PmLBD3 links auxin and brassinosteroid signalling pathways on dwarfism in Prunus mume.
Dwarfing mechanism
Grafting
Hormonal signalling
Prunus mume
Journal
BMC biology
ISSN: 1741-7007
Titre abrégé: BMC Biol
Pays: England
ID NLM: 101190720
Informations de publication
Date de publication:
26 Aug 2024
26 Aug 2024
Historique:
received:
12
03
2024
accepted:
15
08
2024
medline:
26
8
2024
pubmed:
26
8
2024
entrez:
25
8
2024
Statut:
epublish
Résumé
Grafting with dwarf rootstock is an efficient method to control plant height in fruit production. However, the molecular mechanism remains unclear. Our previous study showed that plants with Prunus mume (mume) rootstock exhibited a considerable reduction in plant height, internode length, and number of nodes compared with Prunus persica (peach) rootstock. The present study aimed to investigate the mechanism behind the regulation of plant height by mume rootstocks through transcriptomic and metabolomic analyses with two grafting combinations, 'Longyan/Mume' and 'Longyan/Peach'. There was a significant decrease in brassinolide levels in plants that were grafted onto mume rootstocks. Plant hormone signal transduction and brassinolide production metabolism gene expression also changed significantly. Flavonoid levels, amino acid and fatty acid metabolites, and energy metabolism in dwarf plants decreased. There was a notable upregulation of PmLBD3 gene expression in plant specimens that were subjected to grafting onto mume rootstocks. Auxin signalling cues promoted PmARF3 transcription, which directly controlled this upregulation. Through its binding to PmBAS1 and PmSAUR36a gene promoters, PmLBD3 promoted endogenous brassinolide inactivation and inhibited cell proliferation. Auxin signalling and brassinolide levels are linked by PmLBD3. Our findings showed that PmLBD3 is a key transcription factor that regulates the balance of hormones through the auxin and brassinolide signalling pathways and causes dwarf plants in stone fruits.
Sections du résumé
BACKGROUND
BACKGROUND
Grafting with dwarf rootstock is an efficient method to control plant height in fruit production. However, the molecular mechanism remains unclear. Our previous study showed that plants with Prunus mume (mume) rootstock exhibited a considerable reduction in plant height, internode length, and number of nodes compared with Prunus persica (peach) rootstock. The present study aimed to investigate the mechanism behind the regulation of plant height by mume rootstocks through transcriptomic and metabolomic analyses with two grafting combinations, 'Longyan/Mume' and 'Longyan/Peach'.
RESULTS
RESULTS
There was a significant decrease in brassinolide levels in plants that were grafted onto mume rootstocks. Plant hormone signal transduction and brassinolide production metabolism gene expression also changed significantly. Flavonoid levels, amino acid and fatty acid metabolites, and energy metabolism in dwarf plants decreased. There was a notable upregulation of PmLBD3 gene expression in plant specimens that were subjected to grafting onto mume rootstocks. Auxin signalling cues promoted PmARF3 transcription, which directly controlled this upregulation. Through its binding to PmBAS1 and PmSAUR36a gene promoters, PmLBD3 promoted endogenous brassinolide inactivation and inhibited cell proliferation.
CONCLUSIONS
CONCLUSIONS
Auxin signalling and brassinolide levels are linked by PmLBD3. Our findings showed that PmLBD3 is a key transcription factor that regulates the balance of hormones through the auxin and brassinolide signalling pathways and causes dwarf plants in stone fruits.
Identifiants
pubmed: 39183294
doi: 10.1186/s12915-024-01985-z
pii: 10.1186/s12915-024-01985-z
doi:
Substances chimiques
Brassinosteroids
0
Indoleacetic Acids
0
Plant Proteins
0
Plant Growth Regulators
0
Transcription Factors
0
Steroids, Heterocyclic
0
brassinolide
Y9IQ1L53OX
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Pagination
184Informations de copyright
© 2024. The Author(s).
Références
Luo J, Tang Y, Chu Z, Peng Y, Chen J, Yu H, et al. SlZF3 regulates tomato plant height by directly repressing SlGA20ox4 in the gibberellic acid biosynthesis pathway. Hortic Res. 2023;10:uhad025.
pubmed: 37090098
pmcid: 10116951
doi: 10.1093/hr/uhad025
Hayat F, Ma C, Iqbal S, Ma Y, Khanum F, Tariq R, et al. Comprehensive transcriptome profiling and hormonal signaling reveals important mechanism related to dwarfing effect of rootstocks on scion in Japanese apricot (Prunus mume). Sci Hortic. 2023;321:112267.
doi: 10.1016/j.scienta.2023.112267
Cong L, Ling H, Liu S, Wang A, Zhai R, Yang C, et al. ‘Yunnan’ quince rootstock promoted flower bud formation of ‘Abbé Fetel’ pear by altering hormone levels and PbAGL9 expression. J Plant Physiol. 2023;282:153924.
pubmed: 36805518
doi: 10.1016/j.jplph.2023.153924
Gu Q, Wei Q, Hu Y, Chen M, Chen Z, Zheng S, et al. Physiological and full-length transcriptome analyses reveal the dwarfing regulation in trifoliate orange (Poncirus trifoliata L.). Plants. 2023;12:271.
pubmed: 36678984
pmcid: 9860739
doi: 10.3390/plants12020271
Hayat F, Li J, Iqbal S, Khan U, Ali NA, Peng Y, et al. Hormonal interactions underlying rootstock-induced vigor control in horticultural crops. Appl Sci. 2023;13:1237.
doi: 10.3390/app13031237
Li X, Wang Y, Zhao L, Chen S, Yuan Y, Wei T, et al. Effects of Cerasus humilis (Bge). Sok. Rootstock on peach growth, development, and expression of growth-related genes. Horticulturae. 2023;9:576.
doi: 10.3390/horticulturae9050576
Foster TM, Celton J-M, Chagné D, Tustin DS, Gardiner SE. Two quantitative trait loci, Dw1 and Dw2, are primarily responsible for rootstock-induced dwarfing in apple. Hortic Res. 2015;2:15001.
pubmed: 26504562
pmcid: 4595989
doi: 10.1038/hortres.2015.1
Prassinos C, Ko J-H, Lang G, Iezzoni AF, Han K-H. Rootstock-induced dwarfing in cherries is caused by differential cessation of terminal meristem growth and is triggered by rootstock-specific gene regulation. Tree Physiol. 2009;29:927–36.
pubmed: 19429629
doi: 10.1093/treephys/tpp027
Zhou Y, Underhill SJR. Differential transcription pathways associated with rootstock-induced dwarfing in breadfruit (Artocarpus altilis) scions. BMC Plant Biol. 2021;21:261.
pubmed: 34090350
pmcid: 8178858
doi: 10.1186/s12870-021-03013-6
Tworkoski T, Fazio G. Hormone and growth interactions of scions and size-controlling rootstocks of young apple trees. Plant Growth Regul. 2016;78:105–19.
doi: 10.1007/s10725-015-0078-2
Aloni B, Cohen R, Karni L, Aktas H, Edelstein M. Hormonal signaling in rootstock–scion interactions. Sci Hortic. 2010;127:119–26.
doi: 10.1016/j.scienta.2010.09.003
Yang S, Zhang K, Zhu H, Zhang X, Yan W, Xu N, et al. Melon short internode (CmSi) encodes an ERECTA-like receptor kinase regulating stem elongation through auxin signaling. Hortic Res. 2020;7:202.
pubmed: 33328451
pmcid: 7705010
doi: 10.1038/s41438-020-00426-6
Michalczuk L. Indole-3-acetic acid level in wood, bark and cambial sap of apple rootstocks differing in growth vigour. Acta Physiol Plant. 2002;24:131–6.
doi: 10.1007/s11738-002-0002-z
Song C, Zhang D, Zhang J, Zheng L, Zhao C, Ma J, et al. Expression analysis of key auxin synthesis, transport, and metabolism genes in different young dwarfing apple trees. Acta Physiol Plant. 2016;38:43.
doi: 10.1007/s11738-016-2065-2
Zhang S, Wang S, Xu Y, Yu C, Shen C, Qian Q, et al. The auxin response factor, OsARF19, controls rice leaf angles through positively regulating OsGH3-5 and OsBRI1. Plant Cell Environ. 2015;38:638–54.
pubmed: 24995795
doi: 10.1111/pce.12397
Stortenbeker N, Bemer M. The SAUR gene family: the plant’s toolbox for adaptation of growth and development. J Exp Bot. 2019;70:17–27.
pubmed: 30239806
doi: 10.1093/jxb/ery332
Chae K, Isaacs CG, Reeves PH, Maloney GS, Muday GK, Nagpal P, et al. Arabidopsis SMALL AUXIN UP RNA63 promotes hypocotyl and stamen filament elongation. Plant J. 2012;71:684–97.
pubmed: 22507274
doi: 10.1111/j.1365-313X.2012.05024.x
Hou K, Wu W, Gan S-S. SAUR36, a SMALL AUXIN UP RNA gene, is involved in the promotion of leaf senescence in Arabidopsis. Plant Physiol. 2013;161:1002–9.
pubmed: 23250625
doi: 10.1104/pp.112.212787
Koka CV, Cerny RE, Gardner RG, Noguchi T, Fujioka S, Takatsuto S, et al. A putative role for the tomato genes DUMPY and CURL-3 in brassinosteroid biosynthesis and response. Plant Physiol. 2000;122:85–98.
pubmed: 10631252
pmcid: 58847
doi: 10.1104/pp.122.1.85
Spartz AK, Lee SH, Wenger JP, Gonzalez N, Itoh H, Inzé D, et al. The SAUR19 subfamily of SMALL AUXIN UP RNA genes promote cell expansion. Plant J. 2012;70:978–90.
pubmed: 22348445
pmcid: 3481998
doi: 10.1111/j.1365-313X.2012.04946.x
Stamm P, Kumar PP. Auxin and gibberellin responsive Arabidopsis SMALL AUXIN UP RNA36 regulates hypocotyl elongation in the light. Plant Cell Rep. 2013;32:759–69.
pubmed: 23503980
doi: 10.1007/s00299-013-1406-5
van Mourik H, van Dijk ADJ, Stortenbeker N, Angenent GC, Bemer M. Divergent regulation of Arabidopsis SAUR genes: a focus on the SAUR10-clade. BMC Plant Biol. 2017;17:245.
pubmed: 29258424
pmcid: 5735953
doi: 10.1186/s12870-017-1210-4
Fridman Y, Savaldi-Goldstein S. Brassinosteroids in growth control: how, when and where. Plant Sci. 2013;209:24–31.
pubmed: 23759100
doi: 10.1016/j.plantsci.2013.04.002
Unterholzner SJ, Rozhon W, Papacek M, Ciomas J, Lange T, Kugler KG, et al. Brassinosteroids are master regulators of gibberellin biosynthesis in Arabidopsis. Plant Cell. 2015;27:2261–72.
pubmed: 26243314
pmcid: 4568508
doi: 10.1105/tpc.15.00433
Kim T-W, Guan S, Sun Y, Deng Z, Tang W, Shang J-X, et al. Brassinosteroid signal transduction from cell-surface receptor kinases to nuclear transcription factors. Nat Cell Biol. 2009;11:1254–60.
pubmed: 19734888
pmcid: 2910619
doi: 10.1038/ncb1970
Jager CE, Symons GM, Nomura T, Yamada Y, Smith JJ, Yamaguchi S, et al. Characterization of two brassinosteroid C-6 oxidase genes in pea. Plant Physiol. 2007;143:1894–904.
pubmed: 17322341
pmcid: 1851809
doi: 10.1104/pp.106.093088
Turk EM, Fujioka S, Seto H, Shimada Y, Takatsuto S, Yoshida S, et al. BAS1 and SOB7 act redundantly to modulate Arabidopsis photomorphogenesis via unique brassinosteroid inactivation mechanisms. Plant J. 2005;42:23–34.
pubmed: 15773851
doi: 10.1111/j.1365-313X.2005.02358.x
Yang B, Zhou S, Ou L, Liu F, Yang L, Zheng J, et al. A novel single-base mutation in CaBRI1 confers dwarf phenotype and brassinosteroid accumulation in pepper. Mol Genet Genomics. 2020;295:343–56.
pubmed: 31745640
doi: 10.1007/s00438-019-01626-z
Yang M, Wang X. Multiple ways of BES1/BZR1 degradation to decode distinct developmental and environmental cues in plants. Mol Plant. 2017;10:915–7.
pubmed: 28629641
doi: 10.1016/j.molp.2017.06.005
He G, Liu J, Dong H, Sun J. The blue-light receptor CRY1 interacts with BZR1 and BIN2 to modulate the phosphorylation and nuclear function of BZR1 in repressing BR signaling in Arabidopsis. Mol Plant. 2019;12:689–703.
pubmed: 30763615
doi: 10.1016/j.molp.2019.02.001
Tong H, Xiao Y, Liu D, Gao S, Liu L, Yin Y, et al. Brassinosteroid regulates cell elongation by modulating gibberellin metabolism in rice. Plant Cell. 2014;26:4376–93.
pubmed: 25371548
pmcid: 4277228
doi: 10.1105/tpc.114.132092
Gallego-Bartolomé J, Minguet EG, Grau-Enguix F, Abbas M, Locascio A, Thomas SG, et al. Molecular mechanism for the interaction between gibberellin and brassinosteroid signaling pathways in Arabidopsis. Proc Natl Acad Sci U S A. 2012;109:13446–51.
pubmed: 22847438
pmcid: 3421204
doi: 10.1073/pnas.1119992109
Zhang Y, Li Z, Ma B, Hou Q, Wan X. Phylogeny and functions of LOB domain proteins in plants. Int J Mol Sci. 2020;21:E2278.
doi: 10.3390/ijms21072278
Sun X, Feng Z, Meng L, Zhu J, Geitmann A. Arabidopsis ASL11/LBD15 is involved in shoot apical meristem development and regulates WUS expression. Planta. 2013;237:1367–78.
pubmed: 23397191
doi: 10.1007/s00425-013-1844-x
Zentella R, Zhang Z-L, Park M, Thomas SG, Endo A, Murase K, et al. Global analysis of della direct targets in early gibberellin signaling in Arabidopsis. Plant Cell. 2007;19:3037–57.
pubmed: 17933900
pmcid: 2174696
doi: 10.1105/tpc.107.054999
Ikezaki M, Kojima M, Sakakibara H, Kojima S, Ueno Y, Machida C, et al. Genetic networks regulated by ASYMMETRIC LEAVES1 (AS1) and AS2 in leaf development in Arabidopsis thaliana: KNOX genes control five morphological events. Plant J. 2010;61:70–82.
pubmed: 19891706
doi: 10.1111/j.1365-313X.2009.04033.x
Bell EM, Lin W, Husbands AY, Yu L, Jaganatha V, Jablonska B, et al. Arabidopsis lateral organ boundaries negatively regulates brassinosteroid accumulation to limit growth in organ boundaries. Proc Natl Acad Sci U S A. 2012;109:21146–51.
pubmed: 23213252
pmcid: 3529045
doi: 10.1073/pnas.1210789109
Jeon E, Young Kang N, Cho C, Joon Seo P, Chung Suh M, Kim J. LBD14/ASL17 positively regulates lateral root formation and is involved in ABA response for root architecture in Arabidopsis. Plant Cell Physiol. 2017;58:2190–201.
pubmed: 29040694
doi: 10.1093/pcp/pcx153
Pandey SK, Lee HW, Kim M-J, Cho C, Oh E, Kim J. LBD18 uses a dual mode of a positive feedback loop to regulate ARF expression and transcriptional activity in Arabidopsis. Plant J. 2018;95:233–51.
pubmed: 29681137
doi: 10.1111/tpj.13945
Teng R-M, Yang N, Liu C-F, Chen Y, Wang Y-X, Zhuang J. CsLBD37, a LBD/ASL transcription factor, affects nitrate response and flowering of tea plant. Sci Hortic. 2022;306:111457.
doi: 10.1016/j.scienta.2022.111457
Feng X, Xiong J, Zhang W, Guan H, Zheng D, Xiong H, et al. ZmLBD5, a class-II LBD gene, negatively regulates drought tolerance by impairing abscisic acid synthesis. Plant J. 2022;112:1364–76.
pubmed: 36305873
doi: 10.1111/tpj.16015
Basile B, DeJong TM. Control of fruit tree vigor induced by dwarfing rootstocks. In: Warrington I, editor. Horticultural reviews. 1st ed. Wiley; 2018. p. 39–97.
doi: 10.1002/9781119521082.ch2
Du M, Spalding EP, Gray WM. Rapid auxin-mediated cell expansion. Annu Rev Plant Biol. 2020;71:379–402.
pubmed: 32131604
pmcid: 7733314
doi: 10.1146/annurev-arplant-073019-025907
Hayat F, Iqbal S, Coulibaly D, Razzaq MK, Nawaz MA, Jiang W, et al. An insight into dwarfing mechanism: contribution of scion-rootstock interactions toward fruit crop improvement. Fruit Res. 2021;1:1–11.
doi: 10.48130/FruRes-2021-0003
Kuhn BM, Geisler M, Bigler L, Ringli C. Flavonols accumulate asymmetrically and affect auxin transport in Arabidopsis. Plant Physiol. 2011;156:585–95.
pubmed: 21502189
pmcid: 3177260
doi: 10.1104/pp.111.175976
Brown DE, Rashotte AM, Murphy AS, Normanly J, Tague BW, Peer WA, et al. Flavonoids act as negative regulators of auxin transport in vivo in Arabidopsis. Plant Physiol. 2001;126:524–35.
pubmed: 11402184
pmcid: 111146
doi: 10.1104/pp.126.2.524
Kurepa J, Shull TE, Smalle JA. Friends in arms: flavonoids and the auxin/cytokinin balance in terrestrialization. Plants. 2023;12:517.
pubmed: 36771601
pmcid: 9921348
doi: 10.3390/plants12030517
Peer WA, Murphy AS. Flavonoids and auxin transport: modulators or regulators? Trends Plant Sci. 2007;12:556–63.
pubmed: 18198522
doi: 10.1016/j.tplants.2007.10.003
Zhao X, Sun X-F, Zhao L-L, Huang L-J, Wang P-C. Morphological, transcriptomic and metabolomic analyses of Sophora davidii mutants for plant height. BMC Plant Biol. 2022;22:144.
pubmed: 35337273
pmcid: 8951708
doi: 10.1186/s12870-022-03503-1
Zang X, Liu J, Zhao J, Liu J, Ren J, Li L, et al. Uncovering mechanisms governing stem growth in peanut (Arachis hypogaea L.) with varying plant heights through integrated transcriptome and metabolomics analyses. J Plant Physiol. 2023;287:154052.
pubmed: 37454530
doi: 10.1016/j.jplph.2023.154052
Cui Z, Zhang H, Galarneau E-RA, Yang Y, Li D, Song J, et al. Metabolome analysis reveals important compounds related to dwarfing effect of interstock on scion in pear. Ann Appl Biol. 2021;179:108–22.
doi: 10.1111/aab.12684
Zou T, Zhang K, Zhang J, Liu S, Liang J, Liu J, et al. DWARF AND LOW-TILLERING 2 functions in brassinosteroid signaling and controls plant architecture and grain size in rice. Plant J. 2023;116:1766–83.
pubmed: 37699038
doi: 10.1111/tpj.16464
Zang X, Liu J, Zhao J, Liu J, Ren J, Li L, et al. Uncovering mechanisms governing stem growth in peanut (Arachis hypogaea L.) with varying plant heights through integrated transcriptome and metabolomics analyses. J Plant Physiol. 2023;287:154052.
pubmed: 37454530
doi: 10.1016/j.jplph.2023.154052
Xie Z, Zhang L, Zhang Q, Lu Y, Dong C, Li D, et al. A Glu209Lys substitution in DRG1/TaACT7, which disturbs F-actin organization, reduces plant height and grain length in bread wheat. New Phytol. 2023;240:1913–29.
pubmed: 37668262
doi: 10.1111/nph.19246
El-Kereamy A, Bi Y-M, Mahmood K, Ranathunge K, Yaish MW, Nambara E, et al. Overexpression of the CC-type glutaredoxin, OsGRX6 affects hormone and nitrogen status in rice plants. Front Plant Sci. 2015;6:934.
pubmed: 26579177
pmcid: 4630655
doi: 10.3389/fpls.2015.00934
Luo J, Huang S, Wang M, Zhang R, Zhao D, Yang Y, et al. Characterization of the transcriptome and proteome of Brassica napus reveals the close relation between DW871 dwarfing phenotype and stalk tissue. Plants. 2022;11:413.
pubmed: 35161394
pmcid: 8838640
doi: 10.3390/plants11030413
Guo F, Hou L, Ma C, Li G, Lin R, Zhao Y, et al. Comparative transcriptome analysis of the peanut semi-dwarf mutant 1 reveals regulatory mechanism involved in plant height. Gene. 2021;791:145722.
pubmed: 34010708
doi: 10.1016/j.gene.2021.145722
Um TY, Hong SY, Han JS, Jung KH, Moon S, Choi B-S, et al. Gibberellic acid sensitive dwarf encodes an ARPC2 subunit that mediates gibberellic acid biosynthesis, effects to grain yield in rice. Front Plant Sci. 2022;13:1027688.
pubmed: 36618614
pmcid: 9813395
doi: 10.3389/fpls.2022.1027688
Que F, Wang Y-H, Xu Z-S, Xiong A-S. DcBAS1, a carrot brassinosteroid catabolism gene, modulates cellulose synthesis. J Agric Food Chem. 2019;67:13526–33.
pubmed: 31725271
doi: 10.1021/acs.jafc.9b05241
Lu Q, Shao F, Macmillan C, Wilson IW, van der Merwe K, Hussey SG, et al. Genomewide analysis of the lateral organ boundaries domain gene family in Eucalyptus grandis reveals members that differentially impact secondary growth. Plant Biotechnol J. 2018;16:124–36.
pubmed: 28499078
doi: 10.1111/pbi.12754
Ren H, Willige BC, Jaillais Y, Geng S, Park MY, Gray WM, et al. BRASSINOSTEROID-SIGNALING KINASE 3, a plasma membrane-associated scaffold protein involved in early brassinosteroid signaling. PLoS Genet. 2019;15:e1007904.
pubmed: 30615605
pmcid: 6336344
doi: 10.1371/journal.pgen.1007904
Sakamoto T, Kawabe A, Tokida-Segawa A, Shimizu B, Takatsuto S, Shimada Y, et al. Rice CYP734As function as multisubstrate and multifunctional enzymes in brassinosteroid catabolism. Plant J. 2011;67:1–12.
pubmed: 21418356
doi: 10.1111/j.1365-313X.2011.04567.x
Yang Z, Zhang C, Yang X, Liu K, Wu Z, Zhang X, et al. PAG1, a cotton brassinosteroid catabolism gene, modulates fiber elongation. New Phytol. 2014;203:437–48.
pubmed: 24786710
doi: 10.1111/nph.12824
Ohnishi T, Nomura T, Watanabe B, Ohta D, Yokota T, Miyagawa H, et al. Tomato cytochrome P450 CYP734A7 functions in brassinosteroid catabolism. Phytochemistry. 2006;67:1895–906.
pubmed: 16872648
doi: 10.1016/j.phytochem.2006.05.042
Chen Y, Dan Z, Gao F, Chen P, Fan F, Li S. Rice GROWTH-REGULATING FACTOR7 modulates plant architecture through regulating GA and indole-3-acetic acid metabolism. Plant Physiol. 2020;184:393–406.
pubmed: 32581114
pmcid: 7479900
doi: 10.1104/pp.20.00302
Phillips KA, Skirpan AL, Liu X, Christensen A, Slewinski TL, Hudson C, et al. Vanishing tassel2 encodes a grass-specific tryptophan aminotransferase required for vegetative and reproductive development in maize. Plant Cell. 2011;23:550–66.
pubmed: 21335375
pmcid: 3077783
doi: 10.1105/tpc.110.075267
Yoshikawa T, Ito M, Sumikura T, Nakayama A, Nishimura T, Kitano H, et al. The rice FISH BONE gene encodes a tryptophan aminotransferase, which affects pleiotropic auxin-related processes. Plant J. 2014;78:927–36.
pubmed: 24654985
doi: 10.1111/tpj.12517
Lu G, Coneva V, Casaretto JA, Ying S, Mahmood K, Liu F, et al. OsPIN5b modulates rice (Oryza sativa) plant architecture and yield by changing auxin homeostasis, transport and distribution. Plant J. 2015;83:913–25.
pubmed: 26213119
doi: 10.1111/tpj.12939
Liu Y, Liu Y, He Y, Yan Y, Yu X, Ali M, et al. Cytokinin-inducible response regulator SlRR6 controls plant height through gibberellin and auxin pathways in tomato. J Exp Bot. 2023;74:4471–88.
pubmed: 37115725
doi: 10.1093/jxb/erad159
Lee K-H, Du Q, Zhuo C, Qi L, Wang H. LBD29-involved auxin signaling represses NAC master regulators and fiber wall biosynthesis. Plant Physiol. 2019;181:595–608.
pubmed: 31377726
pmcid: 6776862
doi: 10.1104/pp.19.00148
Okushima Y, Fukaki H, Onoda M, Theologis A, Tasaka M. ARF7 and ARF19 regulate lateral root formation via direct activation of LBD/ASL genes in Arabidopsis. Plant Cell. 2007;19:118–30.
pubmed: 17259263
pmcid: 1820965
doi: 10.1105/tpc.106.047761
Okushima Y, Overvoorde PJ, Arima K, Alonso JM, Chan A, Chang C, et al. Functional genomic analysis of the AUXIN RESPONSE FACTOR gene family members in Arabidopsis thaliana: unique and overlapping functions of ARF7 and ARF19. Plant Cell. 2005;17:444–63.
pubmed: 15659631
pmcid: 548818
doi: 10.1105/tpc.104.028316
Li W, Chu C, Li H, Zhang H, Sun H, Wang S, et al. Near-gapless and haplotype-resolved apple genomes provide insights into the genetic basis of rootstock-induced dwarfing. Nat Genet. 2024;56(3):505–16.
pubmed: 38347217
doi: 10.1038/s41588-024-01657-2
Wang T, Liu L, Wang X, Liang L, Yue J, Li L. Comparative analyses of anatomical structure, phytohormone levels, and gene expression profiles reveal potential dwarfing mechanisms in Shengyin bamboo (Phyllostachys edulis f. tubaeformis). IJMS. 2018;19:1697.
pubmed: 29875341
pmcid: 6032043
doi: 10.3390/ijms19061697
Park J-E, Kim Y-S, Yoon H-K, Park C-M. Functional characterization of a small auxin-up RNA gene in apical hook development in Arabidopsis. Plant Sci. 2007;172:150–7.
doi: 10.1016/j.plantsci.2006.08.005
Spartz AK, Lor VS, Ren H, Olszewski NE, Miller ND, Wu G, et al. Constitutive expression of Arabidopsis SMALL AUXIN UP RNA19 (SAUR19) in tomato confers auxin-independent hypocotyl elongation. Plant Physiol. 2017;173:1453–62.
pubmed: 27999086
doi: 10.1104/pp.16.01514
Spartz AK, Ren H, Park MY, Grandt KN, Lee SH, Murphy AS, et al. SAUR inhibition of PP2C-D phosphatases activates plasma membrane H+-ATPases to promote cell expansion in Arabidopsis. Plant Cell. 2014;26:2129–42.
pubmed: 24858935
pmcid: 4079373
doi: 10.1105/tpc.114.126037
Kim D, Langmead B, Salzberg SL. HISAT: a fast spliced aligner with low memory requirements. Nat Methods. 2015;12:357–60.
pubmed: 25751142
pmcid: 4655817
doi: 10.1038/nmeth.3317
Li B, Dewey CN. RSEM: accurate transcript quantification from RNA-Seq data with or without a reference genome. BMC Bioinf. 2011;12:323.
doi: 10.1186/1471-2105-12-323
Wang Z, Gerstein M, Snyder M. RNA-Seq: a revolutionary tool for transcriptomics. Nat Rev Genet. 2009;10:57–63.
pubmed: 19015660
pmcid: 2949280
doi: 10.1038/nrg2484
Young MD, Wakefield MJ, Smyth GK, Oshlack A. Gene ontology analysis for RNA-seq: accounting for selection bias. Genome Biol. 2010;11(2):R14.
pubmed: 20132535
pmcid: 2872874
doi: 10.1186/gb-2010-11-2-r14
Huo F, Wang X, Han Y, Bai Y, Zhang W, Yuan H, et al. A new derivatization approach for the rapid and sensitive analysis of brassinosteroids by using ultra high performance liquid chromatography-electrospray ionization triple quadrupole mass spectrometry. Talanta. 2012;99:420–5.
pubmed: 22967574
doi: 10.1016/j.talanta.2012.05.073
Hellens RP, Allan AC, Friel EN, Bolitho K, Grafton K, Templeton MD, et al. Transient expression vectors for functional genomics, quantification of promoter activity and RNA silencing in plants. Plant Methods. 2005;1:13.
pubmed: 16359558
pmcid: 1334188
doi: 10.1186/1746-4811-1-13
Lu S, Zhang Y, Zhu K, Yang W, Ye J, Chai L, et al. The citrus transcription factor CsMADS6 modulates carotenoid metabolism by directly regulating carotenogenic genes. Plant Physiol. 2018;176:2657–76.
pubmed: 29463773
pmcid: 5884614
doi: 10.1104/pp.17.01830
Transcriptomic study of different tissues of mume ‘Longyan’ plant grafted on mume rootstock and peach rootstock. NCBI. 2024. https://www.ncbi.nlm.nih.gov/bioproject/?term=PRJNA1055178 .
MTBLS10051: Metabolomics study of different tissues of mume ‘Longyan’ plant grafted on mume rootstock and peach rootstock (root) . EMBL-EBI MetaboLights. 2024. https://www.ebi.ac.uk/metabolights/editor/MTBLS10051/descriptors .
MTBLS10062: Metabolomics study of different tissues of mume ‘Longyan’ plant grafted on mume rootstock and peach rootstock (stem) . EMBL-EBI MetaboLights. 2024. https://www.ebi.ac.uk/metabolights/editor/MTBLS10062/descriptors .
MTBLS10083: Metabolomics study of different tissues of mume ‘Longyan’ plant grafted on mume rootstock and peach rootstock (leaf) . EMBL-EBI MetaboLights. 2024. https://www.ebi.ac.uk/metabolights/editor/MTBLS10083/descriptors .