Genome-wide expression analysis of LBD genes in tomato (Solanum lycopersicum L.) under different light conditions

References

• Wang S, Meng X, Tang Z, Wu Y, Xiao X, Zhang G, Hu L, Liu Z, Lyu J, Yu J, et al. Red and blue LED light supplementation in the morning pre-activates the photosynthetic System of tomato (Solanum lycopersicum L.) leaves and promotes Plant growth. Agronomy. 2022;12(4):897. doi:10.3390/agronomy12040897.
   Google Scholar
• Yang X, Sun H, Hua M, Song L, Du Z, Tong Y, Ma H, Song Z. Effects of supplemental light on tomato growth and the mechanism of the photosystem II apparatus. PLoS ONE. 2022;17(5):e0267989. doi:10.1371/journal.pone.0267989.
   PubMed Web of Science ®Google Scholar
• Dzakovich MP, Ferruzzi MG, Mitchell CA. Manipulating sensory and phytochemical profiles of greenhouse tomatoes using environmentally relevant doses of ultraviolet radiation. J Agr Food Chem. 2016;64(36):6801–10. doi:10.1021/acs.jafc.6b02983.
   PubMed Web of Science ®Google Scholar
• Kochetova GV, Avercheva OV, Bassarskaya EM, Kushunina MA, Zhigalova TV. Effects of red and blue LED light on the growth and photosynthesis of barley (Hordeum vulgare L.) seedlings. J Plant Growth Regul. 2023;42(3):1804–1820. doi:10.1007/s00344-022-10661-x.
   Web of Science ®Google Scholar
• Liu X, Shi R, Gao M, He R, Li Y, Liu H. Effects of LED light quality on the growth of pepper (Capsicum spp.) seedlings and the development after transplanting. Agronomy. 2022;12(10):2269. doi:10.3390/agronomy12102269.
   Google Scholar
• Huché-Thélier L, Crespel L, Le Gourrierec J, Morel P, Sakr S, Leduc N. Light signaling and plant responses to blue and UV radiations—perspectives for applications in horticulture. Environ Exp Bot. 2016;121:22–38. doi:10.1016/j.envexpbot.2015.06.009.
   Web of Science ®Google Scholar
• Lazzarin M, Meisenburg M, Meijer D, Van Ieperen W, Marcelis L, Kappers I, van der Krol AR, van Loon JJA, Dicke M. LEDs make it resilient: effects on plant growth and defense. Trends Plant Sci. 2021;26(5):496–508. doi:10.1016/j.tplants.2020.11.013.
   PubMed Web of Science ®Google Scholar
• Dueck T, Ieperen W, Taulavuori K. Light perception, signalling and plant responses to spectral quality and photoperiod in natural and horticultural environments. Environ Exp Bot. 2016;121:1–150. doi:10.1016/j.envexpbot.2015.06.012.
   Web of Science ®Google Scholar
• Sheerin DJ, Hiltbrunner A. Molecular mechanisms and ecological function of far‐red light signalling. Plant, Cell & Environ. 2017;40(11):2509–2529. doi:10.1111/pce.12915.
   PubMed Web of Science ®Google Scholar
• Huang B, Huang Z, Ma R, Ramakrishnan M, Chen J, Zhang Z, Yrjälä K. Genome-wide identification and expression analysis of LBD transcription factor genes in moso bamboo (Phyllostachys edulis). BMC Plant Biol. 2021;21(1):1–22. doi:10.1186/s12870-021-03078-3.
   PubMed Web of Science ®Google Scholar
• Iwakawa H, Ueno Y, Semiarti E, Onouchi H, Kojima S, Tsukaya H, Hasebe M, Soma T, Ikezaki M, Machida C, et al. The ASYMMETRIC LEAVES2 gene of Arabidopsis thaliana, required for formation of a symmetric flat leaf lamina, encodes a member of a novel family of proteins characterized by cysteine repeats and a leucine zipper. Plant Cell Physiol. 2002;43(5):467–478. doi:10.1093/pcp/pcf077.
   PubMed Web of Science ®Google Scholar
• Feng S, Shi J, Hu Y, Li D, Guo L, Zhao Z, Lee G-S, Qiao Y. Genome-wide analysis of soybean lateral organ boundaries domain gene family reveals the role in phytophthora root and stem rot. Front Plant Sci. 2022;13:865165. doi:10.3389/fpls.2022.865165.
   PubMed Web of Science ®Google Scholar
• Shuai B, Reynaga-Pena CG, Springer PS. The lateral organ boundaries gene defines a novel, plant-specific gene family. Plant Physiol. 2002;129(2):747–61. doi:10.1104/pp.010926.
   PubMed Web of Science ®Google Scholar
• Zheng Y, Jiao C, Sun H, Rosli HG, Pombo MA, Zhang P, Banf M, Dai X, Martin G, Giovannoni J, et al. iTAK: a program for genome-wide prediction and classification of plant transcription factors, transcriptional regulators, and protein kinases. Mol Plant. 2016;9(12):1667–1670. doi:10.1016/j.molp.2016.09.014.
   PubMed Web of Science ®Google Scholar
• Kumar S, Stecher G, Tamura K. MEGA7: molecular evolutionary genetics analysis version 7.0 for bigger datasets. Mol Biol Evol. 2016;33(7):1870–1874. doi:10.1093/molbev/msw054.
   PubMed Web of Science ®Google Scholar
• Hu B, Jin J, Guo A-Y, Zhang H, Luo J, Gao G. GSDS 2.0: an upgraded gene feature visualization server. Bioinformatics. 2015;31(8):1296–1297. doi:10.1093/bioinformatics/btu817.
   PubMed Web of Science ®Google Scholar
• Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren J, Li WW, Noble WS. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 2009;37(Web Server):W202–W208. doi:10.1093/nar/gkp335.
   PubMedGoogle Scholar
• Xie T, Zeng L, Chen X, Rong H, Wu J, Batley J, Jiang J, Wang Y. Genome-wide analysis of the lateral organ boundaries domain gene family in Brassica napus. Genes. 2020;11(3):280. doi:10.3390/genes11030280.
   PubMed Web of Science ®Google Scholar
• Majer C, Hochholdinger F. Defining the boundaries: structure and function of LOB domain proteins. Trends Plant Sci. 2011;16(1):47–52. doi:10.1016/j.tplants.2010.09.009.
   PubMed Web of Science ®Google Scholar
• Li A, Liu A, Du X, Chen J-Y, Yin M, Hu H-Y, Shrestha N, Wu S-D, Wang H-Q, Dou Q-W, et al. A chromosome-scale genome assembly of a diploid alfalfa, the progenitor of autotetraploid alfalfa. Horticul Res. 2020;7(1):194. doi:10.1038/s41438-020-00417-7.
   PubMed Web of Science ®Google Scholar
• Guo M, Thomas J, Collins G, Timmermans MC. Direct repression of KNOX loci by the ASYMMETRIC LEAVES1 complex of Arabidopsis. Plant Cell. 2008;20(1):48–58. doi:10.1105/tpc.107.056127.
   PubMed Web of Science ®Google Scholar
• Chen X, Wang H, Li J, Huang H, Xu L. Quantitative control of ASYMMETRIC LEAVES2 expression is critical for leaf axial patterning in Arabidopsis. J Exp Bot. 2013;64(16):4895–4905. doi:10.1093/jxb/ert278.
   PubMed Web of Science ®Google Scholar
• Rast-Somssich MI, Žádníková P, Schmid S, Kieffer M, Kepinski S, Simon R. The Arabidopsis JAGGED LATERAL ORGANS (JLO) gene sensitizes plants to auxin. J Exp Bot. 2017;68(11):2741–2755. doi:10.1093/jxb/erx131.
   PubMed Web of Science ®Google Scholar
• Rast MI, Simon R. Arabidopsis JAGGED LATERAL ORGANS acts with ASYMMETRIC LEAVES2 to coordinate KNOX and PIN expression in shoot and root meristems. Plant Cell. 2012;24(7):2917–2933. doi:10.1105/tpc.112.099978.
   PubMed Web of Science ®Google Scholar
• Iwakawa H, Iwasaki M, Kojima S, Ueno Y, Soma T, Tanaka H, Semiarti E, Machida Y, Machida C. Expression of the ASYMMETRIC LEAVES2 gene in the adaxial domain of Arabidopsis leaves represses cell proliferation in this domain and is critical for the development of properly expanded leaves. Plant Journal. 2007;51(2):173–84. doi:10.1111/j.1365-313X.2007.03132.x.
   PubMed Web of Science ®Google Scholar
• Yu C, Cai X, Ye Z, Li H. Genome-wide identification and expression profiling analysis of trihelix gene family in tomato. Biochem Bioph Res Co. 2015;468(4):653–659. doi:10.1016/j.bbrc.2015.11.010.
   PubMed Web of Science ®Google Scholar
• Kay SA, Keith B, Shinozaki K, Chye M-L, Chua N-H. The rice phytochrome gene: structure, autoregulated expression, and binding of GT-1 to a conserved site in the 5’ upstream region. Plant Cell. 1989;1(3):351–60. doi:10.1105/tpc.1.3.351.
   PubMed Web of Science ®Google Scholar
• Brewer PB, Howles PA, Dorian K, Griffith ME, Ishida T, Kaplan-Levy RN, Kilinc A, Smyth DR. PETAL LOSS, a trihelix transcription factor gene, regulates perianth architecture in the Arabidopsis flower. Development. 2004;131(16):4035–4045. doi:10.1242/dev.01279.
   PubMed Web of Science ®Google Scholar
• Barr MS, Willmann MR, Jenik PD. Is there a role for trihelix transcription factors in embryo maturation? Plant Signal Behav. 2012;7(2):205–209. doi:10.4161/psb.18893.
   PubMed Web of Science ®Google Scholar
• Breuer C, Kawamura A, Ichikawa T, Tominaga-Wada R, Wada T, Kondou Y, Muto S, Matsui M, Sugimoto K. The trihelix transcription factor GTL1 regulates ploidy-dependent cell growth in the Arabidopsis trichome. Plant Cell. 2009;21(8):2307–22. doi:10.1105/tpc.109.068387.
   PubMed Web of Science ®Google Scholar
• Wang X-H, Li Q-T, Chen H-W, Zhang W-K, Ma B, Chen S-Y, Zhang J-S. Trihelix transcription factor GT-4 mediates salt tolerance via interaction with TEM2 in Arabidopsis. BMC Plant Biol. 2014;14(1):1–14. doi:10.1186/s12870-014-0339-7.
   Google Scholar
• Lu Q, Liu H, Hong Y, Liang X, Li S, Liu H, Li H, Wang R, Deng Q, Jiang H, et al. Genome-wide identification and expression of FAR1 gene family provide insight into pod development in peanut (Arachis hypogaea). Front Plant Sci. 2022;13:893278. doi:10.3389/fpls.2022.893278.
   PubMedGoogle Scholar
• Xie Y, Liu Y, Ma M, Zhou Q, Zhao Y, Zhao B, Wang B, Wei H, Wang H. Arabidopsis FHY3 and FAR1 integrate light and strigolactone signaling to regulate branching. Nat Commun. 2020;11(1):1955. doi:10.1038/s41467-020-15893-7.
   PubMed Web of Science ®Google Scholar
• Xie Y, Zhou Q, Zhao Y, Li Q, Liu Y, Ma M, Wang B, Shen R, Zheng Z, Wang H, et al. FHY3 and FAR1 integrate light signals with the miR156-SPL module-mediated aging pathway to regulate Arabidopsis flowering. Mol Plant. 2020;13(3):483–498. doi:10.1016/j.molp.2020.01.013.
   PubMed Web of Science ®Google Scholar
• Noguero M, Atif RM, Ochatt S, Thompson RD. The role of the DNA-binding one zinc finger (DOF) transcription factor family in plants. Plant Sci. 2013;209:32–45. doi:10.1016/j.plantsci.2013.03.016.
   PubMed Web of Science ®Google Scholar
• Chen P, Yan M, Li L, He J, Zhou S, Li Z, Niu C, Bao C, Zhi F, Ma F, et al. The apple DNA-binding one zinc-finger protein MdDof54 promotes drought resistance. Hortic Res. 2020;7(1):7. doi:10.1038/s41438-020-00419-5.
   PubMed Web of Science ®Google Scholar