol 2011, 53(10):814-823.
39. Mizoi J, Shinozaki K, Yamaguchi-Shinozaki K. AP2/ERF family transcription factors in plant abiotic stress responses. BBA-Gene Regul Mech 2012, 1819(2):86-96.
40. Dubos C, Stracke R, Grotewold E, Weisshaar B, Martin C, Lepiniec L. MYB transcription factors in Arabidopsis. Trends Plant Sci 2010, 15(10):573-581.
41. Kanehisa M, Goto S, Kawashima S, Okuno Y, Hattori M. The KEGG resource for deciphering the genome. Nucleic Acids Res 2004, 32(suppl 1):D277-D280.
42. Gregersen PL, Brinch-Pedersen H, Holm PB. A microarray-based comparative analysis of gene expression profiles during grain development in transgenic and wild type wheat. Transgenic Res 2005, 14(6):887-905.
43. Coll A, Nadal A, Collado R, Capellades G, Messeguer J, Melé E, Palaudelmàs M, Pla M. Gene expression profiles of MON810 and comparable non-GM maize varieties cultured in the field are more similar than are those of conventional lines. Transgenic Res 2009, 18(5):801-808.
44. Coll A, Nadal A, Palaudelmas M, Messeguer J, Melé E, Puigdomenech P, Pla M. Lack of repeatable differential expression patterns between MON810 and comparable commercial varieties of maize. Plant Mol Biol 2008, 68(1):105-117.
45. Abdeen A, Miki B. The pleiotropic effects of the bar gene and glufosinate on the Arabidopsis transcriptome. Plant Biotechnol J 2009, 7(3):266-282.
46. Abdeen A, Schnell J, Miki B. Transcriptome analysis reveals absence of unintended effects in drought-tolerant transgenic plants overexpressing the transcription factor ABF3. BMC Genomics 2010, 11(1):69-89.
47. AC't Hoen P, Ariyurek Y, Thygesen HH, Vreugdenhil E, Vossen RH, de Menezes RX, Boer JM, van Ommen G-JB, den Dunnen JT. Deep sequencing-based expression analysis shows major advances in robustness, resolution and inter-lab portability over five microarray platforms. Nucleic Acid Res 2008, 36(21):e141-e141.
48. Kogel K-H, Voll LM, Schäfer P, Jansen C, Wu Y, Langen G, Imani J, Hofmann J, Schmiedl A, Sonnewald S. Transcriptome and metabolome profiling of field-grown transgenic barley lack induced differences but show cultivar-specific variances. Proc Natl Acad Sci 2010, 107(14):6198-6203.
49. Kauffman HE, Reddy APK, Hsieh SPY, Merca SD. An improved technique for evaluation of resistance of rice varieties to Xhanthomonas oryzae. Plant Dis Rep 1973, 57:537-541.
50. Livak KJ, Schmittgen TD. Analysis of relative gene expression data using real-time quantitative PCR and the 2- ΔΔCT method. Methods 2001, 25(4):402-408.
51. Saeed AI, Bhagabati NK, Braisted JC, Liang W, Sharov V, Howe EA, Li J, Thiagarajan M, White JA, Quackenbush J. TM4 microarray software suite. Methods Enzymol 2006, 411:134-193.
52. Ye J, Fang L, Zheng H, Zhang Y, Chen J, Zhang Z, Wang J, Li S, Li R, Bolund L. WEGO: a web tool for plotting GO annotations. Nucleic Acids Res 2006, 34(suppl 2):W293-W297.
53. Wu J, Mao X, Cai T, Luo J, Wei L. KOBAS server: a web-based platform for automated annotation and pathway identification. Nucleic Acid Res 2006, 34(suppl 2):W720-W724.