Stage and tissue-specific modulation of ten conserved miRNAs and their targets during somatic embryogenesis of Valencia sweet orange

Planta

Volumn 233, Issue 3, 2011, Pages 495-505

  Wu, Xiao Meng ^a   Liu, Mei Ya ^a   Ge, Xiao Xia ^a   Xu, Qiang ^a   Guo, Wen Wu ^a  

^a HUAZHONG AGRICULTURAL UNIVERSITY   (China)

Author keywords

Citrus; MicroRNA; qRT PCR; Somatic embryogenesis; Target unigenes

Indexed keywords

MICRORNA;

ARTICLE; EMBRYO DEVELOPMENT; GENE EXPRESSION REGULATION; GENETICS; METABOLISM; PLANT GENE; PRENATAL DEVELOPMENT; REVERSE TRANSCRIPTION POLYMERASE CHAIN REACTION; SWEET ORANGE;

CITRUS SINENSIS; EMBRYONIC DEVELOPMENT; GENE EXPRESSION REGULATION, DEVELOPMENTAL; GENE EXPRESSION REGULATION, PLANT; GENES, PLANT; MICRORNAS; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION;

CITRUS; CITRUS SINENSIS;

EID: 79951958197     PISSN: 00320935     EISSN: 14322048     Source Type: Journal    
DOI: 10.1007/s00425-010-1312-9     Document Type: Article

References (51)

1. Achard P, Herr A, Baulcombe DC, Harberd NP (2004) Modulation of floral development by a gibberellin-regulated microRNA. Development 131: 3357-3365.
2. Bartel DP (2004) MiRNAs: genomics, biogenesis, mechanism and function. Cell 116: 281-297.
3. Bonnet E, He Y, Billiau K, van de Peer Y (2010) TAPIR, a web server for the prediction of plant microRNA targets, including target mimics. Bioinformatics 26: 1566-1568.
4. Cangahuala-Inocente GC, Villarino A, Seixas D, Dumas-Gaudot E, Terenzi H, Guerra MP (2009) Differential proteomic analysis of developmental stages of Acca sellowiana somatic embryos. Acta Physiol Plant 31: 501-514.
5. Deng XX (1987) Studies on the isolation, regeneration and fusion of protoplasts in citrus. PhD dissertation of Huazhong Agricultural University.
6. Fahlgren N, Montgomery TA, Howell MD, Allen E, Dvorak SK, Alexander AL, Carrington JC (2006) Regulation of AUXIN RESPONSE FACTOR3 by TAS3 ta-siRNA affects developmental timing and patterning in Arabidopsis. Curr Biol 16: 939-944.
7. Gandikota M, Birkenbihl RP, Höhmann S, Cardon GH, Heinz S, Huijser P (2007) The miRNA156/157 recognition element in the 3′ UTR of the Arabidopsis SBP box gene SPL3 prevents early flowering by translational inhibition in seedlings. Plant J 49: 683-693.
8. Ge XX, Fan GE, Chai LJ, Guo WW (2010) Cloning, molecular characterization and expression analysis of a SOMATIC EMBRYOGENESIS RECEPTOR-LIKE KINASE gene (CitSERK1-like) in Valencia sweet orange. Acta Physiol Plant 32: 1197-1207.
9. Ghildiyal M, Zamore PD (2009) Small silencing RNAs: an expanding universe. Nat Rev Genet 10: 94-108.
10. Gmitter FG Jr, Soneji JR, Rao MN (2009) Citrus breeding. In: Jain SM, Priyadarshan PM (eds) Breeding plantation tree crops: temperate species. Springer, New York, pp 105-134.
11. Griffiths-Jones S, Saini HK, van Dongen S, Enright AJ (2008) miRBase: tools for microRNA genomics. Nucleic Acids Res 36: D154-D158.
12. Guan YC, Ren HB, Xie H, Ma ZY, Chen F (2009) Identification and characterization of bZIP-type transcription factors involved in carrot (Daucus carota L.) somatic embryogenesis. Plant J 60: 207-217.
13. Guo WW, Cai XD, Cheng YJ, Grosser JW, Deng XX (2007) Protoplast technology and citrus improvement. In: Xu ZH, Li JY, Xue YB, Yang WC (eds) Biotechnology and sustainable agriculture 2006 and beyond. In: Proc 11th IAPTC& B Congress. Springer, pp 461-464.
14. Hofacker IL, Fontana W, Stadler PF, Bonhoeffer S, Tacker M, Schuster P (1994) Fast folding and comparison of RNA secondary structures. Monatshefte Chemie 125: 167-188.
15. Imin N, Goffard N, Nizamidin M, Rolfe BG (2008) Genome-wide transcriptional analysis of super-embryogenic Medicago truncatula explant cultures. BMC Plant Biol 8: 110.
16. Kalendar R, Lee D, Schulman AH (2009) FastPCR software for PCR primer and probe design and repeat search. Genes Genomes Genomics 3: 1-14.
17. Kayim M, Koc NK (2006) The effects of some carbohydrates on growth and somatic embryogenesis in citrus callus culture. Sci Hortic 109: 29-34.
18. Kikuchi A, Sanuki N, Higashi K, Koshiba T, Kamada H (2006) Abscisic acid and stress treatment are essential for the acquisition of embryogenic competence by carrot somatic cells. Planta 223: 637-645.
19. Kim J, Jung JH, Reyes JL, Kim YS, Kim SY, Chung KS, Kim JA, Lee M, Lee Y, Kim VN, Chua NH, Park CM (2005) MicroRNA-directed cleavage of ATHB15 mRNA regulates vascular development in Arabidopsis inflorescence stems. Plant J 42: 84-94.
20. Lalitha S (2000) Primer Premier 5. Biotech Softw Internet Rep 1: 270-272.
21. Liu Q, Xu J, Liu Y, Zhao X, Deng X, Guo L, Gu J (2007) A novel bud mutation that confers abnormal patterns of lycopene accumulation in sweet orange fruit (Citrus sinensis L. Osbeck). J Exp Bot 58: 4161-4171.
22. Llave C, Xie Z, Kasschau KD, Carrington JC (2002) Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 297: 2053-2056.
23. Luo YC, Zhou H, Li Y, Chen JY, Yang JH, Chen YQ, Qu LH (2006) Rice embryogenic calli express a unique set of miRNAs, suggesting regulatory roles of miRNAs in plant post-embryogenic development. FEBS Lett 580: 5111-5116.
24. Mallory AC, Vaucheret H (2006) Functions of microRNAs and related small RNAs in plants. Nat Genet 38: S31-S36.
25. Mallory AC, Dugas DV, Bartel DP, Bartel B (2004) MicroRNA regulation of NAC-domain targets is required for proper formation and separation of adjacent embryonic, vegetative, and floral organs. Curr Biol 14: 1035-1046.
26. Maul P, Bausher M, McCollum G, Mozoruk J, Niedz R (2006) CsHPt1, a putative histidine-containing phosphotransmitter protein induced during early somatic embryogenesis in Valencia sweet orange. Plant Sci 170: 44-53.
27. Murashige T, Tucker DPH (1969) Growth factors requirement of citrus tissue cultures. In: Chapman HD (ed) Proceedings of the international citrus symposium, vol 3. Riverside, California, pp 1155-1161.
28. Oh TJ, Wartell RM, Cairney J, Pullman GS (2008) Evidence for stage-specific modulation of specific microRNAs (miRNAs) and miRNA processing components in zygotic embryo and female gametophyte of loblolly pine (Pinus taeda). New Phytol 179: 67-80.
29. Pan ZY, Guan R, Zhu SP, Deng XX (2009) Proteomic analysis of somatic embryogenesis in Valencia sweet orange (Citrus sinensis Osbeck). Plant Cell Rep 28: 281-289.
30. Reyes JL, Chua N-H (2007) ABA induction of miR159 controls transcript levels of two MYB factors during Arabidopsis seed germination. Plant J 49: 592-606.
31. Ru P, Xu L, Ma H, Huang H (2006) Plant fertility defects induced by the enhanced expression of microRNA167. Cell Res 16: 457-465.
32. 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.
33. Schwab R, Ossowski S, Riester M, Warthmann N, Weigel D (2006) Highly specific gene silencing by artificial microRNAs in Arabidopsis. Plant Cell 18: 1121-1133.
34. Shimada T, Hirabayashi T, Endo T, Fujii H, Kita M, Omura M (2005) Isolation and characterization of the somatic embryogenesis receptor-like kinase gene homologue (CitSERK1) from Citrus unshiu Marc. Sci Hortic 103: 233-238.
35. Sieber P, Wellmer F, Gheyselinck J, Riechmann JL, Meyerowitz EM (2007) Redundancy and specialization among plant microRNAs: role of the miR164 family in developmental robustness. Development 134: 1051-1060.
36. Smita R, Thomas G, Alexis P, Thomas B, Patrick L, Klaus T (2008) Interplay of miR164, CUP-SHAPED COTYLEDON genes and LATERAL SUPPRESSOR controls axillary meristem formation in Arabidopsis thaliana. Plant J 55: 65-76.
37. Song C, Fang J, Li X, Liu H, Thomas Chao C (2009) Identification and characterization of 27 conserved microRNAs in citrus. Planta 230: 671-685.
38. Song C, Jia Q, Fang J, Li F, Wang C, Zhang Z (2010) Computational identification of citrus microRNAs and target analysis in citrus expressed sequence tags. Plant Biol 12: 927-934.
39. Sunkar R, Zhu JK (2004) Novel and stress-regulated microRNAs and other small RNAs from Arabidopsis. Plant Cell 16: 2001-2019.
40. Sunkar R, Kapoor A, Zhu JK (2006) Posttranscriptional induction of two Cu/Zn superoxide dismutase genes in Arabidopsis is mediated by down regulation of miR398 and important for oxidative stress tolerance. Plant Cell 18: 2051-2065.
41. Takahata K (2008) Isolation of carrot Argonaute1 from subtractive somatic embryogenesis cDNA library. Biosci Biotechnol Biochem 72: 900-904.
42. Vaucheret H, Mallory AC, Bartel DP (2006) AGO1 homeostasis entails coexpression of MIR168 and AGO1 and preferential stabilization of miR168 by AGO1. Mol Cell 22: 129-136.
43. Vernoux T, Benfey PN (2005) Signals that regulate stem cell activity during plant development. Curr Opin Genet Dev 15: 388-394.
44. Wang JW, Czech B, Weigel D (2009) miR156-regulated SPL transcription factors define an endogenous flowering pathway in Arabidopsis thaliana. Cell 138: 738-749.
45. Williams L, Grigg SP, Xie M, Christensen S, Fletcher JC (2005) Regulation of Arabidopsis shoot apical meristem and lateral organ formation by microRNA miR166g and its AtHD-ZIP target genes. Development 132: 3657-3668.
46. Wu G, Poethig RS (2006) Temporal regulation of shoot development in Arabidopsis thaliana by miR156 and its target SPL3. Development 133: 3539-3547.
47. Wu XB, Wang J, Liu JH, Deng XX (2009) Involvement of polyamine biosynthesis in somatic embryogenesis of Valencia sweet orange (Citrus sinensis) induced by glycerol. J Plant Physiol 166: 52-62.
48. Wu XM, Liu MY, Xu Q, Guo WW (2010) Identification and characterization of miRNAs from citrus expressed sequence tags. Tree Genet Genomes. doi: 10. 1007/s11295-010-0319-5.
49. Xu Q, Liu YL, Zhu AD, Wu XM, Ye JL, Yu KQ, Guo WW, Deng XX (2010) Discovery and comparative profiling of microRNAs in a sweet orange red-flesh mutant and its wild type. BMC Genomics 11: 246.
50. Yang XY, Zhang XL (2010) Regulation of somatic embryogenesis in higher plants. Crit Rev Plant Sci 29: 36-57.
51. Zhang Y (2005) miRU: an automated plant miRNA target prediction server. Nucleic Acids Res 33: w701-w704.