Characterization and expression patterns of small RNAs in synthesized Brassica hexaploids

Plant Molecular Biology

Volumn 85, Issue 3, 2014, Pages 287-299

  Shen, Yanyue ^a   Zhao, Qin ^a   Zou, Jun ^b   Wang, Wenliang ^a   Gao, Yi ^a   Meng, Jinling ^b   Wang, Jianbo ^a  

^a WUHAN UNIVERSITY   (China)

^b HUAZHONG AGRICULTURAL UNIVERSITY   (China)

Author keywords

Brassica; High throughput sequencing; MiRNA expression; Non additive expression; Polyploid; SiRNA

Indexed keywords

MICRORNA; PLANT RNA;

ARTICLE; BRASSICA; DOWN REGULATION; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; PHYSIOLOGICAL STRESS; PHYSIOLOGY; POLYPLOIDY;

BRASSICA; DOWN-REGULATION; GENE EXPRESSION REGULATION, PLANT; MICRORNAS; POLYPLOIDY; RNA, PLANT; STRESS, PHYSIOLOGICAL;

EID: 84900865289     PISSN: 01674412     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11103-014-0185-x     Document Type: Article

References (52)

1. Akhunov ED, Sehgal S, Liang HQ, Wang SC, Akhunova AR, Kaur G, Li WL, Forrest KL, See D, Simkova H, Ma YQ, Hayden MJ, Luo MC, Faris JD, Dolezel J, Gill BS (2013) Comparative analysis of syntenic genes in grass genomes reveals accelerated rates of gene structure and coding sequence evolution in polyploid wheat. Plant Physiol 161: 252-265.
2. Allen E, Xie Z, Gustafson AM, Carrington JC (2005) MicroRNA-directed phasing during trans-acting siRNA biogenesis in plants. Cell 121: 207-221.
3. Buggs RJA, Zhang LJ, Miles N, Tate JA, Gao L, Wei W, Schnable PS, Barbazuk WB, Soltis PS, Soltis DE (2011) Transcriptomic shock generates evolutionary novelty in a newly formed, natural allopolyploid plant. Curr Biol 21: 551-556.
4. Carthew RW, Sontheimer EJ (2009) Origins and mechanisms of miRNAs and siRNAs. Cell 136: 642-655.
5. Casneuf T, De Bodt S, Raes J, Maere S, van de Peer Y (2006) Nonrandom divergence of gene expression following gene and genome duplications in the flowering plant Arabidopsis thaliana. Genome Biol 7: R13.
6. Chague V, Just J, Mestiri I, Balzergue S, Tanguy AM, Huneau C, Huteau V, Belcram H, Coriton O, Jahier J, Chalhoub B (2010) Genome-wide gene expression changes in genetically stable synthetic and natural wheat allohexaploids. New Phytol 187: 1181-1194.
7. Chandra A, Dubey A (2010) Effect of ploidy levels on the activities of D1-pyrroline-5-carboxylate synthetase, superoxide dismutase and peroxidase in Cenchrus species grown under water stress. Plant Physiol Bioch 48: 27-34.
8. Chaudhary B, Flagel L, Stupar RM, Udall JA, Verma N, Springer NM, Wendel JF (2009) Reciprocal silencing, transcriptional bias and functional divergence of homeologs in polyploidy cotton (Gossypium). Genetics 182: 503-517.
9. Chen ZJ (2007) Genetic and epigenetic mechanisms for gene expression and phenotypic variation in plant polyploids. Annu Rev Plant Biol 58: 377-406.
10. Chen XM (2009) Small RNAs and their roles in plant development. Annu Rev Cell Dev Bi 25: 21-44.
11. Chen ZJ (2010) Molecular mechanisms of polyploidy and hybrid vigor. Trends Plant Sci 15: 57-71.
12. Chen CF, Ridzon DA, Broomer AJ, Zhou ZH, Lee DH, Ngyyen JT, Barbisin M, Xu NL, Mahuvakar VR, Andersen MR, Lao KQ, Livak KJ, Guegler KJ (2005) Real-time quantification of microRNAs by stem-loop RT-PCR. Nucleic Acids Res 33: e179.
13. Fahlgren N, Howell MD, Kasschau KD, Chapman EJ, Sullivan CM, Cumbie JS, Givan SA, Law TF, Grant SR, Dangel JL, Carrington JC (2007) High-throughput sequencing of Arabidopsis microRNAs: evidence for frequent birth and death of MiRNA genes. PLoS ONE 2: e219.
14. Gardner PP, Daub J, Tate JG, Nawrocki EP, Kolbe DL, Lindgreen S, Wilkinson AC, Finn RD, Griffiths-Jones S, Eddy SR, Bateman A (2009) Rfam: updates to the RNA families database. Nucleic Acids Res 37: D136-D140.
15. Giron D, Frago E, Glevarec G, Pieterse CMJ, Dicke M (2013) Cytokinins as key regulators in plant-microbe-insect interactions: connecting plant growth and defence. Funct Ecol 27: 599-609.
16. Guo M, Rupe MA, Zinselmeier C, Habben J, Bowen BA, Smith OS (2004) Allelic variation of gene expression in maize hybrids. Plant Cell 16: 1707-1716.
17. Ha M, Pang MX, Agarwal V, Chen ZJ (2008) Interspecies regulation of microRNAs and their targets. Biochim Biophys Acta 1779: 735-742.
18. Ha M, Lu J, Tian L, Ramachandran V, Kasschau KD, Chapman EJ, Carrington JC, Chen XM, Wang XJ, Chen ZJ (2009) Small RNAs serve as a genetic buffer against genomic shock in Arabidopsis interspecific hybrids and allopolyploids. Proc Natl Acad Sci USA 106: 17835-17840.
19. He GM, Zhu XP, Elling AA, Chen LB, Wang XF, Guo L, Liang MZ, He H, Zhang HY, Chen FF, Qi YJ, Chen RS, Deng XW (2010) Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids. Plant Cell 22: 17-33.
20. Jiang JJ, Shao YL, Du K, Ran LP, Fang XP, Wang YP (2013) Use of digital gene expression to discriminate gene expression differences in early generations of resynthesized Brassica napus and its diploid progenitors. BMC Genom 14: 72.
21. Kantama L, Junbuathong S, Sakulkoo J, de Jong H, Apisitwanich S (2013) Epigenetic changes and transposon reactivation in Thai rice hybrids. Mol Breed 31: 815-827.
22. Kashkush K, Feldman M, Levy AA (2012) Gene loss, silencing and activation in a newly synthesized wheat allotetraploid. Genetics 160: 1651-1659.
23. Kenan-Eichler M, Leshkowitz D, Tal L, Noor E, Melamed-Bessudo C, Feldman M, Levy AA (2011) Wheat hybridization and polyploidization results in deregulation of small RNAs. Genetics 188: 263-U59.
24. Khraiwesh B, Zhu JK, Zhu J (2012) Role of miRNAs and siRNAs in biotic and abiotic stress responses of plants. Biochim Biophys Acta 1819: 137-148.
25. Li R, Li Y, Kristiansen K, Wang J (2008) SOAP: short oligonucleotide alignment program. Bioinformatics 24: 713-714.
26. Li Y, Varala K, Moose SP, Hudson ME (2012) The Inheritance Pattern of 24 nt siRNA clusters in Arabidopsis hybrids is influenced by proximity to transposable elements. PLoS ONE 7: e47043.
27. Li BS, Duan H, Li JG, Deng XW, Yin WL, Xia XL (2013) Global identification of miRNAs and targets in Populus euphratica under salt stress. Plant Mol Biol 81: 525-539.
28. Manzaneda AJ, Rey PJ, Bastida JM, Weiss-Lehman C, Raskin E, Mitchell-Olda T (2012) Environmental aridity is associated with cytotype segregation and polyploidy occurrence in Brachypodium distachyon (Poaceae). New Phytol 193: 797-805.
29. McClintock B (1984) The significance of responses of the genome to challenge. Science 226: 792-801.
30. Ng DWK, Lu J, Chen ZJ (2012) Big roles for small RNAs in polyploidy, hybrid vigor, and hybrid incompatibility. Curr Opin Plant Biol 15: 154-161.
31. Ni ZF, Kim ED, Ha MS, Lackey E, Liu JX, Zhang YR, Sun QX, Chen ZJ (2009) Altered circadian rhythms regulate growth vigour in hybrids and allopolyploids. Nature 457: 327-331.
32. Qi Y, Denli AM, Hannon GJ (2005) Biochemical specialization within Arabidopsis RNA silencing pathways. Mol Cell 19: 421-428.
33. Qi B, Huang W, Zhu B, Zhong XF, Guo JH, Zhao N, Xu CM, Zhang HK, Pang JS, Han FP, Liu B (2012) Global transgenerational gene expression dynamics in two newly synthesized allohexaploid wheat (Triticum aestivum) lines. BMC Biol 10: 3.
34. Rhoades M, Reinhart B, Lim L, Burge C, Bartel B, Bartel D (2002) Prediction of plant microRNA targets. Cell 110: 513-520.
35. Saleh B, Allario T, Dambier D, Ollitrault P, Morillon R (2008) Tetraploid citrus rootstocks are more tolerant to salt stress than diploid. CR Biol 331: 703-710.
36. Sarilar V, Palacios PM, Rousselet A, Ridel C, Falque M, Eber F, Chevre AM, Joets J, Brabant P, Alix K (2013) Allopolyploidy has a moderate impact on restructuring at three contrasting transposable element insertion sites in resynthesized Brassica napus allotetraploids. New Phytol 198: 593-604.
37. Schwab R, Palatnik JF, Riester M, Schommer C, Schmid M, Schwab R, Palatnik JF, Riester M, Schommer C, Schmid M, Weigel D (2005) Specific effects of microRNAs on the plant transcriptome. Dev Cell 8: 517-527.
38. Sun GL (2012) MicroRNAs and their diverse functions in plants. Plant Mol Biol 80: 17-36.
39. Sun FL, Guo WW, Du JK, Ni ZF, Sun QX, Yao YY (2013) Widespread, abundant, and diverse TE-associated siRNAs in developing wheat grain. Gene 522: 1-7.
40. Sunkar R, Chinnusamy V, Zhu JH, Zhu JK (2007) Small RNAs as big players in plant abiotic stress responses and nutrient deprivation. Trends Plant Sci 12: 301-309.
41. Sunkar R, Zhou X, Zheng Y, Zhang W, Zhu JK (2008) Identification of novel and candidate miRNAs in rice by high throughput sequencing. BMC Plant Biol 8: 25.
42. Tian ET, Jiang YF, Chen LL, Zou J, Liu F, Meng JL (2010) Synthesis of a Brassica trigenomic allohexaploid (B. carinata × B. rapa) de novo and its stability in subsequent generations. Theor Appl Genet 121: 1431-1440.
43. van Laere K, Franca SC, Vansteenkiste H, van Huylenbroeck J, Steppe K, van Labeke MC (2011) Influence of ploidy level on morphology, growth and drought susceptibility in Spathiphyllum wallisii. Acta Physiol Plant 33: 1149-1156.
44. Varkonyi-Gasic E, Wu RM, Wood M, Walton EF, Hellens RP (2007) Protocol: a highly sensitive RT-PCR method for detection and quantification of microRNAs. Plant Methods 3: 12.
45. Vaucheret H (2009) AGO1 homeostasis involves differential production of 21-nt and 22-nt miR168 species by MIR168a and MIR168b. PLoS ONE 4: e6442.
46. Wang JL, Tian L, Lee HS, Wei NE, Jiang HM, Watson B, Madling A, Osborn TC, Doerge RW, Comai L, Chen ZJ (2006) Genomewide nonadditive gene regulation in Arabidopsis allotetraploids. Genetics 172: 507-517.
47. Wendel JF (2000) Genome evolution in polyploids. Plant Mol Biol 42: 225-249.
48. Xu YH, Zhong L, Wu XM, Fang XP, Wang JB (2009) Rapid alterations of gene expression and cytosine methylation in newly synthesized Brassica napus allopolyploids. Planta 229: 471-483.
49. Xu YH, Xu H, Wu XM, Fang XP, Wang JB (2012) Genetic changes following hybridization and genome doubling in synthetic Brassica napus. Biochem Genet 50: 616-624.
50. Yu X, Wang H, Lu YZ, de Ruiter M, Cariaso M, Prins M, van Tunen A, He YK (2012) Identification of conserved and novel microRNAs that are responsive to heat stress in Brassica rapa. J Exp Bot 63: 1025-1038.
51. Zhao CZ, Xia H, Yao YY, Frazier TP, Bi YP, Li AQ, Li MJ, Li CS, Zhang BH, Wang XJ (2010) Deep sequencing identifies novel and conserved microRNAs in peanuts (Arachis hypogaea L.). BMC Plant Biol 10: 3.
52. Zhao Q, Zou J, Meng JL, Mei SY, Wang JB (2013) Tracing the transcriptomic changes in synthetic trigenomic allohexaploids of Brassica using an RNA-Seq approach. PLoS ONE 8: e68883.