Differentiated expression of microRNAs may regulate genotype-dependent traits in cotton

Gene

Volumn 547, Issue 2, 2014, Pages 233-238

  Sun, Runrun ^a,b   Wang, Qinglian ^a   Ma, Jun ^b   He, Qiuling ^b   Zhang, Baohong ^a,b  

^a HENAN INSTITUTE OF SCIENCE AND TECHNOLOGY   (China)

^b EAST CAROLINA UNIVERSITY   (United States)

Author keywords

Expression profile; Floral development; Genotype; MiRNA; Phage change

Indexed keywords

EXPRESSION PROFILE; FLORAL DEVELOPMENT; GENOTYPE; MIRNA; PHAGE CHANGE;

GENE EXPRESSION REGULATION, PLANT; GENOTYPE; GOSSYPIUM; MICRORNAS; RNA, PLANT; TRANSCRIPTION, GENETIC;

EID: 84904440049     PISSN: 03781119     EISSN: 18790038     Source Type: Journal    
DOI: 10.1016/j.gene.2014.06.052     Document Type: Article

References (46)

1. Abdurakhmonov I.Y., Devor E.J., Buriev Z.T., Huang L., Makamov A., Shermatov S.E., Bozorov T., Kushanov F.N., Mavlonov G.T., Abdukarimov A. Small RNA regulation of ovule development in the cotton plant G. hirsutum L. BMC Plant Biol. 2008, 8.
2. Aukerman M.J., Sakai H. Regulation of flowering time and floral organ identity by a microRNA and its APETALA2-like target genes. Plant Cell 2003, 15:2730-2741.
3. Barozai M.Y.K., Irfan M., Yousaf R., Ali I., Qaisar U., Maqbool A., Zahoor M., Rashid B., Hussnain T., Riazuddin S. Identification of micro-RNAs in cotton. Plant Physiol. Biochem. 2008, 46:739-751.
4. Cai Y.-F., He X.-H., Sun Q., Jiang H.-Z., Mo J.-C., Yuan Y.-L., Shi Y.-Z. Differential expression of miRNA during upland cotton gland forming age. Sichuan Daxue Xuebao (Ziran Kexueban) 2011, 48:673-678.
5. Chen X.M. A microRNA as a translational repressor of APETALA2 in Arabidopsis flower development. Science 2004, 303:2022-2025.
6. Ding Y., Tao Y., Zhu C. Emerging roles of microRNAs in the mediation of drought stress response in plants. J. Exp. Bot. 2013, 64:3077-3086.
7. Fang X., Zhao Y., Ma Q., Huang Y., Wang P., Zhang J., Nian H., Yang C. Identification and comparative analysis of cadmium tolerance-associated miRNAs and their targets in two soybean genotypes. Plos One 2013, 8.
8. Frazier T.P., Burklew C.E., Zhang B.H. Titanium dioxide nanoparticles affect the growth and microRNA expression of tobacco (Nicotiana tabacum). Funct. Integr. Genom. 2014, 14:75-83.
9. Gong L., Kakrana A., Arikit S., Meyers B.C., Wendel J.F. Composition and expression of conserved MICRORNA genes in diploid cotton (Gossypium) species. Genome Biol. Evol. 2013, 5:2449-2459.
10. Griffiths-Jones S., Saini H.K., van Dongen S., Enright A.J. miRBase: tools for microRNA genomics. Nucleic Acids Res. 2008, 36:D154-D158.
11. Gupta O.P., Sharma P., Gupta R.K., Sharma I. MicroRNA mediated regulation of metal toxicity in plants: present status and future perspectives. Plant Mol. Biol. 2014, 84:1-18.
12. He X., Cai Y., Sun Q., Yuan Y., Shi Y. MicroRNA expression profiling during upland cotton gland forming age by microarray and quantitative reverse-transcription polymerase chain reaction (qRT-PCR). Afr. J. Biotechnol. 2011, 10:8695-8702.
13. Jeong D.-H., Green P.J. The role of rice microRNAs in abiotic stress responses. J. Plant Biol. 2013, 56:187-197.
14. Khan Barozai M.Y., Irfan M., Yousaf R., Ali I., Qaisar U., Maqbool A., Zahoor M., Rashid B., Hussnain T., Riazuddin S. Identification of micro-RNAs in cotton. Plant Physiol. Biochem. 2008, 46:739-751.
15. Kozomara A., Griffiths-Jones S. miRBase: integrating microRNA annotation and deep-sequencing data. Nucleic Acids Res. 2011, 39:D152-D157.
16. Kwak P.B., Wang Q.Q., Chen X.S., Qiu C.X., Yang Z.M. Enrichment of a set of microRNAs during the cotton fiber development. BMC Genomics 2009, 10.
17. Lee R.C., Feinbaum R.L., Ambros V. The C. elegans heterochronic gene lin-4 encodes small RNAs with antisense complementarity to lin-14. Cell 1993, 75:843-854.
18. Li Q., Jin X., Zhu Y.-X. Identification and analyses of miRNA genes in allotetraploid gossypium hirsutum fiber cells based on the sequenced diploid G. raimondii genome. J. Genet. Genom. 2012, 39:351-360.
19. Luo Y., Guo Z., Li L. Evolutionary conservation of microRNA regulatory programs in plant flower development. Dev. Biol. 2013, 380:133-144.
20. Navarro L., Dunoyer P., Jay F., Arnold B., Dharmasiri N., Estelle M., Voinnet O., Jones J.D.G. A plant miRNA contributes to antibacterial resistance by repressing auxin signaling. Science 2006, 312:436-439.
21. Pang M., Woodward A.W., Agarwal V., Guan X., Ha M., Ramachandran V., Chen X., Triplett B.A., Stelly D.M., Chen Z.J. Genome-wide analysis reveals rapid and dynamic changes in miRNA and siRNA sequence and expression during ovule and fiber development in allotetraploid cotton (Gossypium hirsutum L.). Genome Biol. 2009, 10.
22. Pang M., Xing C., Adams N., Rodriguez-Uribe L., Hughs S.E., Hanson S.F., Zhang J. Comparative expression of miRNA genes and miRNA-based AFLP marker analysis in cultivated tetraploid cottons. J. Plant Physiol. 2011, 168:824-830.
23. Pang M., Hanson S.F., Zhang J. Cloning and expression studies of novel small RNAs in tetraploid cotton. Plant Mol. Biol. Report. 2012, 30:710-718.
24. Pei L., Jin Z., Li K., Yin H., Wang J., Yang A. Identification and comparative analysis of low phosphate tolerance-associated microRNAs in two maize genotypes. Plant Physiol. Biochem. 2013, 70:221-234.
25. Qiu C.X., Xie F.L., Zhu Y.Y., Guo K., Huang S.Q., Nie L., Yang Z.M. Computational identification of microRNAs and their targets in Gossypium hirsutum expressed sequence tags. Gene 2007, 395:49-61.
26. Rai K.M., Singh S.K., Bhardwaj A., Kumar V., Lakhwani D., Srivastava A., Jena S.N., Yadav H.K., Bag S.K., Sawant S.V. Large-scale resource development in Gossypium hirsutum L. by 454 sequencing of genic-enriched libraries from six diverse genotypes. Plant Biotechnol. J. 2013, 11:953-963.
27. Rogers K., Chen X. Biogenesis, turnover, and mode of action of plant microRNAs. Plant Cell 2013, 25:2383-2399.
28. Rubio-Somoza I., Weigel D. MicroRNA networks and developmental plasticity in plants. Trends Plant Sci. 2011, 16:258-264.
29. Schwab R., Palatnik J.F., Riester M., Schommer C., Schmid M., Weigel D. Specific effects of microRNAs on the plant transcriptome. Dev. Cell 2005, 8:517-527.
30. Unver T., Parmaksiz I., Dundar E. Identification of conserved micro-RNAs and their target transcripts in opium poppy (Papaver somniferum L.). Plant Cell Rep. 2010, 29:757-769.
31. Wang J.W., Czech B., Weigel D. miR156-regulated SPL transcription factors define an endogenous flowering pathway in Arabidopsis thaliana. Cell 2009, 138:738-749.
32. Wang M., Wang Q., Wang B. Identification and characterization of microRNAs in Asiatic cotton (Gossypium arboreum L.). Plos One 2012, 7.
33. Wang M., Wang Q., Zhang B. Response of miRNAs and their targets to salt and drought stresses in cotton (Gossypium hirsutum L.). Gene 2013, 530:26-32.
34. Wu G., Park M.Y., Conway S.R., Wang J.W., Weigel D., Poethig R.S. The sequential action of miR156 and miR172 regulates developmental timing in Arabidopsis. Cell 2009, 138:750-759.
35. Xie K.B., Shen J.Q., Hou X., Yao J.L., Li X.H., Xiao J.H., Xiong L.Z. Gradual increase of miR156 regulates temporal expression changes of numerous genes during leaf development in rice. Plant Physiol. 2012, 158:1382-1394.
36. Yanik H., Turktas M., Dundar E., Hernandez P., Dorado G., Unver T. Genome-wide identification of alternate bearing-associated microRNAs (miRNAs) in olive (Olea europaea L.). BMC Plant Biol. 2013, 13.
37. Zhang B., Pan X. Expression of microRNAs in cotton. Mol. Biotechnol. 2009, 42:269-274.
38. Zhang B.H., Pan X.P., Cobb G.P., Anderson T.A. Plant microRNA: a small regulatory molecule with big impact. Dev. Biol. 2006, 289:3-16.
39. Zhang B., Wang Q., Wang K., Pan X., Liu F., Guo T., Cobb G.P., Anderson T.A. Identification of cotton microRNAs and their targets. Gene 2007, 397:26-37.
40. Zhang B.H., Wang Q.L. MicroRNA-based biotechnology for plant improvement. J. Cell. Physiol. 2014, 10.1002/jcp.24685.
41. Zhang B.H., Wang Q.L., Pan X.P. MicroRNAs and their regulatory roles in animals and plants. J. Cell. Physiol. 2007, 210:279-289.
42. Zhang X.H., Zou Z., Gong P.J., Zhang J.H., Ziaf K., Li H.X., Xiao F.M., Ye Z.B. Over-expression of microRNA169 confers enhanced drought tolerance to tomato. Biotechnol. Lett. 2011, 33:403-409.
43. Zhang H., Wan Q., Ye W., Lv Y., Wu H., Zhang T. Genome-wide analysis of small RNA and novel microRNA discovery during fiber and seed initial development in Gossypium hirsutum L. Plos One 2013, 8.
44. Zhou M., Luo H. MicroRNA-mediated gene regulation: potential applications for plant genetic engineering. Plant Mol. Biol. 2013, 83:59-75.
45. Zhou M., Li D.Y., Li Z.G., Hu Q., Yang C.H., Zhu L.H., Luo H. Constitutive expression of a miR319 gene alters plant development and enhances salt and drought tolerance in transgenic creeping bentgrass. Plant Physiol. 2013, 161:1375-1391.
46. Zhu Q.-H., Fan L., Liu Y., Xu H., Llewellyn D., Wilson I. miR482 regulation of NBS-LRR defense genes during fungal pathogen infection in cotton. Plos One 2013, 8.