Spatial and temporal expression modes of MicroRNAs in an elite rice hybrid and its parental lines

Planta

Volumn 238, Issue 2, 2013, Pages 259-269

  Fang, Ruiqiu ^a   Li, Luoye ^a   Li, Jianxiong ^a  

^a SOUTH CHINA INSTITUTE OF BOTANY   (China)

Author keywords

Heterosis; MicroRNA; QTL; Rice

Indexed keywords

MICRORNA; PLANT RNA;

ARTICLE; CHIMERA; CHROMOSOME MAP; CROSS BREEDING; DOMINANT GENE; GENE EXPRESSION REGULATION; GENETICS; GROWTH, DEVELOPMENT AND AGING; HETEROSIS; PHENOTYPE; PLANT GENOME; PLANT LEAF; QUANTITATIVE TRAIT LOCUS; RICE; SEEDLING;

CHIMERA; CHROMOSOME MAPPING; CROSSES, GENETIC; GENE EXPRESSION REGULATION, PLANT; GENES, DOMINANT; GENOME, PLANT; HYBRID VIGOR; MICRORNAS; ORYZA SATIVA; PHENOTYPE; PLANT LEAVES; QUANTITATIVE TRAIT LOCI; RNA, PLANT; SEEDLING;

EID: 84880828505     PISSN: 00320935     EISSN: 14322048     Source Type: Journal    
DOI: 10.1007/s00425-013-1881-5     Document Type: Article

References (50)

1. Bartel DP (2004) MicroRNAs: genomics, giogenesis, mechanism, and function. Cell 116: 281-297.
2. Bartel B, Bartel DP (2003) MicroRNAs: at the root of plant development? Plant Physiol 132: 709-717.
3. Birchler JA, Veitia RA (2010) The gene balance hypothesis: implications for gene regulation, quantitative traits and evolution. New Phytol 186: 54-62.
4. Bruce AB (1910) The Mendelian theory of heredity and the augmentation of vigor. Science 32: 627-628.
5. Bushati N, Cohen SM (2007) MicroRNA functions. Annu Rev Cell Dev Biol 23: 175-205.
6. Chen ZJ (2010) Molecular mechanisms of polyploidy and hybrid vigor. Trends Plant Sci 15: 57-71.
7. Chen F, He G, He H, Chen W, Zhu X, Liang M, Chen L, Deng XW (2010) Expression analysis of miRNAs and highly-expressed small RNAs in two rice subspecies and their reciprocal hybrids. J Integr Plant Biol 5: 971-980.
8. Clark RM, Wagler TN, Quijada P, Doebley J (2006) A distant upstream enhancer at the maize domestication gene tb1 has pleiotropic effects on plant and inflorescent architecture. Nat Genet 38: 594-597.
9. Darwin CR (1876) The effects of cross- and self- fertilization in the Vegetable Kingdom. John Murray, London.
10. Davenport CB (1908) Degeneration, albinism and inbreeding. Science 28: 454-455.
11. Debernardi JM, Rodriguez RE, Mecchia MA, Palatnik JF (2012) Functional specialization of the plant miR396 regulatory network through distinct microRNA-target interactions. PLoS Genet 8: e1002419.
12. Duvick DN (1999) Heterosis: feeding people and protecting natural resources. In: Coors JG, Pandey S (eds) The genetics and exploitation of heterosis in crops. Crop Science Society of America, Madison, pp 19-29.
13. East EM (1936) Heterosis. Genetics 21: 375-397.
14. Fu Z, Jin X, Ding D, Li Y, Fu Z, Tang J (2011) Proteomic analysis of heterosis during maize seed germination. Proteomics 11: 1462-1472.
15. Fujimotoa R, Taylora JM, Shirasawab S, Peacocka WJ, Dennisa ES (2012) Heterosis of Arabidopsis hybrids between C24 and Col is associated with increased photosynthesis capacity. Proc Natl Acad Sci USA 109: 7109-7114.
16. Goff SA (2011) A unifying theory for general multigenic heterosis: energy efficiency, protein metabolism, and implications for molecular breeding. New Phytol 189: 923-937.
17. Goodnight CJ (1999) Epistasis and heterosis. In: Coors JG, Pandey S (eds) Genetic and exploitation of heterosis in crops. ASA-CSSA, Madison, pp 59-67.
18. Ha M, Pang M, Agarwal V, Chen ZJ (2008) Interspecies regulation of microRNAs and their targets. Biochim Biophys Acta 1779: 735-742.
19. Ha M, Lu J, Tian L, Ramachandran V, Kasschau KD, Chapman EJ, Carrington JC, Chen X, 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.
20. He G, Zhu X, Elling AA, Chen L, Wang X, Guo L, Liang M, He H, Zhang H, Chen F, Qi Y, Chen R, Deng XW (2010) Global epigenetic and transcriptional trends among two rice subspecies and their reciprocal hybrids. Plant Cell 22: 17-33.
21. Hoecker N, Keller B, Piepho HP, Hochholdinger F (2006) Manifestation of heterosis during early maize (Zea mays L.) root development. Theor Appl Genet 112: 421-429.
22. Hua JP, Xing YZ, Wu WR, Xu CG, Sun XL, Yu SB, Zhang QF (2003) Single-locus heterotic effects and dominance by dominance interactions can adequately explain the genetic basis of heterosis in an elite rice hybrid. Proc Natl Acad Sci USA 100: 2574-2579.
23. Jiang S, Wells CD, Roach PJ (2011) Starch-binding domain-containing protein 1 (Stbd1) and glycogen metabolism: identification of the Atg8 family interacting motif (AIM) in Stbd1 required for interaction with GABARAPL1. Biochem Biophys Res Commun 413: 420-425.
24. Jones DF (1917) Dominance of linked factors as a means of accounting for heterosis. Genetics 2: 466-479.
25. Jones-Rhoades MW, Bartel DP, Bartel B (2006) MicroRNAs and their regulatory roles in plants. Annu Rev Plant Biol 57: 19-53.
26. Konishi S, Izawa T, Lin SY, Ebana K, Fukuta Y, Sasaki T, Yano M (2006) An SNP caused loss of seed shattering during rice domestication. Science 312: 1392-1396.
27. Lee Y, Kim M, Han J, Yeom KH, Lee S, Baek SH, Kim VN (2004) MicroRNA genes are transcribed by RNA polymerase II. EMBO J 23: 4051-4060.
28. Li JX, Yu SB, Xu CG, Tan YF, Gao YJ, Li XH, Zhang QF, Saghai Maroof MA (2000) Analyzing quantitative trait loci for yield using a vegetatively replicated F2 population from a cross between the parents of an elite rice hybrid. Theor Appl Genet 101: 248-254.
29. Li L, Lu K, Chen Z, Mu T, Hu Z, Li X (2008) Dominance, overdominance and epistasis condition the heterosis in two heterotic rice hybrids. Genetics 180: 1725-1742.
30. Lippman ZB, Zamir D (2007) Heterosis: revisiting the magic. Trends Genet 23: 60-66.
31. -ΔΔCT method. Methods 25: 402-408.
32. Ma Q, Hedden P, Zhang QF (2011) Heterosis in rice seedlings: its relationship to gibberellin content and expression of gibberellin metabolism and signaling genes. Plant Physiol 156: 1905-1920.
33. Meyer RC, Witucka-Wall H, Becher M, Blacha A, Boudichevskaia A, Dörmann P, Fiehn O, Friedel S, von Korff M, Lisec J, Melzer M, Repsilber D, Schmidt R, Scholz M, Selbig J, Willmitzer L, Altmann T (2012) Heterosis manifestation during early Arabidopsis seedling development is characterized by intermediate gene expression and enhanced metabolic activity in the hybrids. Plant J. doi: 10. 1111/j. 1365-313X. 2012. 05021. x.
34. Ng DW, Lu J, Chen ZJ (2012) Big roles for small RNAs in polyploidy, hybrid vigor, and hybrid incompatibility. Curr Opin Plant Biol 15: 154-161.
35. Park W, Li J, Song R, Messing J, Chen X (2002) CARPEL FACTORY, a dicer homolog, and HEN1, a novel protein, act in microRNA metabolism in Arabidopsis thaliana. Curr Biol 12: 1484-1495.
36. Phelps-Durr TL, Thomas J, Vahab P, Timmermans MCP (2005) Maize rough sheath2 and its Arabidopsis orthologue ASYMMETRIC LEAVES1 interact with HIRA, a predicted histone chaperone, to maintain knox gene silencing and determinacy during organogenesis. Plant Cell 17: 2886-2898.
37. Rhoades MW, Reinhart BJ, Lim LP, Burge CB, Bartel B, Bartel DP (2002) Prediction of plant microRNA targets. Cell 110: 513-520.
38. Römisch-Margl L, Spielbauer G, Schützenmeister A, Schwab W, Piepho HP, Genschel U, Gierl A (2010) Heterotic patterns of sugar and amino acid components in developing maize kernels. Theor Appl Genet 120: 369-381.
39. Ru P, Xu L, Ma H, Huang H (2006) Plant fertility defects induced by the enhanced expression of microRNA167. Cell Res 16: 457-465.
40. Ruiz A, Xu X, Carlson M (2011) Roles of two protein phosphatases, Reg1-Glc7 and Sit4, and glycogen synthesis in regulation of SNF1 protein kinase. Proc Natl Acad Sci USA 108: 6349-6354.
41. Schmittgen TD, Jiang J, Liu Q, Yang L (2004) A high-throughput method to monitor the expression of microRNA precursors. Nucleic Acids Res 32: e43.
42. Shi R, Chiang VL (2005) Facile means for quantifying microRNA expression by real-time PCR. Biotechniques 39: 519-525.
43. Shull GH (1908) The composition of a field of maize. Am Breed Assoc Rep 4: 296-301.
44. Stuber CW, Lincoln SE, Wolff DW, Helentjaris T, Lander ES (1992) Identification of genetic factors contributing to heterosis in a hybrid from two elite maize inbred lines using molecular markers. Genetics 132: 823-839.
45. Swanson-Wagner RA, Jia Y, DeCook R, Borsuk LA, Nettleton D, Schnable PS (2006) All possible modes of gene action are observed in a global comparison of gene expression in a maize F1 hybrid and its inbred parents. Proc Natl Acad Sci USA 103: 6805-6810.
46. Swanson-Wagner RA, DeCook R, Jia Y, Bancroft T, Ji T, Zhao X, Nettleton D, Schnable PS (2009) Paternal dominance of trans-eQTL influences gene expression patterns in maize hybrids. Science 326: 1118-1120.
47. Tan YF, Li JX, Yu SB, Xing YZ, Xu CG, Zhang Q (1999) The three important traits for cooking and eating quality of rice grains are controlled by a single locus in an elite rice hybrid, Shanyou 63. Theor Appl Genet 99: 642-648.
48. Wang ZF, Wang JF, Bao YM, Wang FH, Zhang HS (2010) Quantitative trait loci analysis for rice seed vigor during the germination stage. J Zhejiang Univ Sci B 11: 958-964.
49. Xiao J, Li J, Yuan LP, Tanksley SD (1995) Dominance is the major genetic basis of heterosis in rice as revealed by QTL analysis using molecular markers. Genetics 140: 745-754.
50. Yu SB, Li JX, Xu CG, Tan YF, Gao YJ, Li XH, Zhang QF, Saghai Maroof MA (1997) Importance of epistasis as the genetic basis of heterosis in an elite rice hybrid. Proc Natl Acad Sci USA 94: 9226-9231.