甘蓝型油菜开花相关基因的鉴定及进化与表达分析
来源： 时间：2025-09-10 23:51
[1] Srikanth A, Schmid M . Regulation of flowering time: all roads lead to Rome. Cell Mol Life Sci, 2011,68:2013-2037.
doi: 10.1007/s00018-011-0673-y[2] Koornneef M, Alonso B C, Peeters A J M, Soppe W . Genetic control of flowering time in Arabidopsis. Annu Rev Plant Physiol Plant Mol Biol, 1998,49:345-370.
doi: 10.1146/annurev.arplant.49.1.345[3] Bouche F, Lobet G, Tocquin P, Perilleux C . FLOR-ID: an interactive database of flowering-time gene networks in Arabidopsis thaliana. Nucl Acids Res, 2016,44:1167-1171.[4] Blumel M, Dally N, Jung C . Flowering time regulation in crops-what did we learn from Arabidopsis?. Curr Opin Biotechnol, 2015,32:121-129.
doi: 10.1016/j.copbio.2014.11.023[5] Fornara F, de Montaigu A, Coupland G . SnapShot: control of flowering in Arabidopsis. Cell, 2010,141:550-550.
doi: 10.1016/j.cell.2010.04.024[6] Peng F Y, Hu Z, Yang R C . Genome-wide comparative analysis of flowering-related genes in Arabidopsis, wheat, and barley. Int J Plant Genomics, 2015,15:1-17.[7] Raman H, Raman R, Coombes N, Song J, Prangnell R, Bandaranayake C, Tahira R, Sundaramoorthi V, Killian A, Meng J, Dennis E S, Balasubramanian S . Genome-wide association analyses reveal complex genetic architecture underlying natural variation for flowering time in canola. Plant Cell Environ, 2016,39:1228-1239.
doi: 10.1111/pce.12644[8] Xu L, Hu K, Zhang Z, Guan C, Chen S, Hua W, Li J, Wen J, Yi B, Shen J, Ma C, Tu J, Fu T . Genome-wide association study reveals the genetic architecture of flowering time in rapeseed (Brassica napus L.). DNA Res, 2016,23:43-52.[9] Wang J, Qiu Y, Cheng F, Chen X, Zhang X, Wang H, Song J, Duan M, Yang H, Li X . Genome-wide identification, characterization, and evolutionary analysis of flowering genes in radish (Raphanus sativus L.). BMC Genomics, 2017,18:981, doi: 10.1186/s12864-017-4377-z.[10] Yang Z . PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol, 2007,24:1586-1591.
doi: 10.1093/molbev/msm088[11] Liang Y, Wan N, Cheng Z, Mo Y, Liu B, Liu H, Raboanatahiry N, Yin Y, Li M . Whole-genome identification and expression pattern of the vicinal oxygen chelate family in rapeseed (Brassica napus L.). Front Plant Sci, 2017,8:745, doi: 10.3389/fpls.2017.00745.[12] Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley D R, Pimentel H, Salzberg S L, Rinn J L, Pachter L . Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc, 2012,7:562-578.
doi: 10.1038/nprot.2012.016[13] Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg S L . TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol, 2013,14:R36.
doi: 10.1186/gb-2013-14-4-r36[14] Song Y H, Ito S, Imaizumi T . Flowering time regulation: photoperiod- and temperature-sensing in leaves. Trends Plant Sci, 2013,18:575-583.
doi: 10.1016/j.tplants.2013.05.003[15] Wenkel S, Turck F, Singer K, Gissot L, Le Gourrierec J, Samach A, Coupland G . CONSTANS and the CCAAT box binding complex share a functionally important domain and interact to regulate flowering of Arabidopsis. Plant Cell, 2006,18:2971-2984.
doi: 10.1105/tpc.106.043299[16] Dong M A, Farre E M, Thomashow M F . Circadian clock-associated 1 and late elongated hypocotyl regulate expression of the C-repeat binding factor (CBF) pathway in Arabidopsis. Proc Natl Acad Sci USA, 2011,108:7241-7246.
doi: 10.1073/pnas.1103741108[17] Sawa M, Kay S A . GIGANTEA directly activates flowering locus T in Arabidopsis thaliana. Proc Natl Acad Sci USA, 2011,108:11698-11703.[18] Nagel D H, Doherty C J, Pruneda P J L, Schmitz R J, Ecker J R, Kay S A . Genome-wide identification of CCA1 targets uncovers an expanded clock network in Arabidopsis. Proc Natl Acad Sci USA, 2015,112:4802-4810.
doi: 10.1073/pnas.1513609112[19] Baudry A, Ito S, Song Y H, Strait A A, Kiba T, Lu S, Henriques R, Pruneda P J L, Chua N H, Tobin E M, Kay S A, Imaizumi T . F-box proteins FKF1 and LKP2 act in concert with ZEITLUPE to control Arabidopsis clock progression. Plant Cell, 2010,22:606-622.
doi: 10.1105/tpc.109.072843[20] Lou P, Wu J, Cheng F, Cressman L G, Wang X , McClung C R. Preferential retention of circadian clock genes during diploidization following whole genome triplication in Brassica rapa. Plant Cell, 2012,24:2415-2426.[21] Johanson U, West J, Lister C, Michaels S, Amasino R, Dean C . Molecular analysis of FRIGIDA, a major determinant of natural variation in Arabidopsis flowering time. Science, 2000,290:344-347.
doi: 10.1126/science.290.5490.344[22] Noh B, Lee S H, Kim H J, Yi G, Shin E A, Lee M, Jung K J, Doyle M R, Amasino R M, Noh Y S . Divergent roles of a pair of homologous jumonji/zinc-finger-class transcription factor proteins in the regulation of Arabidopsis flowering time. Plant Cell, 2004,16:2601-2613.
doi: 10.1105/tpc.104.025353[23] Simpson G G . The autonomous pathway: epigenetic and post- transcriptional gene regulation in the control of Arabidopsis flowering time. Curr Opin Plant Biol, 2004,7:570-574.
doi: 10.1016/j.pbi.2004.07.002[24] Parcy F . Flowering: a time for integration. Int J Dev Biol, 2005,49:585-593.
doi: 10.1387/ijdb.041930fp[25] Kim S, Soltis P S, Wall K, Soltis D E . Phylogeny and domain evolution in the APETALA2-like gene family. Mol Biol Evol, 2006,23:107-120.
doi: 10.1093/molbev/msj014[26] Mitchum M G, Yamaguchi S, Hanada A, Kuwahara A, Yoshioka Y, Kato T, Tabata S, Kamiya Y, Sun T P . Distinct and overlapping roles of two gibberellin 3-oxidases in Arabidopsis development. Plant J, 2006,45:804-818.
doi: 10.1111/tpj.2006.45.issue-5[27] Ariizumi T, Murase K, Sun T P, Steber C M . Proteolysis- independent downregulation of DELLA repression in Arabidopsis by the gibberellin receptor GIBBERELLIN INSENSITIVE DWARF1. Plant Cell, 2008,20:2447-2459.
doi: 10.1105/tpc.108.058487[28] Achard P, Vriezen W H, Van D S D, Harberd N P . Ethylene regulates arabidopsis development via the modulation of DELLA protein growth repressor function. Plant Cell, 2003,15:2816-2825.
doi: 10.1105/tpc.015685[29] Samach A, Wigge P A . Ambient temperature perception in plants. Curr Opin Plant Biol, 2005,8:483-486.
doi: 10.1016/j.pbi.2005.07.011[30] Thines B C, Youn Y, Duarte M I, Harmon F G . The time of day effects of warm temperature on flowering time involve PIF4 and PIF5. J Exp Bot, 2014,65:1141-1151.
doi: 10.1093/jxb/ert487[31] Lee J H, Yoo S J, Park S H, Hwang I, Lee J S, Ahn J H . Role of SVP in the control of flowering time by ambient temperature in Arabidopsis. Genes Dev, 2007,21:397-402.
doi: 10.1101/gad.1518407[32] Yan Y, Shen L, Chen Y, Bao S, Thong Z, Yu H . A MYB-domain protein EFM mediates flowering responses to environmental cues in Arabidopsis. Dev Cell, 2014,30:437-448.
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doi: 10.1111/tpj.2011.65.issue-3[37] Jung J H, Seo Y H, Seo P J, Reyes J L, Yun J, Chua N H, Park C M . The GIGANTEA-regulated microRNA172 mediates photoperiodic flowering independent of CONSTANS in Arabidopsis. Plant Cell, 2007,19:2736-2748.
doi: 10.1105/tpc.107.054528[38] Mathieu J, Yant L J, Murdter F, Kuttner F, Schmid M . Repression of flowering by the miR172 target SMZ. PLoS Biol, 2009,7:e1000148.
doi: 10.1371/journal.pbio.1000148[39] 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.
doi: 10.1016/j.cell.2009.06.014[40] Matsoukas I G, Massiah A J, Thomas B . Starch metabolism and antiflorigenic signals modulate the juvenile-to-adult phase transition in Arabidopsis. Plant Cell Environ, 2013,36:1802-1811.
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doi: 10.1016/j.devcel.2009.03.011
doi: 10.1007/s00018-011-0673-y[2] Koornneef M, Alonso B C, Peeters A J M, Soppe W . Genetic control of flowering time in Arabidopsis. Annu Rev Plant Physiol Plant Mol Biol, 1998,49:345-370.
doi: 10.1146/annurev.arplant.49.1.345[3] Bouche F, Lobet G, Tocquin P, Perilleux C . FLOR-ID: an interactive database of flowering-time gene networks in Arabidopsis thaliana. Nucl Acids Res, 2016,44:1167-1171.[4] Blumel M, Dally N, Jung C . Flowering time regulation in crops-what did we learn from Arabidopsis?. Curr Opin Biotechnol, 2015,32:121-129.
doi: 10.1016/j.copbio.2014.11.023[5] Fornara F, de Montaigu A, Coupland G . SnapShot: control of flowering in Arabidopsis. Cell, 2010,141:550-550.
doi: 10.1016/j.cell.2010.04.024[6] Peng F Y, Hu Z, Yang R C . Genome-wide comparative analysis of flowering-related genes in Arabidopsis, wheat, and barley. Int J Plant Genomics, 2015,15:1-17.[7] Raman H, Raman R, Coombes N, Song J, Prangnell R, Bandaranayake C, Tahira R, Sundaramoorthi V, Killian A, Meng J, Dennis E S, Balasubramanian S . Genome-wide association analyses reveal complex genetic architecture underlying natural variation for flowering time in canola. Plant Cell Environ, 2016,39:1228-1239.
doi: 10.1111/pce.12644[8] Xu L, Hu K, Zhang Z, Guan C, Chen S, Hua W, Li J, Wen J, Yi B, Shen J, Ma C, Tu J, Fu T . Genome-wide association study reveals the genetic architecture of flowering time in rapeseed (Brassica napus L.). DNA Res, 2016,23:43-52.[9] Wang J, Qiu Y, Cheng F, Chen X, Zhang X, Wang H, Song J, Duan M, Yang H, Li X . Genome-wide identification, characterization, and evolutionary analysis of flowering genes in radish (Raphanus sativus L.). BMC Genomics, 2017,18:981, doi: 10.1186/s12864-017-4377-z.[10] Yang Z . PAML 4: phylogenetic analysis by maximum likelihood. Mol Biol Evol, 2007,24:1586-1591.
doi: 10.1093/molbev/msm088[11] Liang Y, Wan N, Cheng Z, Mo Y, Liu B, Liu H, Raboanatahiry N, Yin Y, Li M . Whole-genome identification and expression pattern of the vicinal oxygen chelate family in rapeseed (Brassica napus L.). Front Plant Sci, 2017,8:745, doi: 10.3389/fpls.2017.00745.[12] Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley D R, Pimentel H, Salzberg S L, Rinn J L, Pachter L . Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nat Protoc, 2012,7:562-578.
doi: 10.1038/nprot.2012.016[13] Kim D, Pertea G, Trapnell C, Pimentel H, Kelley R, Salzberg S L . TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions. Genome Biol, 2013,14:R36.
doi: 10.1186/gb-2013-14-4-r36[14] Song Y H, Ito S, Imaizumi T . Flowering time regulation: photoperiod- and temperature-sensing in leaves. Trends Plant Sci, 2013,18:575-583.
doi: 10.1016/j.tplants.2013.05.003[15] Wenkel S, Turck F, Singer K, Gissot L, Le Gourrierec J, Samach A, Coupland G . CONSTANS and the CCAAT box binding complex share a functionally important domain and interact to regulate flowering of Arabidopsis. Plant Cell, 2006,18:2971-2984.
doi: 10.1105/tpc.106.043299[16] Dong M A, Farre E M, Thomashow M F . Circadian clock-associated 1 and late elongated hypocotyl regulate expression of the C-repeat binding factor (CBF) pathway in Arabidopsis. Proc Natl Acad Sci USA, 2011,108:7241-7246.
doi: 10.1073/pnas.1103741108[17] Sawa M, Kay S A . GIGANTEA directly activates flowering locus T in Arabidopsis thaliana. Proc Natl Acad Sci USA, 2011,108:11698-11703.[18] Nagel D H, Doherty C J, Pruneda P J L, Schmitz R J, Ecker J R, Kay S A . Genome-wide identification of CCA1 targets uncovers an expanded clock network in Arabidopsis. Proc Natl Acad Sci USA, 2015,112:4802-4810.
doi: 10.1073/pnas.1513609112[19] Baudry A, Ito S, Song Y H, Strait A A, Kiba T, Lu S, Henriques R, Pruneda P J L, Chua N H, Tobin E M, Kay S A, Imaizumi T . F-box proteins FKF1 and LKP2 act in concert with ZEITLUPE to control Arabidopsis clock progression. Plant Cell, 2010,22:606-622.
doi: 10.1105/tpc.109.072843[20] Lou P, Wu J, Cheng F, Cressman L G, Wang X , McClung C R. Preferential retention of circadian clock genes during diploidization following whole genome triplication in Brassica rapa. Plant Cell, 2012,24:2415-2426.[21] Johanson U, West J, Lister C, Michaels S, Amasino R, Dean C . Molecular analysis of FRIGIDA, a major determinant of natural variation in Arabidopsis flowering time. Science, 2000,290:344-347.
doi: 10.1126/science.290.5490.344[22] Noh B, Lee S H, Kim H J, Yi G, Shin E A, Lee M, Jung K J, Doyle M R, Amasino R M, Noh Y S . Divergent roles of a pair of homologous jumonji/zinc-finger-class transcription factor proteins in the regulation of Arabidopsis flowering time. Plant Cell, 2004,16:2601-2613.
doi: 10.1105/tpc.104.025353[23] Simpson G G . The autonomous pathway: epigenetic and post- transcriptional gene regulation in the control of Arabidopsis flowering time. Curr Opin Plant Biol, 2004,7:570-574.
doi: 10.1016/j.pbi.2004.07.002[24] Parcy F . Flowering: a time for integration. Int J Dev Biol, 2005,49:585-593.
doi: 10.1387/ijdb.041930fp[25] Kim S, Soltis P S, Wall K, Soltis D E . Phylogeny and domain evolution in the APETALA2-like gene family. Mol Biol Evol, 2006,23:107-120.
doi: 10.1093/molbev/msj014[26] Mitchum M G, Yamaguchi S, Hanada A, Kuwahara A, Yoshioka Y, Kato T, Tabata S, Kamiya Y, Sun T P . Distinct and overlapping roles of two gibberellin 3-oxidases in Arabidopsis development. Plant J, 2006,45:804-818.
doi: 10.1111/tpj.2006.45.issue-5[27] Ariizumi T, Murase K, Sun T P, Steber C M . Proteolysis- independent downregulation of DELLA repression in Arabidopsis by the gibberellin receptor GIBBERELLIN INSENSITIVE DWARF1. Plant Cell, 2008,20:2447-2459.
doi: 10.1105/tpc.108.058487[28] Achard P, Vriezen W H, Van D S D, Harberd N P . Ethylene regulates arabidopsis development via the modulation of DELLA protein growth repressor function. Plant Cell, 2003,15:2816-2825.
doi: 10.1105/tpc.015685[29] Samach A, Wigge P A . Ambient temperature perception in plants. Curr Opin Plant Biol, 2005,8:483-486.
doi: 10.1016/j.pbi.2005.07.011[30] Thines B C, Youn Y, Duarte M I, Harmon F G . The time of day effects of warm temperature on flowering time involve PIF4 and PIF5. J Exp Bot, 2014,65:1141-1151.
doi: 10.1093/jxb/ert487[31] Lee J H, Yoo S J, Park S H, Hwang I, Lee J S, Ahn J H . Role of SVP in the control of flowering time by ambient temperature in Arabidopsis. Genes Dev, 2007,21:397-402.
doi: 10.1101/gad.1518407[32] Yan Y, Shen L, Chen Y, Bao S, Thong Z, Yu H . A MYB-domain protein EFM mediates flowering responses to environmental cues in Arabidopsis. Dev Cell, 2014,30:437-448.
doi: 10.1016/j.devcel.2014.07.004[33] Paul M J, Primavesi L F, Jhurreea D, Zhang Y . Trehalose metabolism and signaling. Annu Rev Plant Biol, 2008,59:417-441.
doi: 10.1146/annurev.arplant.59.032607.092945[34] Dalchau N, Baek S J, Briggs H M, Robertson F C, Dodd A N, Gardner M J, Stancombe M A, Haydon M J, Stan G B, Goncalves J M, Webb A A . The circadian oscillator gene GIGANTEA mediates a long-term response of the Arabidopsis thaliana circadian clock to sucrose. Proc Natl Acad Sci USA, 2011,108:5104-5109.[35] Wahl V, Ponnu J, Schlereth A, Arrivault S, Langenecker T, Franke A, Feil R, Lunn J E, Stitt M, Schmid M . Regulation of flowering by trehalose-6-phosphate signaling in Arabidopsis thaliana. Science, 2013,339:704-707.[36] Seo P J, Ryu J, Kang S K, Park C M . Modulation of sugar metabolism by an INDETERMINATE DOMAIN transcription factor contributes to photoperiodic flowering in Arabidopsis. Plant J, 2011,65:418-429.
doi: 10.1111/tpj.2011.65.issue-3[37] Jung J H, Seo Y H, Seo P J, Reyes J L, Yun J, Chua N H, Park C M . The GIGANTEA-regulated microRNA172 mediates photoperiodic flowering independent of CONSTANS in Arabidopsis. Plant Cell, 2007,19:2736-2748.
doi: 10.1105/tpc.107.054528[38] Mathieu J, Yant L J, Murdter F, Kuttner F, Schmid M . Repression of flowering by the miR172 target SMZ. PLoS Biol, 2009,7:e1000148.
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