Transcriptome profiles reveal that gibberellin-related genes regulate weeping traits in crape myrtle

Abstract

Plant architecture includes vital traits that influence and benefit crops, and economically important trees. Different plant architectures provide natural beauty. Weeping ornamental plants are aesthetically appealing to people. The regulatory mechanism controlling the weeping trait is poorly understood in crape myrtle. To investigate the weeping trait mechanism, transcriptional profiling of different organs in weeping and upright crape myrtle was performed based on phenotype. Phenotypic and histological analyses demonstrated that endodermal cells were absent, and that new shoot phenotypes could be rescued by the GA₃ treatment of weeping plants. The transcriptional analysis and coexpression network analysis (WGCNA) of differentially expressed genes indicated that GA synthesis and signal transduction pathways play a role in weeping traits. When the expression level of a negative element of GA signaling, LfiGRAS1, was reduced by virus-induced gene silencing (VIGS), new branches grew in infected plants in a negatively geotropic manner. An integrated analysis implied that GA had a strong influence on weeping crape myrtle by interacting with other factors. This study helps to elucidate the mechanism governing the weeping trait and can improve the efficiency of breeding in Lagerstroemia.

References

[1] Wang, B., Smith, S. M. & Li, J. Genetic regulation of shoot architecture. Annu. Rev. Plant Biol. 69, 437-468, https://doi.org/10.1146/annurev-arplant-042817-040422 (2018).

[2] Petersen, R. & Krost, C. Tracing a key player in the regulation of plant architecture: the columnar growth habit of apple trees (Malus x domestica). Planta 238, 1-22, https://doi.org/10.1007/s00425-013-1898-9 (2013).

[3] Busov, V. B., Brunner, A. M. & Strauss, S. H. Genes for control of plant stature and form. N. Phytol. 177, 589-607, https://doi.org/10.1111/j.1469-8137.2007.02324.x (2008).

[4] Dong, Z. et al. Maize LAZY1 mediates shoot gravitropism and inflorescence development through regulating auxin transport, auxin signaling, and light response. Plant Physiol. 163, 1306-1322, https://doi.org/10.1104/pp.113.227314 (2013).

[5] Li, P. et al. LAZY1 controls rice shoot gravitropism through regulating polar auxin transport. Cell Res. 17, 402-410, https://doi.org/10.1038/cr.2007.38 (2007).

[6] Taniguchi, M. et al. The Arabidopsis LAZY1 family plays a key role in gravity signaling within statocytes and in branch angle control of roots and shoots. Plant Cell 29, 1984-1999, https://doi.org/10.1105/tpc.16.00575 (2017).

[7] Yoshihara, T. & Iino, M. Identification of the gravitropism-related rice gene LAZY1 and elucidation of LAZY1-dependent and -independent gravity signaling pathways. Plant Cell Physiol. 48, 678-688, https://doi.org/10.1093/pcp/pcm042 (2007).

[8] Yoshihara, T., Spalding, E. P. & Iino, M. AtLAZY1 is a signaling component required for gravitropism of the Arabidopsis thaliana inflorescence. Plant J. 74, 267-279, https://doi.org/10.1111/tpj.12118 (2013).

[9] Xu, D. et al. PzTAC and PzLAZY from a narrow-crown poplar contribute to regulation of branch angles. Plant Physiol. Biochem. 118, 571-578, https://doi.org/10.1016/j.plaphy.2017.07.011 (2017).

[10] Dardick, C. et al. PpeTAC1 promotes the horizontal growth of branches in peach trees and is a member of a functionally conserved gene family found in diverse plants species. Plant J. 75, 618-630, https://doi.org/10.1111/tpj.12234 (2013).

[11] Dong, H. et al. A novel tiller angle gene, TAC3, together with TAC1 and D2 largely determine the natural variation of tiller angle in rice cultivars. PLoS Genet. 12, e1006412, https://doi.org/10.1371/journal.pgen.1006412 (2016).

[12] Ku, L. et al. Cloning and characterization of a putative TAC1 ortholog associated with leaf angle in maize (Zea mays L.). PLoS ONE 6, e20621, https://doi.org/10.1371/journal.pone.0020621 (2011).

[13] Waite, J. M. & Dardick, C. TILLER ANGLE CONTROL 1 modulates plant architecture in response to photosynthetic signals. J. Exp. Bot. 69, 4935-4944, https://doi.org/10.1093/jxb/ery253 (2018).

[14] Yu, B. et al. TAC1, a major quantitative trait locus controlling tiller angle in rice. Plant J. 52, 891-898, https://doi.org/10.1111/j.1365-313X.2007.03284.x (2007).

[15] Hollender, C. A. et al. Loss of a highly conserved sterile alpha motif domain gene (WEEP) results in pendulous branch growth in peach trees. Proc. Natl Acad. Sci. USA 115, E4690-E4699, https://doi.org/10.1073/pnas.1704515115 (2018).

[16] Gao, J. et al. GmILPA1, encoding an APC8-like protein, controls leaf petiole angle in soybean. Plant Physiol. 174, 1167-1176, https://doi.org/10.1104/pp.16.00074 (2017).

[17] Wu, X., Tang, D., Li, M., Wang, K. & Cheng, Z. Loose plant architecture1, an INDETERMINATE DOMAIN protein involved in shoot gravitropism, regulates plant architecture in rice. Plant Physiol. 161, 317-329, https://doi.org/10.1104/pp.112.208496 (2013).

[18] Jin, J. et al. Genetic control of rice plant architecture under domestication. Nat. Genet. 40, 1365-1369, https://doi.org/10.1038/ng.247 (2008).

[19] Tan, L. et al. Control of a key transition from prostrate to erect growth in rice domestication. Nat. Genet. 40, 1360-1364, https://doi.org/10.1038/ng.197 (2008).

[20] Xie, C., Zhang, G., An, L., Chen, X. & Fang, R. Phytochrome-interacting factor-like protein OsPIL15 integrates light and gravitropism to regulate tiller angle in rice. Planta 250, 105-114, https://doi.org/10.1007/s00425-019-03149-8 (2019).

[21] Yoshida, M., Yamamoto, H., Okuyama, T. & Nakamura, T. Negative gravitropism and growth stress in GA3-treated branches of Prunus spachiana Kitamura f. spachiana Plenarosea. J. Wood Sci. 45, 368-372, https://doi.org/10.1007/bf01177907 (1999).

[22] Nakamura, T. et al. The effects of GA3 on weeping of growing shoots of the Japanese cherry, Prunus spachiana. Plant Cell Physiol. 35, 523-527, https://doi.org/10.1007/s00417-002-0444-4 (1994).

[23] Kei-Ichi, B., Adachi, K., Take, T., Yokoyama, T. & Nakamura, T. Induction of tension wood in GA3-treated branches of the weeping type of Japanese cherry, Prunus spachiana. Plant Cell Physiol. 36, 983-988, https://doi.org/10.1093/oxfordjournals.pcp.a078870 (1995).

[24] Mami, S., Yuriko, N., Hiroshi, N. & Teruko, N. Expression of gibberellin 3 beta-hydroxylase gene in a gravi-response mutant, weeping Japanese flowering cherry. Biol. Sci. Space 18, 261-266, https://doi.org/10.2187/bss.18.261 (2004).

[25] Wolbang, C. M., Davies, N. W., Taylor, S. A. & Ross, J. J. Gravistimulation leads to asymmetry of both auxin and gibberellin levels in barley pulvini. Physiol. Plant 131, 140-148, https://doi.org/10.1111/j.1399-3054.2007.00931.x (2007).

[26] Nugroho, W. D. et al. Gibberellin is required for the formation of tension wood and stem gravitropism in Acacia mangium seedlings. Ann. Bot. 110, 887-895, https://doi.org/10.1093/aob/mcs148 (2012).

[27] Hollender, C. A. & Dardick, C. Molecular basis of angiosperm tree architecture. N. Phytol. 206, 541-556, https://doi.org/10.1111/nph.13204 (2015).

[28] Liu, J., Zeng, Y., Yan, P., He, C. & Zhang, J. Transcriptional and hormonal regulation of weeping trait in Salix matsudana. Genes (Basel) 8, https://doi.org/10.3390/genes8120359 (2017).

[29] Krost, C. et al. Evaluation of the hormonal state of columnar apple trees (Malus x domestica) based on high throughput gene expression studies. Plant Mol. Biol. 81, 211-220, https://doi.org/10.1007/s11103-012-9992-0 (2013).

[30] Wang, Q., Little, C. H. A. & Oden, P. C. Control of longitudinal and cambial growth by gibberellins and indole-3-acetic acid in current-year shoots of Pinus sylvestris. Tree Physiol. 17, 715, https://doi.org/10.1093/treephys/17.11.715 (1997).

[31] Gerttula, S. et al. Transcriptional and hormonal regulation of gravitropism of woody stems in populus. Plant Cell 27, 2800-2813, https://doi.org/10.1105/tpc.15.00531 (2015).

[32] Ju, Y. et al. Transcriptome analysis of the genes regulating phytohormone and cellular patterning in Lagerstroemia plant architecture. Sci. Rep. 8, 15162, https://doi.org/10.1038/s41598-018-33506-8 (2018).

[33] Ye, Y. J. et al. Screening of molecular markers linked to dwarf trait in crape myrtle by bulked segregant analysis. Genet. Mol. Res 14, 4369-4380, https://doi.org/10.4238/2015.April.30.10 (2015).

[34] Ye, Y. et al. Identification and validation of SNP markers linked to dwarf traits using SLAF-Seq technology in Lagerstroemia. PLoS ONE 11, e0158970, https://doi.org/10.1371/journal.pone.0158970 (2016).

[35] Zheng, T. et al. Screening of applicable SSR molecular markers linked to creeping trait in crape myrtle. Forests 10, https://doi.org/10.3390/f10050429 (2019).

[36] Quevillon, E. et al. InterProScan: protein domains identifier. Nucleic Acids Res. 33, W116-W120, https://doi.org/10.1093/nar/gki442 (2005).

[37] Conesa, A. et al. Blast2GO: a universal tool for annotation, visualization and analysis in functional genomics research. Bioinformatics 21, 3674-3676, https://doi.org/10.1093/bioinformatics/bti610 (2005).

[38] Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357-359, https://doi.org/10.1038/nmeth.1923 (2012).

[39] Li, B. & Dewey, C. N. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinformatics 12, 323, https://doi.org/10.1186/1471-2105-12-323 (2011).

[40] Leng, N. et al. EBSeq: an empirical Bayes hierarchical model for inference in RNA-seq experiments. Bioinformatics 29, 1035-1043, https://doi.org/10.1093/bioinformatics/btt087 (2013).

[41] Langfelder, P. & Horvath, S. WGCNA: an R package for weighted correlation network analysis. BMC Bioinformatics 9, 559, https://doi.org/10.1186/1471-2105-9-559 (2008).

[42] Wang, Y. et al. GSA: Genome Sequence Archive. Genomics Proteomics Bioinformatics 15, 14-18, https://doi.org/10.1016/j.gpb.2017.01.001 (2017).

[43] Members, B. I. G. D. C. Database resources of the BIG Data Center in 2019. Nucleic Acids Res. 47, D8-D14, https://doi.org/10.1093/nar/gky993 (2019).

[44] Zheng, T. et al. Reference gene selection for qRT-PCR analysis of flower development in Lagerstroemia indica and L. speciosa. PLoS ONE 13, e0195004, https://doi.org/10.1371/journal.pone.0195004 (2018).

[45] Livak, K. J. & Schmittgen, T. D. Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) method. Methods 25, 402-408, https://doi.org/10.1006/meth.2001.1262 (2001).

[46] Fu, D. Q., Zhu, B. Z., Zhu, H. L., Jiang, W. B. & Luo, Y. B. Virus-induced gene silencing in tomato fruit. Plant J. 43, 299-308, https://doi.org/10.1111/j.1365-313X.2005.02441.x (2005).

[47] Senthil-Kumar, M. & Mysore, K. S. Tobacco rattle virus-based virus-induced gene silencing in Nicotiana benthamiana. Nat. Protoc. 9, 1549-1562, https://doi.org/10.1038/nprot.2014.092 (2014).

[48] Fukaki, H. et al. Genetic evidence that the endodermis is essential for shoot gravitropism in Arabidopsis thaliana. Plant J. Cell Mol. Biol. 14, 425-430 (1998).

[49] Helariutta, Y. et al. The SHORT-ROOT gene controls radial patterning of the Arabidopsis root through radial signaling. Cell 101, 555-567 (2000).

[50] Di Laurenzio, L. et al. The SCARECROW gene regulates an asymmetric cell division that is essential for generating the radial organization of the Arabidopsis root. Cell 86, 423-433 (1996).

[51] Kitazawa, D. et al. Shoot circumnutation and winding movements require gravisensing cells. Proc. Natl Acad. Sci. USA 102, 18742-18747 (2005).

[52] Kitazawa, D. et al. The gravity-regulated growth of axillary buds is mediated by a mechanism different from decapitation-induced release. Plant Cell Physiol. 49, 891-900, https://doi.org/10.1093/pcp/pcn063 (2008).

[53] Chen, J. et al. Isolation of prostrate turfgrass mutants via screening of dwarf phenotype and characterization of a perennial ryegrass prostrate mutant. Hortic. Res. 3, 16003, https://doi.org/10.1038/hortres.2016.3 (2016).

[54] Thomas, S. G., Phillips, A. L. & Hedden, P. Molecular cloning and functional expression of gibberellin 2-oxidases, multifunctional enzymes involved in gibberellin deactivation. Proc. Natl Acad. Sci. USA 96, 4698-4703, https://doi.org/10.1073/pnas.96.8.4698 (1999).

[55] Olszewski, N., Sun, T.-p & Gubler, F. Supplement: signal transduction || gibberellin signaling: biosynthesis, catabolism, and response pathways. Plant Cell 14, S61-S80, https://doi.org/10.2307/3871750 (2002).

[56] Ni, J. et al. Gibberellin promotes shoot branching in the perennial woody plant Jatropha curcas. Plant Cell Physiol. 56, 1655-1666, https://doi.org/10.1093/pcp/pcv089 (2015).

[57] Cheng, J. et al. A single nucleotide mutation in GID1c disrupts its interaction with DELLA1 and causes a GA-insensitive dwarf phenotype in peach. Plant Biotechnol. J. https://doi.org/10.1111/pbi.13094 (2019).

[58] Busov, V. B. et al. Activation tagging of a dominant gibberellin catabolism gene (GA 2-oxidase) from poplar that regulates tree stature. Plant Physiol. 132, 1283-1291, https://doi.org/10.1104/pp.103.020354 (2003).

[59] Lo, S. F. et al. A novel class of gibberellin 2-oxidases control semidwarfism, tillering, and root development in rice. Plant Cell 20, 2603-2618, https://doi.org/10.1105/tpc.108.060913 (2008).

[60] Wuddineh, W. A. et al. Identification and overexpression of gibberellin 2-oxidase (GA2ox) in switchgrass (Panicum virgatum L.) for improved plant architecture and reduced biomass recalcitrance. Plant Biotechnol. J. 13, 636-647, https://doi.org/10.1111/pbi.12287 (2015).

[61] Bennett, T. et al. Strigolactone regulates shoot development through a core signalling pathway. Biol. Open 5, 1806-1820 (2016).

[62] McGinnis, K. M. et al. The Arabidopsis SLEEPY1 gene encodes a putative F-box subunit of an SCF E3 ubiquitin ligase. Plant Cell 15, 1120-1130, https://doi.org/10.1105/tpc.010827 (2003).

[63] Wang, H. et al. Fasciclin-like arabinogalactan proteins, PtFLAs, play important roles in GA-mediated tension wood formation in Populus. Sci. Rep. 7, 6182, https://doi.org/10.1038/s41598-017-06473-9 (2017).

[64] Funada, R. et al. Gibberellin-induced formation of tension wood in angiosperm trees. Planta 227, 1409-1414, https://doi.org/10.1007/s00425-008-0712-6 (2008).

[65] Jiang, S., Xu, K., Wang, Y. Z., Ren, Y. P. & Gu, S. Role of GA3, GA4 and uniconazole-P in controlling gravitropism and tension wood formation in Fraxinus mandshurica Rupr. var. japonica Maxim. seedlings. J. Integr. Plant Biol. 50, 19-28, https://doi.org/10.1111/j.1744-7909.2007.00552.x (2008).

[66] de Lucas, M. & Prat, S. PIFs get BRright: PHYTOCHROME INTERACTING FACTORs as integrators of light and hormonal signals. N. Phytol. 202, 1126-1141, https://doi.org/10.1111/nph.12725 (2014).

[67] Feng, S. et al. Coordinated regulation of Arabidopsis thaliana development by light and gibberellins. Nature 451, 475-479, https://doi.org/10.1038/nature06448 (2008).

[68] Djakovic-Petrovic, T., de Wit, M., Voesenek, L. A. & Pierik, R. DELLA protein function in growth responses to canopy signals. Plant J. 51, 117-126, https://doi.org/10.1111/j.1365-313X.2007.03122.x (2007).

[69] de Lucas, M. et al. A molecular framework for light and gibberellin control of cell elongation. Nature 451, 480-484, https://doi.org/10.1038/nature06520 (2008).