|
Abdel-Latif A, Osman G. 2017. Comparison of three genomic DNA extraction methods to obtain high DNA quality from maize. Plant Methods, 13, 1.
Agustí M, Mesejo C, Muñoz‐Fambuena N, Vera‐Sirera F, de Lucas M, Martínez‐Fuentes A, Reig C, Iglesias D J, Primo‐Millo E, Blázquez M A. 2020. Fruit-dependent epigenetic regulation of flowering in Citrus. New Phytologist, 225, 376–384.
Albani M C, Coupland G. 2010. Comparative analysis of flowering in annual and perennial plants. Current Topics in Developmental Biology, 91, 323–348.
Amasino R M, Michaels S D. 2010. The timing of flowering. Plant Physiology, 154, 516–520.
Anders S, Huber W. 2010. Differential expression analysis for sequence count data. Genome Biology, 11, R106.
Andrés F, Coupland G. 2012. The genetic basis of flowering responses to seasonal cues. Nature Reviews Genetics, 13, 627.
Chahtane H, Zhang B, Norberg M. 2018. LEAFY activity is post-transcriptionally regulated by BLADE ON PETIOLE2 and CULLIN3 in Arabidopsis. New Phytologist, 220, 2.
Chen F, Zhang X, Liu X, Zhang L. 2017. Evolutionary analysis of MIKCc-type MADS-box genes in gymnosperms and angiosperms. Frontiers in Plant Science, 8, 895.
Chen X, Qi S, Zhang D, Li Y, An N, Zhao C, Zhao J, Shah K, Han M, Xing L. 2018. Comparative RNA-sequencing-based transcriptome profiling of buds from profusely flowering QA and weakly flowering ‘Nagafu no. 2’ apple varieties reveals novel insights into the regulatory mechanisms underlying floral induction. BMC Plant Biology, 18, 370.
Daccord N, Celton J M, Linsmith G, Becker C, Choisne N, Schijlen E, van de Geest H, Bianco L, Micheletti D, Velasco R, Di Pierro E A, Gouzy J, Rees D J G, Guérif P, Muranty H, Durel C E, Laurens F, Lespinasse Y, Gaillard S, Aubourg S, et al. 2017. High-quality de novo assembly of the apple genome and methylome dynamics of early fruit development. Nature Genetics, 49, 1099–1106.
Davière J M, Wild M, Regnault T, Baumberger N, Eisler H, Genschik P, Achard P. 2014. Class I TCP-DELLA interactions in inflorescence shoot apex determine plant height. Current Biology, 24, 1923–1928.
Djilianov D L, Dobrev P I, Moyankova D P, Vankova R, Georgieva D T, Gajdošová S, Motyka V. 2013. Dynamics of endogenous phytohormones during desiccation and recovery of the resurrection plant species Haberlea rhodopensis. Journal of Plant Growth Regulation, 32, 564–574.
Dobrev P I, Vankova R. 2012. Quantification of abscisic acid, cytokinin, and auxin content in salt-stressed plant tissues. In: Plant Salt Tolerance. Springer, Berlin, Germany. pp. 251–261.
Dorca-Fornell C, Gregis V, Grandi V, Coupland G, Colombo L, Kater MM. 2011. The Arabidopsis SOC1-like genes AGL42, AGL71 and AGL72 promote flowering in the shoot apical and axillary meristems. The Plant Journal, 67, 1006–1017.
Du Z, Zhou X, Ling Y, Zhang Z, Su Z. 2010. agriGO: A GO analysis toolkit for the agricultural community. Nucleic Acids Research, 38, W64–W70.
Huang F, Yuan W Y, Tian S, Zheng Q J, He Y H. 2019. SIN3 LIKE genes mediate long-day induction of flowering but inhibit the floral transition in short days through histone deacetylation in Arabidopsis. The Plant Journal, 100, 101–113.
FAO. 2023. FAOSTAT. [2023-6-1]. http://www.fao.org/faostat
Feng H, Conneely K N, Wu H. 2014. A Bayesian hierarchical model to detect differentially methylated loci from single nucleotide resolution sequencing data. Nucleic Acids Research, 42, e69.
Fernandez D E, Wang C T, Zheng Y, Adamczyk B J, Singhal R, Hall P K, Perry S E. 2014. The MADS-domain factors AGAMOUS-LIKE15 and AGAMOUS-LIKE18, along with SHORT VEGETATIVE PHASE and AGAMOUS-LIKE24, are necessary to block floral gene expression during the vegetative phase. Plant Physiology, 165, 1591–1603.
Gallusci P, Hodgman C, Teyssier E, Seymour G B. 2016. DNA methylation and chromatin regulation during fleshy fruit development and ripening. Frontiers in Plant Science, 7, 807.
González-Grandío E, Pajoro A, Franco-Zorrilla JM, Tarancón C, Cubas P. 2016. Abscisic acid signaling is controlled by a BRANCHED1/HD-ZIP I cascade in Arabidopsis axillary buds. Proceedings of the National Academy of Sciences of the United States of America, 114, 201613199.
González-Grandío E, Poza-Carrion C, Sorzano COS, Cubas P. 2013. BRANCHED1 promotes axillary bud dormancy in response to shade in Arabidopsis. Plant Cell, 25, 834–850.
Haberman A, Ackerman M, Crane O, Kelner JJ, Costes E, Samach A. 2016. Different flowering response to various fruit loads in apple cultivars correlates with degree of transcript reaccumulation of a TFL1-encoding gene. Plant Journal, 87, 161–173.
Han Q, Bartels A, Cheng X, Meyer A, An Y Q C, Hsieh T F, Xiao W. 2019. Epigenetics regulates reproductive development in plants. Plants, 8, 564.
He Y. 2015. Enabling photoperiodic control of flowering by timely chromatin silencing of the florigen gene. Nucleus, 6, 179–182.
Hill K, Wang H, Perry S E. 2008. A transcriptional repression motif in the MADS factor AGL15 is involved in recruitment of histone deacetylase complex components. Plant Journal, 53, 172–185.
Hou X, Zhou J, Liu C, Liu L, Shen L, Yu H. 2014. Nuclear factor Y-mediated H3K27me3 demethylation of the SOC1 locus orchestrates flowering responses of Arabidopsis. Nature Communications, 5, 4601.
Huijser P, Schmid M. 2011. The control of developmental phase transitions in plants. Development, 138, 4117–4129.
Hyun Y, Richter R, Vincent C, Martinez-Gallegos R, Porri A, Coupland G. 2016. Multi-layered regulation of SPL15 and cooperation with SOC1 integrate endogenous flowering pathways at the Arabidopsis shoot meristem. Developmental Cell, 37, 254–266.
Jeong J H, Song H R, Ko J H, Jeong Y M, Kwon Y E, Seol J H, Amasino R M, Noh B, Noh Y S. 2009. Repression of FLOWERING LOCUS T chromatin by functionally redundant histone H3 lysine 4 demethylases in Arabidopsis. PLoS ONE, 4, e8033.
Jung C. 2017. Flowering time regulation: Agrochemical control of flowering. Nature Plants, 3, 17045.
Kanehisa M, Sato Y, Kawashima M, Furumichi M, Tanabe M. 2016. KEGG as a reference resource for gene and protein annotation. Nucleic Acids Research, 44, D457–D462.
Kim J Y, Oh J E, Noh Y S, Noh B. 2015. Epigenetic control of juvenile-to-adult phase transition by the Arabidopsis SAGA-like complex. The Plant Journal, 83, 537–545.
Krueger F, Andrews S R. 2011. Bismark: A flexible aligner and methylation caller for Bisulfite-Seq applications. Bioinformatics, 27, 1571–1572.
Li D, Zhang H, Mou M, Chen Y, Xiang S, Chen L, Yu D. 2019. Arabidopsis class II TCP transcription factors integrate with the FT–FD module to control flowering. Plant Physiology, 181, 97–111.
Li R, Yu C, Li Y, Lam T W, Yiu S M, Kristiansen K, Wang J. 2009. SOAP2: An improved ultrafast tool for short read alignment. Bioinformatics, 25, 1966–1967.
Liu R, How-Kit A, Stammitti L, Teyssier E, Rolin D, Mortain-Bertrand A, Halle S, Liu M, Kong J, Wu C, Degraeve-Guibault C, Chapman N H, Maucourt M, Hodgman T C, Tost J, Bouzayen M, Hong Y, Seymour G B, Giovannoni J J, Gallusci P. 2015. A DEMETER-like DNA demethylase governs tomato fruit ripening. Proceedings of the National Academy of Sciences of the United States of America, 112, 10804–10809.
Lopez-Gonzalez L, Mouriz A, Narro-Diego L, Bustos R, Martinez-Zapater J M, Jarillo J A, Pineiro M. 2014. Chromatin-dependent repression of the Arabidopsis floral integrator genes involves plant specific PHD-containing proteins. Plant Cell, 26, 3922–3938.
Meijón M, Cañal M J, Valledor L, Rodríguez R, Feito I. 2011. Epigenetic and physiological effects of gibberellin inhibitors and chemical pruners on the floral transition of azalea. Physiologia Plantarum, 141, 276–288.
Monniaux M, Mckim S M, Cartolano M, Thévenon E, Parcy F, Tsiantis M, Hay A. 2017. Conservation vs divergence in LEAFY and APETALA1 functions between Arabidopsis thaliana and Cardamine hirsuta. New Phytologist, 216, 549–561.
Mortazavi A, Williams B A, McCue K, Schaeffer L, Wold B. 2008. Mapping and quantifying mammalian transcriptomes by RNA-Seq. Nature Methods, 5, 621–628.
Narsai R, Secco D, Schultz M D, Ecker J R, Lister R, Whelan J. 2017. Dynamic and rapid changes in the transcriptome and epigenome during germination and in developing rice (Oryza sativa) coleoptiles under anoxia and re-oxygenation. The Plant Journal, 89, 805–824.
Ni J, Gao C, Chen M S, Pan B Z, Xu Z F. 2015. Gibberellin promotes shoot branching in the perennial woody plant Jatropha curcas. Plant and Cell Physiology, 56, 1655–1666.
Park Y, Wu H. 2016. Differential methylation analysis for BS-seq data under general experimental design. Bioinformatics, 32, 1–10.
Pastore J J, Limpuangthip A, Yamaguchi N, Wu M F, Sang Y, Han S K, Malaspina L, Chavdaroff N, Yamaguchi A, Wagner D. 2011. LATE MERISTEM IDENTITY2 acts together with LEAFY to activate APETALA1. Development, 138, 3189–3198.
Pazhouhandeh M, Molinier J, Berr A, Genschik P. 2011. MSI4/FVE interacts with CUL4-DDB1 and a PRC2-like complex to control epigenetic regulation of flowering time in Arabidopsis. Proceedings of the National Academy of Sciences of the United States of America, 108, 3430–3435.
Qin Z, Wu J, Geng S, Feng N, Chen F, Kong X, Song G, Chen K, Li A, Mao L, Wu L. 2017. Regulation of FT splicing by an endogenous cue in temperate grasses. Nature Communications, 8, 14320.
Qiu Y, Guan SC, Wen C, Li P, Gao Z, Chen X. 2019. Auxin and cytokinin coordinate the dormancy and outgrowth of axillary bud in strawberry runner. BMC Plant Biology, 19, 528.
van Rongen M, Bennett T, Ticchiarelli F, Leyser O. 2019. Connective auxin transport contributes to strigolactone-mediated shoot branching control independent of the transcription factor BRC1. PLoS Genetics, 15, e1008023.
Rothkegel K, Sánchez E, Montes C, Greve M, Tapia S, Bravo S, Prieto H, Almeida A M. 2017. DNA methylation and small interference RNAs participate in the regulation of MADS-box genes involved in dormancy in sweet cherry (Prunus avium L.). Tree Physiology, 37, 1739–1751.
Sacharowski S P, Gratkowska D M, Sarnowska E A, Kondrak P, Jancewicz I, Porri A, Bucior E, Rolicka A T, Franzen R, Kowalczyk J. 2015. SWP73 subunits of Arabidopsis SWI/SNF chromatin remodeling complexes play distinct roles in leaf and flower development. Plant Cell, 27, 1889–1906.
Sánchez-Taltavull D, Ramachandran P, Lau N, Perkins T J. 2016. Bayesian correlation analysis for sequence count data. PLoS ONE, 11, e0163595.
Seymour G, Poole M, Manning K, King G J. 2008. Genetics and epigenetics of fruit development and ripening. Current Opinion in Plant Biology, 11, 58–63.
Shen J, Zhang Y, Ge D, Wang Z, Song W, Gu R, Che G, Cheng Z, Liu R, Zhang X. 2019. CsBRC1 inhibits axillary bud outgrowth by directly repressing the auxin efflux carrier CsPIN3 in cucumber. Proceedings of the National Academy of Sciences of the United States of America, 116, 17105–17114.
Shen L, Kang Y G G, Liu L, Yu H. 2011. The J-domain protein J3 mediates the integration of flowering signals in Arabidopsis. Plant Cell, 23, 499–514.
Smaczniak C, Immink R G H, Angenent G C, Kaufmann K. 2012. Developmental and evolutionary diversity of plant MADS-domain factors: Insights from recent studies. Development, 139, 3081–3098.
Stes E, Depuydt S, De Keyser A, Matthys C, Audenaert K, Yoneyama K, Werbrouck S, Goormachtig S, Vereecke D. 2015. Strigolactones as an auxiliary hormonal defence mechanism against leafy gall syndrome in Arabidopsis thaliana. Journal of Experimental Botany, 66, 5123–5134.
Waldie T, Leyser O. 2018. Cytokinin targets auxin transport to promote shoot branching. Plant Physiology, 177, 803–818.
Wang B, Smith S M, Li J. 2018. Genetic regulation of shoot architecture. Annual Review of Plant Biology, 69, 437–468.
Wang L, Kong D, Lv Q, Niu G Q, Han T, Zhao X, Meng S, Cheng Q, Guo S, Du J. 2017. Tetrahydrofolate modulates floral transition through epigenetic silencing. Plant Physiology, 174, 1274–1284.
Wang Z, Meng D, Wang A, Li T, Jiang S, Cong P, Li T. 2013. The methylation of the PcMYB10 promoter is associated with green-skinned sport in max red bartlett pear. Plant Physiology, 162, 885–896.
Wu H, Xu T, Feng H, Chen L, Li B, Yao B, Qin Z, Jin P, Conneely K N. 2015. Detection of differentially methylated regions from whole-genome bisulfite sequencing data without replicates. Nucleic Acids Research, 43, e141.
Xing L, Li Y, Qi S, Zhang C, Ma W, Zuo X, Liang J, Gao C, Jia P, Shah K, Zhang D, An N, Zhao C, Han M, Zhao J. 2019a. Comparative RNA-sequencing and DNA methylation analyses of apple (Malus domestica Borkh.) buds with diverse flowering capabilities reveal novel insights into the regulatory mechanisms of flower bud formation. Plant Cell Physiology, 60, 1702–1721.
Xing L, Zhang D, Qi S, Chen X, An N, Li Y, Zhao C, Han M, Zhao J. 2019b. Transcription profiles reveal the regulatory mechanisms of spur bud changes and flower induction in response to shoot bending in apple (Malus domestica Borkh.). Plant Molecular Biology, 99, 45–66.
Xing L, Zhang D, Song X, Weng K, Shen Y, Li Y, Zhao C, Ma J, An N, Han M. 2016a. Genome-wide sequence variation identification and floral-associated trait comparisons based on the re-sequencing of the ‘Nagafu No. 2’ and QA varieties of apple (Malus domestica Borkh.). Frontiers in Plant Science, 7, 908.
Xing L, Zhang D, Zhao C, Li Y, Ma J, An N, Han M. 2016b. Shoot bending promotes flower bud formation by miRNA-mediated regulation in apple (Malus domestica Borkh.). Plant Biotechnology Journal, 14, 749–770.
Xing L B, Zhang D, Li Y M, Shen Y W, Zhao C P, Ma J J, An N, Han M Y. 2015. Transcription profiles reveal sugar and hormone signaling pathways mediating flower induction in apple (Malus domestica Borkh.). Plant and Cell Physiology, 56, 2052–2068.
Xing M Q, Zhang Y J, Zhou S R, Hu W Y, Wu X T, Ye Y J, Wu X X, Xiao Y P, Li X, Xue H W. 2015. Global analysis reveals the crucial roles of DNA methylation during rice seed development. Plant Physiology, 168, 1417–1432.
Xu J, Xu H, Xu Q, Deng X. 2015. Characterization of DNA methylation variations during fruit development and ripening of sweet orange. Plant Molecular Biology Reporter, 33, 1–11.
Xu M, Hu T, Smith M R, Poethig R S. 2016. Epigenetic regulation of vegetative phase change in Arabidopsis. The Plant Cell, 28, 28–41.
Yang W, Pallas B, Durand J B, Martinez S, Han M, Costes E. 2016. The impact of long-term water stress on tree architecture and production is related to changes in transitions between vegetative and reproductive growth in the ‘Granny Smith’ apple cultivar. Tree Physiology, 36, 1369–1381.
Yao T, Park B S, Mao H Z, Seo J S, Ohama N, Li Y, Yu N, Mustafa N F B, Huang C H, Chua N H. 2019. Regulation of flowering time by SPL10/MED25 module in Arabidopsis. New Phytologist, 224, 493–504.
Zhao T, Holmer R, de Bruijn S, Angenent G C, van den Burg H A, Schranz M E. 2017. Phylogenomic synteny network analysis of MADS-box transcription factor genes reveals lineage-specific transpositions, ancient tandem duplications, and deep positional conservation. Plant Cell, 29, 1278–1292.
Zicola J, Liu L Y, Tänzler P, Turck F. 2019. Targeted DNA methylation represses two enhancers of FLOWERING LOCUS T in Arabidopsis thaliana. Nature Plants, 5, 300–307.
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