Models of Flowering Gene Networks and Their Adaptation for the Analysis of Vernalization Mechanisms in Legumes
- Authors: Gursky V.V1, Duk M.A1,2, Bankin M.P2, Samsonova M.G2, Surkova S.Y.2
-
Affiliations:
- Ioffe Institute
- Peter the Great St. Petersburg Polytechnic University
- Issue: Vol 69, No 5 (2024)
- Pages: 1037-1043
- Section: Complex systems biophysics
- URL: https://kld-journal.fedlab.ru/0006-3029/article/view/676158
- DOI: https://doi.org/10.31857/S0006302924050112
- EDN: https://elibrary.ru/MJUAIS
- ID: 676158
Cite item
Abstract
Keywords
About the authors
V. V Gursky
Ioffe InstituteSt. Petersburg, 194021 Russia
M. A Duk
Ioffe Institute; Peter the Great St. Petersburg Polytechnic UniversitySt. Petersburg, 194021 Russia; St. Petersburg, 195251 Russia
M. P Bankin
Peter the Great St. Petersburg Polytechnic UniversitySt. Petersburg, 195251 Russia
M. G Samsonova
Peter the Great St. Petersburg Polytechnic UniversitySt. Petersburg, 195251 Russia
S. Yu Surkova
Peter the Great St. Petersburg Polytechnic University
Email: surkova_syu@spbstu.ru
St. Petersburg, 195251 Russia
References
- Jung C. and Müller A. E. Flowering time control and applications in plant breeding. Trends Plant Sci., 14 (10), 563–573 (2009). doi: 10.1016/j.tplants.2009.07.005
- Taylor C. M., Kamphuis L. G., Zhang W., Garg G., Berger J. D., Mousavi-Derazmahalleh M., Bayer P. E., Edwards D., Singh K. B., Cowling W. A., and Nelson M. N. INDEL variation in the regulatory region of the major flowering time gene LanFTc1 is associated with vernalization response and flowering time in narrow-leafed lupin (Lupinus angustifolius L.). Plant Cell Environ., 42 (1), 174–187 (2019). doi: 10.1111/pce.13320
- Fudge J. B., Lee R. H., Laurie R. E., Mysore K. S., Wen J., Weller J. L., and Macknight R. C. Medicago truncatula SOC1 genes are up-regulated by environmental cues that promote flowering. Frontiers in plant science, 9, 496 (2018). doi: 10.3389/fpls.2018.00496
- Gao B., Bian X. C., Yang F., Chen M. X., Das D., Zhu X. R., Jiang Y., Zhang J., Cao Y. Y., and Wu C. F. Comprehensive transcriptome analysis of faba bean in response to vernalization. Planta, 251 (1), 22 (2019). doi: 10.1007/s00425-019-03308-x
- Yuan X., Wang Q., Yan B., Zhang J., Xue C., Chen J., Lin Y., Zhang X., Shen W., and Chen X. Single-molecule real-time and Illumina-based RNA sequencing data identified vernalization-responsive candidate genes in faba bean (Vicia faba L.). Frontiers in genetics, 12, 656137 (2021). doi: 10.3389/fgene.2021.656137
- Rychel-Bielska S., Plewiński P., Kozak B., Galek R., and Ksiażkiewicz M. Photoperiod and vernalization control of flowering-related genes: A case study of the narrow-leafed lupin (Lupinus angustifolius L.). Front. Plant Sci., 11, 572135 (2020). doi: 10.3389/fpls.2020.572135
- Sung S. and Amasino R. M. Vernalization and epigenetics: how plants remember winter. Curr. Opin. Plant Biol., 7 (1), 4–10 (2004). doi: 10.1016/j.pbi.2003.11.010
- Kim D. H., Doyle M. R., Sung S., and Amasino R. M. Vernalization: winter and the timing of flowering in plants. Annu. Rev. Cell Develop. Biol., 25, 277–299 (2009). doi: 10.1146/annurev.cellbio.042308.113411
- Sharma N., Geuten, K., Giri B. S., and Varma A. The molecular mechanism of vernalization in Arabidopsis and cereals: role of flowering locus C and its homologs. Physiol. plantarum, 170 (3), 373–383 (2020). doi: 10.1111/ppl.13163
- Yan L., Fu D., Li C., Blechl A., Tranquilli G., Bonafede M., Sanchez A., Valarik M., Yasuda S., and Dubcovsky J. The wheat and barley vernalization gene VRN3 is an orthologue of FT. Proc. Natl. Acad. Sci. USA, 103 (51), 19581–19586 (2006). doi: 10.1073/pnas.0607142103
- Surkova S. Y. and Samsonova M. G. Mechanisms of vernalization-induced flowering in legumes. Int. J. Mol. Sci., 23 (17), 9889 (2022). doi: 10.3390/ijms23179889
- Sharma S. and Upadhyaya H. D. Vernalization and photoperiod response in annual wild Cicer species and cultivated chickpea. Crop Sci., 55 (5), 2393–2400 (2015). doi: 10.2135/cropsci2014.09.0598
- Pinhasi van-Oss R., Sherman A., Zhang H. B., Vandemark G., Coyne C., and Abbo S. Plant Breeding, 135 (1), 102–110 (2016). doi: 10.1111/pbr.12325
- Berger J. D., Buck R., Henzell J. M., and Turner N. C. Evolution in the genus Cicer – vernalisation response and low temperature pod set in chickpea (C. arietinum L.) and its annual wild relatives. Austr. J. Agricult. Res., 56, 1191–1200 (2005). doi: 10.1071/ar05089
- Gaur P. M., Jukanti A. K., and Varshney R.K. Impact of genomic technologies on chickpea breeding strategies. Agronomy, 2 (3), 199–221 (2012). doi: 10.3390/agronomy2030199
- Samineni S., Kamatam S., Thudi M., Varshney R. K., and Gaur P. M. Vernalization response in chickpea is controlled by a major QTL. Euphytica, 207, 453–461 (2016). doi: 10.1007/s10681-015-1571-4
- Wigge P. A., Kim M. C., Jaeger K. E., Busch, W., Schmid M., Lohmann J. U., and Weigel D. Integration of spatial and temporal information during floral induction in Arabidopsis. Science, 309 (5737), 1056– 1059 (2005). doi: 10.1126/science.1114358
- Weller J. L. and Ortega R. Genetic control of flowering time in legumes. Frontiers in plant science, 6, 207 (2015). doi: 10.3389/fpls.2015.00207
- Benlloch R., Berbel A., Ali L., Gohari G., Millán T., and Madueño F. Genetic control of inflorescence architecture in legumes. Frontiers in plant science, 6, 543 (2015). doi: 10.3389/fpls.2015.00543
- Lee J. H., Hong S. M., Yoo S. J., Park O. K., Lee J. S., and Ahn J. H. Integration of floral inductive signals by flowering locus T and suppressor of overexpression of Constans 1. Physiol. Plantarum, 126 (4), 475–483 (2006). doi: 10.1111/j.1399-3054.2006.00619.x
- Hecht V., Foucher F., Ferrándiz C., Macknight R., Navarro C., Morin J., Vardy M. E., Ellis N., Beltrán J. P., Rameau C., and Weller J. L. Conservation of Arabidopsis flowering genes in model legumes. Plant Physiol., 137 (4), 1420–1434 (2005). doi: 10.1104/pp.104.057018
- Hecht V., Laurie R. E., Vander Schoor J. K., Ridge S., Knowles C. L., Liew L. C., Sussmilch F. C., Murfet I. C., Macknight R. C., and Weller J. L. The pea GIGAS gene is a FLOWERING LOCUS T homolog necessary for graft-transmissible specification of flowering but not for responsiveness to photoperiod. Plant Cell, 23 (1), 147–161 (2011). doi: 10.1105/tpc.110.081042
- Laurie R. E., Diwadkar P., Jaudal M., Zhang L., Hecht V., Wen J., Tadege M., Mysore K. S., Putterill J., Weller J. L., and Macknight R. C. The Medicago FLOWERING LOCUS T homolog, MtFTa1, is a key regulator of flowering time. Plant Physiol., 156 (4), 2207–2224 (2011). doi: 10.1104/pp.111.180182
- N elson M. N., Książkiewicz M., Rychel S., Besharat N., Taylor C. M., Wyrwa K., Jost R., Erskine W., Cowling W. A., Berger J. D., Batley J., Weller J. L., Naganowska B., and Wolko B. The loss of vernalization requirement in narrow-leafed lupin is associated with a deletion in the promoter and de-repressed expression of a Flowering Locus T (FT) homologue. New Phytologist, 213 (1), 220–232 (2017). doi: 10.1111/nph.14094
- Weller J. L. and Macknight R. C. Functional genomics and flowering time in Medicago truncatula: An overview. Methods Mol. Biol., 1822, 261–271 (2018). doi: 10.1007/978-1-4939-8633-0_17
- Searle I., He Y., Turck F., Vincent C., Fornara F., Kröber S., Amasino R. A., and Coupland G. The transcription factor FLC confers a flowering response to vernalization by repressing meristem competence and systemic signaling in Arabidopsis. Genes Develop., 20 (7), 898–912 (2006). doi: 10.1101/gad.373506
- Mateos J. L., Madrigal P., Tsuda K., Rawat V., Richter R., Romera-Branchat M., Fornara F., Schneeberger K., Krajewski P., and Coupland G. Combinatorial activities of SHORT VEGETATIVE PHASE and FLOWERING LOCUS C define distinct modes of flowering regulation in Arabidopsis. Genome Biol., 16 (1), 31 (2015). doi: 10.1186/s13059-015-0597-1
- Welch S. M., Roe J. L., and Dong Z. A genetic neural network model of flowering time control in Arabidopsis thaliana. Agron. J., 95 (1), 71–81 (2003). doi: 10.2134/agronj2003.0071
- Salazar J. D., Saithong T., Brown P. E., Foreman J., Locke J. C., Halliday K. J., Carré I. A., Rand D. A., and Millar A. J. Prediction of photoperiodic regulators from quantitative gene circuit models. Cell, 139 (6), 1170–1179 (2009). doi: 10.1016/j.cell.2009.11.029
- Jaeger K. E., Pullen N., Lamzin S., Morris R. J., and Wigge P. A. Interlocking feedback loops govern the dynamic behavior of the floral transition in Arabidopsis. Plant Cell, 25 (3), 820–833 (2013). doi: 10.1105/tpc. 113.109355
- Pullen N., Jaeger K. E., Wigge P. A., and Morris R. J. Simple network motifs can capture key characteristics of the floral transition in Arabidopsis. Plant Signal. Behav., 8 (11), e26149 (2013). doi: 10.4161/psb.26149
- van Dijk A. D. J. and Molenaar J. Floral pathway integrator gene expression mediates gradual transmission of environmental and endogenous cues to flowering time. Peer J., 5, e3197 (2017). doi: 10.7717/peerj.3197
- Valentim F. L., van Mourik S., Posé D., Kim M. C., Schmid M., van Ham R. C., Busscher M., SanchezPerez G. F., Molenaar J., Angenent G. C., Immink R. G., and van Dijk A. D. A quantitative and dynamic model of the Arabidopsis flowering time gene regulatory network. PLoS One, 10 (2), e0116973 (2015). doi: 10.1371/journal.pone.0116973
- Wang C. C., Chang P. C., Ng K. L., Chang C. M., Sheu P. C., and Tsai J. J. A model comparison study of the flowering time regulatory network in Arabidopsis. BMC Systems Biol., 8, 15 (2014). doi: 10.1186/1752-0509-8-15
- Wenden B., Dun E. A., Hanan J., Andrieu B., Weller J. L., Beveridge C. A., and Rameau C. Computational analysis of flowering in pea (Pisum sativum). New Phytologist, 184 (1), 153–167 (2009). doi: 10.1111/j.1469-8137.2009.02952.x
- Sussmilch F. C., Berbel A., Hecht V., Vander Schoor J. K., Ferrándiz C., Madueño F., and Weller J. L. Pea VEGETATIVE2 is an FD homolog that is essential for flowering and compound inflorescence development. Plant Cell, 27 (4), 1046–1060 (2015). doi: 10.1105/tpc. 115.136150
- Pavlinova P., Samsonova M. G., and Gursky V. V. Dynamical modeling of the core gene network controlling transition to flowering in Pisum sativum. Front. Genetics, 12, 614711 (2021). doi: 10.3389/fgene.2021.614711
- Gursky V. V., Kozlov K. N., Nuzhdin S. V., and Samsonova M. G. Dynamical modeling of the core gene network controlling flowering suggests cumulative activation from the FLOWERING LOCUS T gene homologs in chickpea. Front. Genetics, 9, 547 (2018). doi: 10.3389/fgene.2018.00547
- Ridge S., Deokar A., Lee R., Daba K., Macknight R. C., Weller J. L., and Tar'an B. The chickpea early flowering 1 (Efl1) locus is an ortholog of Arabidopsis ELF3. Plant Physiol., 175 (2), 802–815 (2017). doi: 10.1104/pp.17.00082
- Подольный Б. С., Гурский В. В. и Самсонова М. Г. Анализ экспрессии генов цветения в сорте нута CDC Frontier методами машинного обучения. Биофизика, 65 (2), 263–276 (2020). doi: 10.1134/S0006350920020189
- Helliwell C. A., Wood C. C., Robertson M., Peacock J. W., and Dennis E. S. The Arabidopsis FLC protein interacts directly in vivo with SOC1 and FT chromatin and is part of a high-molecular-weight protein complex. Plant J., 46 (2), 183–192 (2006). doi: 10.1111/j.1365-313X.2006.02686.x
Supplementary files
