Assessment of genetic diversity among cereals and millets based on PCR amplification using Dof (DNA binding with One Finger) transcription factor gene-specific primers

Plant Systematics and Evolution

Volumn 301, Issue 2, 2015, Pages 833-840

  Kushwaha, Hariom ^a,b   Jillo, Kedir Woliy ^a   Singh, Vinay Kumar ^a,c   Kumar, Anil ^a   Yadav, Dinesh ^a,d  

^a G B PANT UNIVERSITY OF AGRICULTURE AND TECHNOLOGY   (India)

^b INSTITUTE OF MICROBIAL TECHNOLOGY   (India)

^c BANARAS HINDU UNIVERSITY   (India)

^d D D U GORAKHPUR UNIVERSITY   (India)

Author keywords

Bands; Cluster; Diversity; Dof; PCR

Indexed keywords

EID: 84939898154     PISSN: 03782697     EISSN: 16156110     Source Type: Journal    
DOI: 10.1007/s00606-014-1095-8     Document Type: Article

References (51)

1. Burland TG (2000) DNASTAR’s Lasergene sequence analysis software. Methods Mol Biol 132:71–91
2. Cai X, Zhang Y, Zhang C et al (2013) Genome-wide analysis of plant-specific Dof transcription factor family in tomato. J Integr Plant Biol 55:552–566
3. Chen X, Wang D, Liu C et al (2012) Maize transcription factor Zmdof1 involves in the regulation of Zm401 gene. Plant Growth Regul 66:271–284
4. Chen H, Ahmad M, Rim Y, Lucas WJ, Kim JY (2013) Evolutionary and molecular analysis of Dof transcription factors identified a conserved motif for intercellular protein trafficking. New Phytol 198:1250–1260
5. Guo Y, Qiu LJ (2013) Genome-wide analysis of the Dof transcription factor gene family reveals soybean-specific duplicable and functional characteristics. PLoS One 8:76809. doi:10.1371/journal.pone.0076809
6. Guo Y, Qin G, Gu H, Qu LJ (2009) Dof5.6/HCA2, a Dof transcription factor gene, regulates interfascicular cambium formation and vascular tissue development in Arabidopsis. Plant Cell 21:3518–3534
7. Gupta S, Kushwaha H, Singh VK et al (2014) Genome wide in silico characterization of Dof transcription factor gene family of sugarcane and its comparative phylogenetic analysis with Arabidopsis, Rice and Sorghum. Sugar Tech. doi:10.1007/s12355-013-0288-8
8. Hernando-Amado S, Gonzalez-Calle V, Carbonero P, Barrero-Sicilia C (2012) The family of DOF transcription factors in Brachypodium distachyon: phylogenetic comparison with rice and barley DOFs and expression profiling. BMC Plant Biol 12:202
9. Jaccard P (1908) Nouvelles recherches sur la distribuition florale. Bull Soc Vaud Sci Nat 44:223–270
10. Karp A, Kresovich S, Bhat KV, Ayad WG, Hodgkin T (1997) Molecular tools in plant genetic resources conservation: a guide to the technologies. IPGRI, Rome
11. Kellogg EA (1998) Relationships of cereal crops and other grasses. Proc Natl Acad Sci USA 95:2005–2010
12. Kim HS, Kim SJ, Abbasi N et al (2010) The DOF transcription factor Dof5.1 influences leaf axial patterning by promoting Revoluta transcription in Arabidopsis. Plant J 64:524–535
13. Kumar J, Verma V, Qazi GN, Gupta PK (2007) Genetic diversity in cymbopogon species using PCR-based functional markers. J Plant Biochem Biotechnol 16:119–122
14. Kushwaha H, Gupta N, Singh VK, Kumar A, Yadav D (2008) In silico analysis of PCR amplified DOF (DNA binding with one finger) transcription factor domain and cloned genes from cereals and millets. Online J Bioinform 9:130–143
15. Kushwaha H, Gupta S, Singh VK, Rastogi S, Yadav D (2011) Genome wide identification of Dof transcription factor gene family in sorghum and its comparative phylogenetic analysis with rice and Arabidopsis. Mol Biol Rep 38:5037–5053
16. Kushwaha H, Gupta S, Singh VK et al (2013) Cloning, in silico characterization and prediction of three dimensional structure of SbDof1, SbDof19, SbDof23 and SbDof24 proteins from sorghum [Sorghum bicolor (L.) Moench]. Mol Biotechnol 54:1–12
17. Le Hir R, Bellini C (2013) The plant-specific dof transcription factors family: new players involved in vascular system development and functioning in Arabidopsis. Front Plant Sci 4:164
18. Libault M, Joshi T, Benedito VA et al (2009) Legume transcription factor genes: what makes legumes so special? Plant Physiol 151:991–1001
19. Lijavetzky D, Carbonero P, Vicente-Carbajosa J (2003) Genome-wide comparative phylogenetic analysis of the rice and Arabidopsis Dof gene families. BMC Evol Biol 3:17
20. Moreno-Risueno MA, Diaz I, Carrillo L, Fuentes R, Carbonero P (2007a) The HvDOF19 transcription factor mediates the abscisic acid-dependent repression of hydrolase genes in germinating barley aleurone. Plant J 51:352–365
21. Moreno-Risueno MA, Martinez M, Vicente-Carbajosa J, Carbonero P (2007b) The family of DOF transcription factors: from green unicellular algae to vascular plants. Mol Genet Genomics 277:379–390
22. Murray MG, Thompson WF (1980) Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8:4321–4325
23. Negi J, Moriwaki K, Konishi M et al (2013) A Dof transcription factor, SCAP1, is essential for the development of functional stomata in Arabidopsis. Curr Biol 23:479–484
24. Noguero M, Atif RM, Ochatt S, Thompson RD (2013) The role of the DNA-binding One Zinc Finger (DOF) transcription factor family in plants. Plant Sci 209:32–45
25. Powell W, Morgante M, Andre C et al (1996) The comparison of RFLP, RAPD, AFLP and SSR microsatellite marker for germplasm analysis. Mol Breed 2:225–238
26. Rohlf FJ (2001) NTSYS-pc numerical taxonomy and multivariate analysis system, Version 5.1. Exeter Publishing Ltd., Setauket
27. Rueda-Lopez M, Crespillo R, Canovas FM, Avila C (2008) Differential regulation of two glutamine synthetase genes by a single Dof transcription factor. Plant J 56:73–85
28. Rueda-Lopez M, Garcia-Gutierrez A, Canovas FM, Avila C (2013) The family of Dof transcription factors in pine. Trees 27:1547–1557
29. Sambrook J, Russell DW (2001) Molecular cloning: a laboratory manual, 3rd edn. Cold Spring Harbor Laboratory Press, Cold Spring Harbor
30. Santos LA, de Sounza SR, Fernandes MS (2012) OsDof25 expression alters carbon and nitrogen metabolism in Arabidopsis under high N-supply. Plant Biotechnol Rep 6:327–337
31. Shaw LM, McIntyre CL, Gresshoff PM, Xue GP (2009) Members of the Dof transcription factor family in Triticum aestivum are associated with light-mediated gene regulation. Funct Integr Genomics 9:485–498
32. Shigyo M, Tabei N, Yoneyama T, Yanagisawa S (2007) Evolutionary processes during the formation of the plant-specific Dof transcription factor family. Plant Cell Physiol 48:179–185
33. Skirycz A, Reichelt M, Burow M et al (2006) DOF transcription factor AtDof1.1 (OBP2) is part of a regulatory network controlling glucosinolate biosynthesis in Arabidopsis. Plant J 47:10–24
34. Skirycz A, Jozefczuk S, Stobiecki M et al (2007) Transcription factor AtDOF4;2 affects phenylpropanoid metabolism in Arabidopsis thaliana. New Phytol 175:425–438
35. Somerville C, Somerville S (1999) Plant functional genomics. Science 285:380–383
36. Takahashi N, Kong S, Umeda M (2013) Dof transcription factors control the expression of the anaphase promoting complex/cyclosome activator CCS52A1. Plant Biotechnol 30:407–410
37. Takatsuji H (1998) Zinc-finger transcription factors in plants. Cell Mol Life Sci 54:582–596
38. Tanksley SD, McCouch SR (1997) Seed banks and molecular maps: unlocking genetic potential from the wild. Science 277:1063–1066
39. 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
40. Untergasser A, Nijveen H, Rao X et al (2007) Primer3Plus, an enhanced web interface to Primer3. Nucleic Acids Res 35:W71–W74
41. Wang HW, Zhang B, Hao YJ et al (2007) The soybean Dof-type transcription factor genes, GmDof4 and GmDof11, enhance lipid content in the seeds of transgenic Arabidopsis plants. Plant J 52:716–729
42. Watanabe KN, Iwanaga M (1999) Plant genetic resources and its global contribution. Plant Biotechnol 16:7–13
43. Yanagisawa S (1995) A novel DNA-binding domain that may form a single zinc finger motif. Nucleic Acids Res 23:3403–3410
44. Yanagisawa S (2002) The Dof family of plant transcription factors. Trends Plant Sci 7:555–560
45. Yanagisawa S (2004) Dof domain proteins: plant-specific transcription factors associated with diverse phenomena unique to plants. Plant Cell Physiol 45:386–391
46. Yanagisawa S, Schmidt RJ (1999) Diversity and similarity among recognition sequences of Dof transcription factors. Plant J 17:209–214
47. Yanagisawa S, Akiyama A, Kisaka H, Uchimiya H, Miwa T (2004) Metabolic engineering with Dof1 transcription factor in plants: improved nitrogen assimilation and growth under low-nitrogen conditions. Proc Natl Acad Sci USA 101:7833–7838
48. Yang X, Tuskan GA, Cheng MZ (2006) Divergence of the Dof gene families in poplar, Arabidopsis, and rice suggests multiple modes of gene evolution after duplication. Plant Physiol 142:820–830
49. Yang J, Yang MF, Wang D, Chen F, Shen SH (2010) JcDof1, a Dof transcription factor gene, is associated with the light-mediated circadian clock in Jatropha curcas. Physiol Plant 139:324–334
50. Yap I, Nelson RJ (1996) Winboot: a program for performing bootstrap analysis of binary data to determine the confidence of UPGMA-based dendrograms. Discussion paper series No 14. IRRI, Manila
51. Zou HF, Zhang YQ, Wei W et al (2013) The transcription factor AtDOF4.2 regulates shoot branching and seed coat formation in Arabidopsis. Biochem J 449:373–388