Understanding the genetic and epigenetic architecture in complex network of rice flowering pathways
详细信息 查看全文
- 作者：Changhui Sun (1)
Dan Chen (1)
Jun Fang (2)
Pingrong Wang (1)
Xiaojian Deng (1)
Chengcai Chu (2) - 关键词：rice ; flowering time ; genetic network ; chromatin modifications ; Arabidopsis ; florigen
- 刊名：Protein & Cell
- 出版年：2014
- 出版时间：December 2014
- 年：2014
- 卷：5
- 期：12
- 页码：889-898
- 全文大小：667 KB
- 参考文献：1. Andres F, Galbraith DW, Talon M, Domingo C (2009) Analysis of / PHOTOPERIOD SENSITIVITY5 sheds light on the role of phytochromes in photoperiodic flowering in rice. Plant Physiol 151:681鈥?90 CrossRef
2. Brambilla V, Fornara F (2013) Molecular control of flowering in response to day length in rice. J Integr Plant Biol 55:410鈥?18 CrossRef
3. Buckler ES, Holland JB, Bradbury PJ, Acharya CB, Brown PJ, Browne C, Ersoz E, Flint-Garcia S, Garcia A, Glaubitz JC, Goodman MM, Harjes C, Guill K, Kroon DE, Larsson S, Lepak NK, Li H, Mitchell SE, Pressoir G, Peiffer JA, Rosas MO, Rocheford TR, Romay MC, Romero S, Salvo S, Sanchez Villeda H, da Silva HS, Sun Q, Tian F, Upadyayula N, Ware D, Yates H, Yu J, Zhang Z, Kresovich S, McMullen MD (2009) The genetic architecture of maize flowering time. Science 325:714鈥?18 CrossRef
4. Cajlachjan MC (1937) Concerning the hormonal nature of plant development processes. Compt Rend Acad Sci URSS 16:227鈥?30
5. Chardon F, Damerval C (2005) Phylogenomic analysis of the PEBP gene family in cereals. J Mol Evol 61:579鈥?90 CrossRef
6. Choi SC, Lee S, Kim S-R, Lee Y-S, Liu C, Cao X, An G (2014) Trithorax group protein OsTrx1 controls flowering time in rice via interaction with Ehd3. Plant Physiol 164(3):1326鈥?337 CrossRef
7. Colasanti J, Yuan Z, Sundaresan V (1998) The indeterminate gene encodes a zinc finger protein and regulates a leaf-generated signal required for the transition to flowering in maize. Cell 93:593鈥?03 CrossRef
8. Colasanti J, Tremblay R, Wong AY, Coneva V, Kozaki A, Mable BK (2006) The maize / INDETERMINATE1 flowering time regulator defines a highly conserved zinc finger protein family in higher plants. BMC Genomics 7:158 CrossRef
9. Corbesier L, Vincent C, Jang S, Fornara F, Fan Q, Searle I, Giakountis A, Farrona S, Gissot L, Turnbull C, Coupland G (2007) FT protein movement contributes to long-distance signaling in floral induction of Arabidopsis. Science 316:1030鈥?033 CrossRef
10. Dai C, Xue HW (2010) Rice / early flowering1, a CKI, phosphorylates DELLA protein SLR1 to negatively regulate gibberellin signalling. EMBO J 29:1916鈥?927 CrossRef
11. Dai X, Ding Y, Tan L, Fu Y, Liu F, Zhu Z, Sun X, Sun X, Gu P, Cai H, Sun C (2012) / LHD1, an allele of / DTH8/ / Ghd8, controls late heading date in common wild rice ( / Oryza rufipogon). J Integr Plant Biol 54:790鈥?99 CrossRef
12. Doi K, Izawa T, Fuse T, Yamanouchi U, Kubo T, Shimatani Z, Yano M, Yoshimura A (2004) / Ehd1, a B-type response regulator in rice, confers short-day promotion of flowering and controls / FT-like gene expression independently of / Hd1. Genes Dev 18:926鈥?36 CrossRef
13. Ebana K, Shibaya T, Wu J, Matsubara K, Kanamori H, Yamane H, Yamanouchi U, Mizubayashi T, Kono I, Shomura A, Ito S, Ando T, Hori K, Matsumoto T, Yano M (2011) Uncovering of major genetic factors generating naturally occurring variation in heading date among Asian rice cultivars. Theor Appl Genet 122:1199鈥?210 CrossRef
14. Fujino K, Yamanouchi U, Yano M (2013) Roles of the / Hd5 gene controlling heading date for adaptation to the northern limits of rice cultivation. Theor Appl Genet 126:611鈥?18 CrossRef
15. Gao H, Zheng XM, Fei G, Chen J, Jin M, Ren Y, Wu W, Zhou K, Sheng P, Zhou F, Jiang L, Wang J, Zhang X, Guo X, Wang JL, Cheng Z, Wu C, Wang H, Wan JM (2013) / Ehd4 encodes a novel and / Oryza-genus-specific regulator of photoperiodic flowering in rice. PLoS Genet 9:e1003281 CrossRef
16. Hayama R, Yokoi S, Tamaki S, Yano M, Shimamoto K (2003) Adaptation of photoperiodic control pathways produces short-day flowering in rice. Nature 422:719鈥?22 CrossRef
17. He Y (2009) Control of the transition to flowering by chromatin modifications. Mol Plant 2:554鈥?64 CrossRef
18. Hori K, Kataoka T, Miura K, Yamaguchi M, Saka N, Nakahara T, Sunohara Y, Ebana K, Yano M (2012) Variation in heading date conceals quantitative trait loci for other traits of importance in breeding selection of rice. Breed Sci 62:223鈥?34 CrossRef
19. Hori K, Ogiso-Tanaka E, Matsubara K, Yamanouchi U, Ebana K, Yano M (2013) / Hd16, a gene for casein kinase I, is involved in the control of rice flowering time by modulating the day-length response. Plant J 76:36鈥?6
20. Ishikawa R, Aoki M, Kurotani K, Yokoi S, Shinomura T, Takano M, Shimamoto K (2011) Phytochrome B regulates / Heading date 1 ( / Hd1)-mediated expression of rice florigen / Hd3a and critical day length in rice. Mol Genet Genomics 285:461鈥?70 CrossRef
21. Itoh H, Izawa T (2013) The coincidence of critical day length recognition for florigen gene expression and floral transition under long-day conditions in rice. Mol Plant 6:635鈥?49 CrossRef
22. Itoh H, Nonoue Y, Yano M, Izawa T (2010) A pair of floral regulators sets critical day length for Hd3a florigen expression in rice. Nat Genet 42:635鈥?38 CrossRef
23. Izawa T (2007) Adaptation of flowering-time by natural and artificial selection in Arabidopsis and rice. J Exp Bot 58:3091鈥?097 CrossRef
24. Izawa T, Oikawa T, Sugiyama N, Tanisaka T, Yano M, Shimamoto K (2002) Phytochrome mediates the external light signal to repress / FT orthologs in photoperiodic flowering of rice. Genes Dev 16:2006鈥?020 CrossRef
25. Kim SL, Lee S, Kim HJ, Nam HG, An G (2007) / OsMADS51 is a short-day flowering promoter that functions upstream of / Ehd1, / OsMADS14, and / Hd3a. Plant Physiol 145:1484鈥?494 CrossRef
26. Kim SK, Yun CH, Lee JH, Jang YH, Park HY, Kim JK (2008) / OsCO3, a / CONSTANS-LIKE gene, controls flowering by negatively regulating the expression of / FT-like genes under SD conditions in rice. Planta 228:355鈥?65 CrossRef
27. Kojima S, Takahashi Y, Kobayashi Y, Monna L, Sasaki T, Araki T, Yano M (2002) / Hd3a, a rice ortholog of the Arabidopsis / FT gene, promotes transition to flowering downstream of / Hd1 under short-day conditions. Plant Cell Physiol 43:1096鈥?105 CrossRef
28. Komiya R, Ikegami A, Tamaki S, Yokoi S, Shimamoto K (2008) / Hd3a and / RFT1 are essential for flowering in rice. Development 135:767鈥?74 CrossRef
29. Komiya R, Yokoi S, Shimamoto K (2009) A gene network for long-day flowering activates / RFT1 encoding a mobile flowering signal in rice. Development 136:3443鈥?450 CrossRef
30. Koo BH, Yoo SC, Park JW, Kwon CT, Lee BD, An G, Zhang Z, Li J, Li Z, Paek NC (2013) Natural variation in / OsPRR37 regulates heading date and contributes to rice cultivation at a wide range of latitudes. Mol Plant 6:1877鈥?888 CrossRef
31. Kwon CT, Yoo SC, Koo BH, Cho SH, Park JW, Zhang Z, Li J, Li Z, Paek NC (2013) Natural variation in / Early flowering1 contributes to early flowering in japonica rice under long days. Plant Cell Environ 37:101鈥?12 CrossRef
32. Lee S, Kim J, Han JJ, Han MJ, An G (2004) Functional analyses of the flowering time gene / OsMADS50, the putative / SUPPRESSOR OF OVEREXPRESSION OF CO 1/ / AGAMOUS-LIKE 20 ( / SOC1/ / AGL20) ortholog in rice. Plant J 38:754鈥?64 CrossRef
33. Lee YS, Jeong DH, Lee DY, Yi J, Ryu CH, Kim SL, Jeong HJ, Choi SC, Jin P, Yang J, Cho LH, Choi H, An G (2010) / OsCOL4 is a constitutive flowering repressor upstream of / Ehd1 and downstream of / OsphyB. Plant J 63:18鈥?0
34. Li D, Yang C, Li X, Gan Q, Zhao X, Zhu L (2009) Functional characterization of rice / OsDof12. Planta 229:1159鈥?169 CrossRef
35. Li W, Han Y, Tao F, Chong K (2011) Knockdown of SAMS genes encoding S-adenosyl-l-methionine synthetases causes methylation alterations of DNAs and histones and leads to late flowering in rice. J Plant Physiol 168:1837鈥?843 CrossRef
36. Lin S, Sasaki T, Yano M (1998) Mapping quantitative trait loci controlling seed dormancy and heading date in rice, / Oryza sativa L., using backcross inbred lines. Theor Appl Genet 96:997鈥?003 CrossRef
37. Lin HX, Yamamoto T, Sasaki T, Yano M (2000) Characterization and detection of epistatic interactions of 3 QTLs, Hd1, Hd2, and Hd3, controlling heading date in rice using nearly isogenic lines. Theor Appl Genet 101:1021鈥?028 CrossRef
38. Lin H, Liang Z-W, Sasaki T, Yano M (2003) Fine mapping and characterization of quantitative trait loci / Hd4 and / Hd5 controlling heading date in rice. Breed Sci 53:51鈥?9 CrossRef
39. Liu C, Lu F, Cui X, Cao X (2010) Histone methylation in higher plants. Annu Rev Plant Biol 61:395鈥?20 CrossRef
40. Liu T, Liu H, Zhang H, Xing Y (2013) Validation and characterization of / Ghd7.1, a major quantitative trait locus with pleiotropic effects on spikelets per panicle, plant height, and heading date in rice ( / Oryza sativa L.). J Integr Plant Biol 55:917鈥?27
41. Matsubara K, Yamanouchi U, Wang ZX, Minobe Y, Izawa T, Yano M (2008) / Ehd2, a rice ortholog of the maize / ID1 gene, promotes flowering by upregulating / Ehd1. Plant Physiol 148:1425鈥?435 CrossRef
42. Matsubara K, Yamanouchi U, Nonoue Y, Sugimoto K, Wang ZX, Minobe Y, Yano M (2011) / Ehd3, encoding a plant homeodomain finger-containing protein, is a critical promoter of rice flowering. Plant J 66:603鈥?12 CrossRef
43. Matsubara K, Ogiso-Tanaka E, Hori K, Ebana K, Ando T, Yano M (2012) Natural variation in / Hd17, a homolog of Arabidopsis / ELF3 that is involved in rice photoperiodic flowering. Plant Cell Physiol 53:709鈥?16 CrossRef
44. Ng DW, Wang T, Chandrasekharan MB, Aramayo R, Kertbundit S, Hall TC (2007) Plant SET domain-containing proteins: structure, function and regulation. Biochim Biophys Acta 1769:316鈥?29 CrossRef
45. Nonoue Y, Fujino K, Hirayama Y, Yamanouchi U, Lin SY, Yano M (2008) Detection of quantitative trait loci controlling extremely early heading in rice. Theor Appl Genet 116:715鈥?22 CrossRef
46. Ogiso E, Takahashi Y, Sasaki T, Yano M, Izawa T (2010) The role of casein kinase II in flowering time regulation has diversified during evolution. Plant Physiol 152:808鈥?20 CrossRef
47. Park SJ, Kim SL, Lee S, Je BI, Piao HL, Park SH, Kim CM, Ryu CH, Park SH, Xuan YH, Colasanti J, An G, Han CD (2008) Rice / Indeterminate 1 ( / OsId1) is necessary for the expression of / Ehd1 ( / Early heading date 1) regardless of photoperiod. Plant J 56:1018鈥?029 CrossRef
48. Peng LT, Shi ZY, Li L, Shen GZ, Zhang JL (2007) Ectopic expression of / OsLFL1 in rice represses / Ehd1 by binding on its promoter. Biochem Biophys Res Commun 360:251鈥?56 CrossRef
49. Peng LT, Shi ZY, Li L, Shen GZ, Zhang JL (2008) Overexpression of transcription factor / OsLFL1 delays flowering time in Oryza sativa. J Plant Physiol 165:876鈥?85 CrossRef
50. Ryu CH, Lee S, Cho LH, Kim SL, Lee YS, Choi SC, Jeong HJ, Yi J, Park SJ, Han CD, An G (2009) / OsMADS50 and / OsMADS56 function antagonistically in regulating long day (LD)-dependent flowering in rice. Plant Cell Environ 32:1412鈥?427 CrossRef
51. Saito H, Ogiso-Tanaka E, Okumoto Y, Yoshitake Y, Izumi H, Yokoo T, Matsubara K, Hori K, Yano M, Inoue H, Tanisaka T (2012) / Ef7 encodes an ELF3-like protein and promotes rice flowering by negatively regulating the floral repressor gene / Ghd7 under both short- and long-day conditions. Plant Cell Physiol 53:717鈥?28 CrossRef
52. Salome PA, Bomblies K, Laitinen RA, Yant L, Mott R, Weigel D (2011) Genetic architecture of flowering-time variation in / Arabidopsis thaliana. Genetics 188:421鈥?33 CrossRef
53. Shibaya T, Nonoue Y, Ono N, Yamanouchi U, Hori K, Yano M (2011) Genetic interactions involved in the inhibition of heading by heading date QTL, / Hd2 in rice under long-day conditions. Theor Appl Genet 123:1133鈥?143 CrossRef
54. Sui P, Shi J, Gao X, Shen WH, Dong A (2012) H3K36 methylation is involved in promoting rice flowering. Mol Plant 6:975鈥?77 CrossRef
55. Sun C, Fang J, Zhao T, Xu B, Zhang F, Liu L, Tang J, Zhang G, Deng X, Chen F, Qian Q, Cao X, Chu C (2012) The histone methyltransferase / SDG724 mediates H3K36me2/3 deposition at / MADS50 and / RFT1 and promotes flowering in rice. Plant Cell 24:3235鈥?247 CrossRef
56. Takahashi Y, Shimamoto K (2011) / Heading date 1 ( / Hd1), an ortholog of Arabidopsis / CONSTANS, is a possible target of human selection during domestication to diversify flowering times of cultivated rice. Genes Genet Syst 86:175鈥?82 CrossRef
57. Takahashi Y, Shomura A, Sasaki T, Yano M (2001) / Hd6, a rice quantitative trait locus involved in photoperiod sensitivity, encodes the alpha subunit of protein kinase CK2. Proc Natl Acad Sci USA 98:7922鈥?927 CrossRef
58. Takahashi Y, Teshima KM, Yokoi S, Innan H, Shimamoto K (2009) Variations in Hd1 proteins, / Hd3a promoters, and / Ehd1 expression levels contribute to diversity of flowering time in cultivated rice. Proc Natl Acad Sci USA 106:4555鈥?560 CrossRef
59. Takimoto A, Ikeda K (1961) Effect of twilight on photoperiodic induction in some short day plants. Plant Cell Physiol 2:213鈥?29
60. Tamaki S, Matsuo S, Wong HL, Yokoi S, Shimamoto K (2007) Hd3a protein is a mobile flowering signal in rice. Science 316:1033鈥?036 CrossRef
61. Tsuji H, Taoka K, Shimamoto K (2011) Regulation of flowering in rice: two florigen genes, a complex gene network, and natural variation. Curr Opin Plant Biol 14:45鈥?2 CrossRef
62. Tsuji H, Taoka K, Shimamoto K (2013) Florigen in rice: complex gene network for florigen transcription, florigen activation complex, and multiple functions. Curr Opin Plant Biol 16:228鈥?35 CrossRef
63. Wang J, Hu J, Qian Q, Xue HW (2012) LC2 and OsVIL2 promote rice flowering by photoperoid-induced epigenetic silencing of / OsLF. Mol Plant 6:514鈥?27 CrossRef
64. Wei X, Xu J, Guo H, Jiang L, Chen S, Yu C, Zhou Z, Hu P, Zhai H, Wan J (2010) / DTH8 suppresses flowering in rice, influencing plant height and yield potential simultaneously. Plant Physiol 153:1747鈥?758 CrossRef
65. Wu C, You C, Li C, Long T, Chen G, Byrne ME, Zhang Q (2008) / RID1, encoding a Cys2/His2-type zinc finger transcription factor, acts as a master switch from vegetative to floral development in rice. Proc Natl Acad Sci USA 105:12915鈥?2920 CrossRef
66. Wu W, Zheng XM, Lu G, Zhong Z, Gao H, Chen L, Wu C, Wang HJ, Wang Q, Zhou K, Wang JL, Wu F, Zhang X, Guo X, Cheng Z, Lei C, Lin Q, Jiang L, Wang H, Ge S, Wan J (2013) Association of functional nucleotide polymorphisms at / DTH2 with the northward expansion of rice cultivation in Asia. Proc Natl Acad Sci USA 110:2775鈥?780 CrossRef
67. Xu L, Zhao Z, Dong A, Soubigou-Taconnat L, Renou JP, Steinmetz A, Shen WH (2008) Di- and tri- but not monomethylation on histone H3 lysine 36 marks active transcription of genes involved in flowering time regulation and other processes in / Arabidopsis thaliana. Mol Cell Biol 28:1348鈥?360 CrossRef
68. Xue W, Xing Y, Weng X, Zhao Y, Tang W, Wang L, Zhou H, Yu S, Xu C, Li X, Zhang Q (2008) Natural variation in / Ghd7 is an important regulator of heading date and yield potential in rice. Nat Genet 40:761鈥?67 CrossRef
69. Yamamoto T, Lin H, Sasaki T, Yano M (2000) Identification of heading date quantitative trait locus / Hd6 and characterization of its epistatic interactions with / Hd2 in rice using advanced backcross progeny. Genetics 154:885鈥?91
70. Yan WH, Wang P, Chen HX, Zhou HJ, Li QP, Wang CR, Ding ZH, Zhang YS, Yu SB, Xing YZ, Zhang QF (2011) A major QTL, / Ghd8, plays pleiotropic roles in regulating grain productivity, plant height, and heading date in rice. Mol Plant 4:319鈥?30 CrossRef
71. Yan W, Liu H, Zhou X, Li Q, Zhang J, Lu L, Liu T, Zhang C, Zhang Z, Shen G, Yao W, Chen H, Yu S, Xie W, Xing Y (2013) Natural variation in Ghd7.1 plays an important role in grain yield and adaptation in rice. Cell Res 23:969鈥?71 CrossRef
72. Yang J, Lee S, Hang R, Kim SR, Lee YS, Cao X, Amasino R, An G (2012) OsVIL2 functions with PRC2 to induce flowering by repressing / OsLFL1 in rice. Plant J 73:566鈥?78 CrossRef
73. Yang Y, Peng Q, Chen GX, Li XH, Wu CY (2013) / OsELF3 is involved in circadian clock regulation for promoting flowering under long-day conditions in rice. Mol Plant 6:202鈥?15 CrossRef
74. Yano M, Harushima Y, Nagamura Y, Kurata N, Minobe Y, Sasaki T (1997) Identification of quantitative trait loci controlling heading date in rice using a high-density linkage map. Theor Appl Genet 95:1025鈥?032 CrossRef
75. Yano M, Katayose Y, Ashikari M, Yamanouchi U, Monna L, Fuse T, Baba T, Yamamoto K, Umehara Y, Nagamura Y, Sasaki T (2000) / Hd1, a major photoperiod sensitivity quantitative trait locus in rice, is closely related to the Arabidopsis flowering time gene / CONSTANS. Plant Cell 12:2473鈥?484 CrossRef
76. Zhao Z, Yu Y, Meyer D, Wu C, Shen WH (2005) Prevention of early flowering by expression of / FLOWERING LOCUS C requires methylation of histone H3 K36. Nat Cell Biol 7:1256鈥?260 CrossRef
77. Zhao XL, Shi ZY, Peng LT, Shen GZ, Zhang JL (2011) An atypical HLH protein OsLF in rice regulates flowering time and interacts with OsPIL13 and OsPIL15. Nat Biotechnol 28:788鈥?97
78. Zhao J, Huang X, Ouyang X, Chen W, Du A, Zhu L, Wang S, Deng XW, Li S (2012) / OsELF3-1, an ortholog of / Arabidopsis early flowering 3, regulates rice circadian rhythm and photoperiodic flowering. PLoS ONE 7:e43705 CrossRef - 作者单位：Changhui Sun (1)
Dan Chen (1)
Jun Fang (2)
Pingrong Wang (1)
Xiaojian Deng (1)
Chengcai Chu (2)
1. Rice Research Institute, Sichuan Agricultural University, Chengdu, 611130, China
2. State Key Laboratory of Plant Genomics and Center for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China - ISSN：1674-8018
文摘