Genome-wide analysis of the auxin response factor (ARF) gene family in maize (Zea mays)

Plant Growth Regulation

Volumn 63, Issue 3, 2011, Pages 225-234

  Liu, Yan ^a   Jiang, HaiYang ^a   Chen, Wenjuan ^a   Qian, Yexiong ^a   Ma, Qing ^a   Cheng, Beijiu ^a   Zhu, Suwen ^a  

^a ANHUI AGRICULTURAL UNIVERSITY   (China)

Author keywords

Duplication; EST; Expression; Phylogenetic analysis; ZmARF

Indexed keywords

ARABIDOPSIS; ORYZA SATIVA; ZEA MAYS;

EID: 79952745764     PISSN: 01676903     EISSN: 15735087     Source Type: Journal    
DOI: 10.1007/s10725-010-9519-0     Document Type: Article

References (34)

1. Abel S, Theologis A (1996) Early genes and auxin action. Plant Physiol 111: 9-17.
2. Bennetzen JL, Chandler VL, Schnable PS (2001) National science foundation-sponsored workshop report. Maize genome sequencing project. Plant Physiol 127: 1572-1578.
3. De Smet I, Jürgens G (2007) Patterning the axis in plants-auxin in control. Curr Opin Genet Dev 17: 337-343.
4. Gu Q, Ferrándiz C, Yanofsky MF, Martienssen R (1998) The FRUITFULL MADS-box gene mediates cell differentiation during Arabidopsis fruit development. Development 125: 1509-1517.
5. Guilfoyle T, Hagen G, Ulmasov T, Murfett J (1998a) How does auxin turn on genes? Plant Physiol 118: 341-347.
6. Guilfoyle T, Ulmasov T, Hagen G (1998b) The ARF family of transcription factors and their role in plant hormone-responsive transcription. Cell Mol Life Sci 54: 619-627.
7. Hagen G, Guilfoyle T (2002) Auxin-responsive gene expression: genes, promoters and regulatory factors. Plant Mol Biol 49: 373-385.
8. Jain M, Kaur N, Tyagi AK, Khurana JP (2006) The auxin-responsive GH3 gene family in rice (Oryza sativa). Funct Integr Genomics 6: 36-46.
9. Kim J, Harter K, Theologis A (1997) Protein-protein interactions among the Aux/IAA proteins. Proc Natl Acad Sci USA 94: 11786-11791.
10. Li Y, Liu ZB, Shi X, Hagen G, Guilfoyle TJ (1994) An auxin-inducible element in soybean SAUR promoters. Plant Physiol 106: 37-43.
11. Lynch M, Conery JS (2000) The evolutionary fate and consequences of duplicate genes. Science 290: 1151-1155.
12. Nakano T, Suzuki K, Fujimura T, Shinshi H (2006) Genome-wide analysis of the ERF gene family in Arabidopsis and rice. Plant Physiol 140: 411-432.
13. Okushima Y, Overvoorde PJ, Arima K et al (2005) Functional genomic analysis of the AUXIN RESPONSE FACTOR gene family members in Arabidopsis thaliana: unique and overlapping functions of ARF7 and ARF19. Plant Cell 17: 444-463.
14. Ouellet F, Overvoorde PJ, Theologis A (2001) IAA17/AXR3: biochemical insight into an auxin mutant phenotype. Plant Cell 13: 829-841.
15. Overvoorde PJ, Okushima Y, Alonso JM et al (2005) Functional genomic analysis of the AUXIN/INDOLE-3-ACETIC ACID gene family members in Arabidopsis thaliana. Plant Cell 17: 2300-3282.
16. Raes J, Vandepoele K, Simillion C, Saeys Y, van de Peer Y (2003) Investigating ancient duplication events in the Arabidopsis genome. J Struct Funct 3: 117-129.
17. Reed JW (2001) Roles and activities of Aux/IAA proteins in Arabidopsis. Trend Plant Sci 6: 420-425.
18. Schnable PS, Ware D, Fulton RS et al (2009) The B73 maize genome: complexity, diversity, and dynamics. Science 326: 1112-1115.
19. Simillion C, Vandepoele K, van Montagu MC, Zabeau M, van de Peer Y (2002) The hidden duplication past of Arabidopsis thaliana. Proc Natl Acad Sci USA 99: 13627-13632.
20. Tamura K, Dudley J, Nei M, Kumar S (2007) MEGA4: molecular evolutionary genetics analysis (MEGA) software version 4. 0. Mol Biol Evol 24: 1596-1599.
21. Terol J, Domingo C, Talon M (2006) The GH3 family in plants: genome wide analysis in rice and evolutionary history based on EST analysis. Gene 371: 279-290.
22. Thompson JD, Higgins DG, Gibson TJ (1994) CLUSTAL W: improving the sensitivity of progressive multiple sequence alignment through sequence weighting, position-specific gap penalties and weight matrix choice. Nucleic Acids Res 22: 4673-4680.
23. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG (1997) The CLUSTAL_X windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res 25: 4876-4882.
24. Tiwari SB, Hagen G, Guilfoyle TJ (2003) The roles of auxin response factor domains in auxin-responsive transcription. Plant Cell 15: 533-543.
25. Udaya C, Stephen P, Amy M (2007) Genome-wide analysis of Aux/IAA and ARF gene families in Populus trichocarpa. BMC Plant Biol 7: 59.
26. Ulmasov T, Hagen G, Guilfoyle TJ (1997a) ARF1, a transcription factor that binds to auxin response elements. Science 276: 1865-1868.
27. Ulmasov T, Murfett J, Hagen G, Guilfoyle TJ (1997b) Aux/IAA proteins repress expression of reporter genes containing natural and highly active synthetic auxin response elements. Plant Cell 9: 1963-1971.
28. Ulmasov T, Hagen G, Guilfoyle TJ (1999) Dimerization and DNA binding of auxin response factors. Plant J 19: 309-319.
29. Vision TJ, Brown DG, Tanksley SD (2000) The origins of genomic duplications in Arabidopsis. Science 290: 2114-2117.
30. Wang Y, Deng D, Bian Y, Lv Y, Xie Q (2010) Genome-wide analysis of primary auxin-responsive Aux/IAA gene family in maize (Zea maysL.). Mol Biol Rep Epub. A head of print Accessed 16 Mar 2010.
31. Wang X, Shi X, Hao B, Ge S, Luo J (2005) Duplication and DNA segmental loss in the rice genome: implications for diploidization. New Phytol 165: 937-946.
32. Wang D, Pei K, Fu Y, Sun Z, Li S, Liu H, Tang K, Han B, Tao Y (2007) Genome-wide analysis of the auxin response factors (ARF) gene family in rice (Oryza sativa). Gene 394: 13-24.
33. Woodward AW, Bartel B (2005) Auxin: regulation, action, and interaction. Ann Bot (Lond) 95: 707-735.
34. Yang SH, Zhang XH, Yue JX, Tian DC, Chen JQ (2008) Recent duplications dominate NBS-encoding gene expansion in two woody species. Mol Genet Genomics 280: 187-198.