Fruit-dependent epigenetic regulation of flowering in Citrus

[EN] In many perennial plants, seasonal flowering is primarily controlled by environmental conditions, but in certain polycarpic plants, environmental signals are locally gated by the presence of developing fruits initiated in the previous season through an unknown mechanism. Polycarpy is defined as the ability of plants to undergo several rounds of reproduction during their lifetime, alternating vegetative and reproductive meristems in the same individual. To understand how fruits regulate flowering in polycarpic plants, we focused on alternate bearing in Citrus trees that had been experimentally established as fully flowering or nonflowering. We found that the presence of the fruit causes epigenetic changes correlating with the induction of the CcMADS19 floral repressor, which prevents the activation of the floral promoter CiFT2 even in the presence of the floral inductive signals. By contrast, newly emerging shoots display an opposite epigenetic scenario associated with CcMADS19 repression, thereby allowing the activation of CiFT2 the following cold season.We thank Francisco Madueno (IBMCP-UPV) for useful comments on the manuscript. The work described in this paper was partially supported by grants BFU2016-80621-P (to MAB) and UNIPA C-XXVI, Italy (to NM-F). We also acknowledge financial support by the Spanish Ministry of Economy and Competitiveness through grant nos RTA2009-00147-CO2 and RTA2013-00024-CO2 (to MA, CM, CR and AM-F).Agustí Fonfría, M.; Mesejo Conejos, C.; Muñoz-Fambuena, N.; Vera Sirera, FJ.; De Lucas, M.; Martinez Fuentes, A.; Reig Valor, C.... (2020). Fruit-dependent epigenetic regulation of flowering in Citrus. New Phytologist. 225(1):376-384. https://doi.org/10.1111/nph.160443763842251Albani, M. C., & Coupland, G. (2010). Comparative Analysis of Flowering in Annual and Perennial Plants. Plant Development, 323-348. doi:10.1016/s0070-2153(10)91011-9Andrés, F., & Coupland, G. (2012). The genetic basis of flowering responses to seasonal cues. Nature Reviews Genetics, 13(9), 627-639. doi:10.1038/nrg3291Balanzà, V., Martínez-Fernández, I., Sato, S., Yanofsky, M. F., Kaufmann, K., Angenent, G. C., … Ferrándiz, C. (2018). Genetic control of meristem arrest and life span in Arabidopsis by a FRUITFULL-APETALA2 pathway. Nature Communications, 9(1). doi:10.1038/s41467-018-03067-5Bergonzi, S., Albani, M. C., Loren van Themaat, E. V., Nordström, K. J. V., Wang, R., Schneeberger, K., … Coupland, G. (2013). Mechanisms of Age-Dependent Response to Winter Temperature in Perennial Flowering of Arabis alpina. Science, 340(6136), 1094-1097. doi:10.1126/science.1234116Berry, S., & Dean, C. (2015). Environmental perception and epigenetic memory: mechanistic insight throughFLC. The Plant Journal, 83(1), 133-148. doi:10.1111/tpj.12869Blázquez, M. A., Ahn, J. H., & Weigel, D. (2003). A thermosensory pathway controlling flowering time in Arabidopsis thaliana. Nature Genetics, 33(2), 168-171. doi:10.1038/ng1085Bratzel, F., & Turck, F. (2015). Molecular memories in the regulation of seasonal flowering: from competence to cessation. Genome Biology, 16(1). doi:10.1186/s13059-015-0770-6Chang, S., & Pikaard, C. S. (2005). Transcript Profiling in Arabidopsis Reveals Complex Responses to Global Inhibition of DNA Methylation and Histone Deacetylation*[boxs]. Journal of Biological Chemistry, 280(1), 796-804. doi:10.1074/jbc.m409053200Charnov, E. L., & Schaffer, W. M. (1973). Life-History Consequences of Natural Selection: Cole’s Result Revisited. The American Naturalist, 107(958), 791-793. doi:10.1086/282877Chica, E. J., & Albrigo, L. G. (2013). Expression of Flower Promoting Genes in Sweet Orange during Floral Inductive Water Deficits. Journal of the American Society for Horticultural Science, 138(2), 88-94. doi:10.21273/jashs.138.2.88Clough, S. J., & Bent, A. F. (1998). Floral dip: a simplified method forAgrobacterium-mediated transformation ofArabidopsis thaliana. The Plant Journal, 16(6), 735-743. doi:10.1046/j.1365-313x.1998.00343.xCole, L. C. (1954). The Population Consequences of Life History Phenomena. The Quarterly Review of Biology, 29(2), 103-137. doi:10.1086/400074Deng, W., Ying, H., Helliwell, C. A., Taylor, J. M., Peacock, W. J., & Dennis, E. S. (2011). FLOWERING LOCUS C (FLC) regulates development pathways throughout the life cycle of Arabidopsis. Proceedings of the National Academy of Sciences, 108(16), 6680-6685. doi:10.1073/pnas.1103175108Du, J., Johnson, L. M., Jacobsen, S. E., & Patel, D. J. (2015). DNA methylation pathways and their crosstalk with histone methylation. Nature Reviews Molecular Cell Biology, 16(9), 519-532. doi:10.1038/nrm4043Earley, K. W., Haag, J. R., Pontes, O., Opper, K., Juehne, T., Song, K., & Pikaard, C. S. (2006). Gateway-compatible vectors for plant functional genomics and proteomics. The Plant Journal, 45(4), 616-629. doi:10.1111/j.1365-313x.2005.02617.xJean Finnegan, E., Kovac, K. A., Jaligot, E., Sheldon, C. C., James Peacock, W., & Dennis, E. S. (2005). The downregulation of FLOWERING LOCUS C (FLC) expression in plants with low levels of DNA methylation and by vernalization occurs by distinct mechanisms. The Plant Journal, 44(3), 420-432. doi:10.1111/j.1365-313x.2005.02541.xFinnegan, E. J., & Dennis, E. S. (2007). Vernalization-Induced Trimethylation of Histone H3 Lysine 27 at FLC Is Not Maintained in Mitotically Quiescent Cells. Current Biology, 17(22), 1978-1983. doi:10.1016/j.cub.2007.10.026Forment, J., Gadea, J., Huerta, L., Abizanda, L., Agusti, J., Alamar, S., … Beltran, J. P. (2005). Development of a citrus genome-wide EST collection and cDNA microarray as resources for genomic studies. Plant Molecular Biology, 57(3), 375-391. doi:10.1007/s11103-004-7926-1Gramzow, L., & Theißen, G. (2015). Phylogenomics reveals surprising sets of essential and dispensable clades of MIKCc-group MADS-box genes in flowering plants. Journal of Experimental Zoology Part B: Molecular and Developmental Evolution, 324(4), 353-362. doi:10.1002/jez.b.22598Hartmann, U., Hohmann, S., Nettesheim, K., Wisman, E., Saedler, H., & Huijser, P. (2000). Molecular cloning of SVP: a negative regulator of the floral transition in Arabidopsis. The Plant Journal, 21(4), 351-360. doi:10.1046/j.1365-313x.2000.00682.xHou, X.-J., Liu, S.-R., Khan, M. R. G., Hu, C.-G., & Zhang, J.-Z. (2013). Genome-Wide Identification, Classification, Expression Profiling, and SSR Marker Development of the MADS-Box Gene Family in Citrus. Plant Molecular Biology Reporter, 32(1), 28-41. doi:10.1007/s11105-013-0597-9Jia, H., & Wang, N. (2014). Targeted Genome Editing of Sweet Orange Using Cas9/sgRNA. PLoS ONE, 9(4), e93806. doi:10.1371/journal.pone.0093806Jones, P. A. (2012). Functions of DNA methylation: islands, start sites, gene bodies and beyond. Nature Reviews Genetics, 13(7), 484-492. doi:10.1038/nrg3230Lee, J., He, K., Stolc, V., Lee, H., Figueroa, P., Gao, Y., … Deng, X. W. (2007). Analysis of Transcription Factor HY5 Genomic Binding Sites Revealed Its Hierarchical Role in Light Regulation of Development. The Plant Cell, 19(3), 731-749. doi:10.1105/tpc.106.047688Martínez-Alcántara, B., Iglesias, D. J., Reig, C., Mesejo, C., Agustí, M., & Primo-Millo, E. (2015). Carbon utilization by fruit limits shoot growth in alternate-bearing citrus trees. Journal of Plant Physiology, 176, 108-117. doi:10.1016/j.jplph.2014.12.001Martínez-Fuentes, A., Mesejo, C., Reig, C., & Agustí, M. (2010). Timing of the inhibitory effect of fruit on return bloom of ‘Valencia’ sweet orange (Citrus sinensis (L.) Osbeck). Journal of the Science of Food and Agriculture, 90(11), 1936-1943. doi:10.1002/jsfa.4038Moss, G. I. (1969). Influence of Temperature and Photoperiod on Flower Induction and Inflorescence Development in Sweet Orange (Citrus SinensisL. Osbeck). Journal of Horticultural Science, 44(4), 311-320. doi:10.1080/00221589.1969.11514314Muñoz-Fambuena, N., Mesejo, C., Carmen González-Mas, M., Primo-Millo, E., Agustí, M., & Iglesias, D. J. (2011). Fruit regulates seasonal expression of flowering genes in alternate-bearing ‘Moncada’ mandarin. Annals of Botany, 108(3), 511-519. doi:10.1093/aob/mcr164Nelson, J. D. (2006). Fast chromatin immunoprecipitation assay. Nucleic Acids Research, 34(1), e2-e2. doi:10.1093/nar/gnj004Nishikawa, F., Endo, T., Shimada, T., Fujii, H., Shimizu, T., Omura, M., & Ikoma, Y. (2007). Increased CiFT abundance in the stem correlates with floral induction by low temperature in Satsuma mandarin (Citrus unshiu Marc.). Journal of Experimental Botany, 58(14), 3915-3927. doi:10.1093/jxb/erm246Pien, S., Fleury, D., Mylne, J. S., Crevillen, P., Inzé, D., Avramova, Z., … Grossniklaus, U. (2008). ARABIDOPSIS TRITHORAX1 Dynamically RegulatesFLOWERING LOCUS CActivation via Histone 3 Lysine 4 Trimethylation. The Plant Cell, 20(3), 580-588. doi:10.1105/tpc.108.058172Reeves, P. A., He, Y., Schmitz, R. J., Amasino, R. M., Panella, L. W., & Richards, C. M. (2007). Evolutionary Conservation of the FLOWERING LOCUS C-Mediated Vernalization Response: Evidence From the Sugar Beet (Beta vulgaris). Genetics, 176(1), 295-307. doi:10.1534/genetics.106.069336Ruelens, P., de Maagd, R. A., Proost, S., Theißen, G., Geuten, K., & Kaufmann, K. (2013). FLOWERING LOCUS C in monocots and the tandem origin of angiosperm-specific MADS-box genes. Nature Communications, 4(1). doi:10.1038/ncomms3280Sgamma, T., Jackson, A., Muleo, R., Thomas, B., & Massiah, A. (2014). TEMPRANILLO is a regulator of juvenility in plants. Scientific Reports, 4(1). doi:10.1038/srep03704Shalom, L., Samuels, S., Zur, N., Shlizerman, L., Zemach, H., Weissberg, M., … Sadka, A. (2012). Alternate Bearing in Citrus: Changes in the Expression of Flowering Control Genes and in Global Gene Expression in ON- versus OFF-Crop Trees. PLoS ONE, 7(10), e46930. doi:10.1371/journal.pone.0046930Sheldon, C. C., Rouse, D. T., Finnegan, E. J., Peacock, W. J., & Dennis, E. S. (2000). The molecular basis of vernalization: The central role of FLOWERING LOCUS C (FLC). Proceedings of the National Academy of Sciences, 97(7), 3753-3758. doi:10.1073/pnas.97.7.3753Suárez-López, P., Wheatley, K., Robson, F., Onouchi, H., Valverde, F., & Coupland, G. (2001). CONSTANS mediates between the circadian clock and the control of flowering in Arabidopsis. Nature, 410(6832), 1116-1120. doi:10.1038/35074138Tamada, Y., Yun, J.-Y., Woo, S. chul, & Amasino, R. M. (2009). ARABIDOPSIS TRITHORAX-RELATED7 Is Required for Methylation of Lysine 4 of Histone H3 and for Transcriptional Activation of FLOWERING LOCUS C . The Plant Cell, 21(10), 3257-3269. doi:10.1105/tpc.109.070060Wang, R., Farrona, S., Vincent, C., Joecker, A., Schoof, H., Turck, F., … Albani, M. C. (2009). PEP1 regulates perennial flowering in Arabis alpina. Nature, 459(7245), 423-427. doi:10.1038/nature07988Wells, C. E., Vendramin, E., Jimenez Tarodo, S., Verde, I., & Bielenberg, D. G. (2015). A genome-wide analysis of MADS-box genes in peach [Prunus persica (L.) Batsch]. BMC Plant Biology, 15(1), 41. doi:10.1186/s12870-015-0436-2Whittaker, C., & Dean, C. (2017). The FLC Locus: A Platform for Discoveries in Epigenetics and Adaptation. Annual Review of Cell and Developmental Biology, 33(1), 555-575. doi:10.1146/annurev-cellbio-100616-060546Yang, H., Howard, M., & Dean, C. (2014). Antagonistic Roles for H3K36me3 and H3K27me3 in the Cold-Induced Epigenetic Switch at Arabidopsis FLC. Current Biology, 24(15), 1793-1797. doi:10.1016/j.cub.2014.06.047Zhou, C.-M., Zhang, T.-Q., Wang, X., Yu, S., Lian, H., Tang, H., … Wang, J.-W. (2013). Molecular Basis of Age-Dependent Vernalization in Cardamine flexuosa. Science, 340(6136), 1097-1100. doi:10.1126/science.123434