Anderson N A, Bonawitz N D, Nyffeler K, Chapple C. 2015. Loss of FERULATE 5-HYDROXYLASE leads to mediator-dependent inhibition of soluble phenylpropanoid biosynthesis in Arabidopsis. Plant Physiology, 169, 1557–1567.
Brown D E, Rashotte A M, Murphy A S, Normanly J, Tague B W, Peer W A, Taiz L, Muday G K. 2001. Flavonoids act as negative regulators of auxin transport in vivo in Arabidopsis. Plant Physiology, 126, 524–535.
Casanova-Saez R, Mateo-Bonmati E, Ljung K. 2021. Auxin metabolism in plants. Cold Spring Harbor Perspectives in Biology, 13, a039867.
Chapple C C, Vogt T, Ellis B E, Somerville C R. 1992. An Arabidopsis mutant defective in the general phenylpropanoid pathway. Plant Cell, 4, 1413–1424.
Chen W, Gong L, Guo Z, Wang W, Zhang H, Liu X, Yu S, Xiong L, Luo J. 2013. A novel integrated method for large-scale detection, identification, and quantification of widely targeted metabolites: Application in the study of rice metabolomics. Molecular Plant, 6, 1769–1780.
Chen Y, Fan X, Song W, Zhang Y, Xu G. 2012. Over-expression of OsPIN2 leads to increased tiller numbers, angle and shorter plant height through suppression of OsLAZY1. Plant Biotechnol Journal, 10, 139–149
Choe S, Dilkes B P, Fujioka S, Takatsuto S, Sakurai A, Feldmann K A. 1998. The DWF4 gene of Arabidopsis encodes a cytochrome P450 that mediates multiple 22 alpha-hydroxylation steps in brassinosteroid biosynthesis. Plant Cell, 10, 231–243.
Clouse S D, Langford M, McMorris T C. 1996. A brassinosteroid-insensitive mutant in Arabidopsis thaliana exhibits multiple defects in growth and development. Plant Physiology, 111, 671–678.
Dharmasiri N, Dharmasiri S, Weijers D, Lechner E, Yamada M, Hobbie L, Ehrismann J S, Jurgens G, Estelle M. 2005. Plant development is regulated by a family of auxin receptor F box proteins. Developmental Cell, 9, 109–119.
Dong X C, Qian T F, Chu J P, Zhang X, Liu Y J, Dai X L, He M R. 2023. Late sowing enhances lodging resistance of wheat plants by improving the biosynthesis and accumulation of lignin and cellulose. Journal of Integrative Agriculture, 22, 1351–1365.
Du M M, Spalding E P, Gray W M. 2020. Rapid auxin-mediated cell expansion. Annual Review of Plant Biology, 71, 379–402.
Duke S O. 2018. The history and current status of glyphosate. Pest Management Science, 74, 1027–1034.
Duke S O, Powles S B. 2008. Glyphosate: A once-in-a-century herbicide. Pest Management Science, 64, 319–325.
Fang S, Yao J, Li Y, Zhu S, Pan J, Li Q, Wang W, Kong J, He L, Zhang Y, Chen W. 2022. Fine mapping and characterization of the Crinkled Dwarf gene in cotton. Industrial Crops and Products, 184, 115034.
Farquharson K L. 2014. SAUR19 links auxin and plasma membrane H+-ATPases in cell expansion. Plant Cell, 26, 1835.
Fernandez-Moreno P T, Alcantara-de la Cruz R, Smeda R J, De Prado R. 2017. Differential resistance mechanisms to glyphosate result in fitness cost for Lolium perenne and L. multiflorum. Frontiers in Plant Science, 8, 1796.
Filiz E, Koc I. 2016. Genome-wide identification and comparative analysis of EPSPS (aroA) genes in different plant species. Journal of Plant Biochemistry and Biotechnology, 25, 21–29.
Franke R, Humphreys J M, Hemm M R, Denault J W, Ruegger M O, Cusumano J C, Chapple C. 2002. The Arabidopsis REF8 gene encodes the 3-hydroxylase of phenylpropanoid metabolism. The Plant Journal, 30, 33–45.
Fraser C M, Chapple C. 2011. The phenylpropanoid pathway in Arabidopsis. Arabidopsis Book, 9, e0152.
Friml J, Yang X, Michniewicz M, Weijers D, Quint A, Tietz O, Benjamins R, Ouwerkerk P B, Ljung K, Sandberg G, Hooykaas P J, Palme K, Offringa R. 2004. A PINOID-dependent binary switch in apical–basal PIN polar targeting directs auxin efflux. Science, 306, 862–865.
Fu L I, Yan D, Gao L F, Liu P, Zhao G Y, Jia J Z, Ren Z L. 2022. TaIAA15 genes regulate plant architecture in wheat. Journal of Integrative Agriculture, 21, 1243–1252.
Fulton T M, Chunwongse J, Tanksley S D. 1995. Microprep protocol for extraction of DNA from tomato and other herbaceous plants. Plant Molecular Biology Reporter, 13, 207–209.
Gencsoylu I. 2009. Effect of plant growth regulators on agronomic characteristics, lint quality, pests, and predators in cotton. Journal of Plant Growth Regulation, 28, 147–153.
Gong L S, Qu S J, Huang G M, Guo Y L, Zhang M C, Li Z H, Zhou Y Y, Duan L S. 2021. Improving maize grain yield by formulating plant growth regulator strategies in North China. Journal of Integrative Agriculture, 20, 622–632.
Griffiths J, Murase K, Rieu I, Zentella R, Zhang Z L, Powers S J, Gong F, Phillips A L, Hedden P, Sun T P, Thomas S G. 2006. Genetic characterization and functional analysis of the GID1 gibberellin receptors in Arabidopsis. Plant Cell, 18, 3399–3414.
Hedden P. 2003. The genes of the green revolution. Trends in Genetics, 19, 5–9.
Helliwell C A, Sheldon C C, Olive M R, Walker A R, Zeevaart J A, Peacock W J, Dennis E S. 1998. Cloning of the Arabidopsis ent-kaurene oxidase gene GA3. Proceedings of the National Academy of Sciences of the United States of America, 95, 9019–9024.
Hirano K, Yoshida H, Aya K, Kawamura M, Hayashi M, Hobo T, Sato-Izawa K, Kitano H, Ueguchi-Tanaka M, Matsuoka M. 2017. SMALL ORGAN SIZE 1 and SMALL ORGAN SIZE 2/DWARF AND LOW-TILLERING form a complex to integrate auxin and brassinosteroid signaling in rice. Molecular Plant, 10, 590–604.
Hoffmann L, Besseau S, Geoffroy P, Ritzenthaler C, Meyer D, Lapierre C, Pollet B, Legrand M. 2004. Silencing of hydroxycinnamoyl-coenzyme A shikimate/quinate hydroxycinnamoyltransferase affects phenylpropanoid biosynthesis. Plant Cell, 16, 1446–1465.
Huang G, Huang J Q, Chen X Y, Zhu Y X. 2021. Recent advances and future perspectives in cotton research. Annual Review of Plant Biology, 72, 437–462.
Huang G, Zhu Y X. 2021. Breeding cotton with superior fiber quality: Identification and utilization of multiple elite loci and exotic genetic resources. Science China (Life Science), 64, 1197–1198.
Ingold E, Sugiyama M, Komamine A. 1990. L-alpha-Aminooxy-beta-phenylpropionic acid inhibits lignification but not the differentiation to tracheary elements of isolated mesophyll cells of Zinnia elegans. Physiologia Plantarum, 78, 67–74.
Ji G, Liang C, Cai Y, Pan Z, Meng Z, Li Y, Jia Y, Miao Y, Pei X, Gong W, Wang X, Gao Q, Peng Z, Wang L, Sun J, Geng X, Wang P, Chen B, Wang P, Zhu T, et al. 2021. A copy number variant at the HPDA-D12 locus confers compact plant architecture in cotton. New Phytologist, 229, 2091–2103.
Jing C, Ma X J, Di J C, Chen X S. 2011. Gene mapping of an ultra-dwarf mutant in upland cotton. Hereditas, 33, 1393–1397.
Kakiuchi Y, Galis I, Tamogami S, Wabiko H. 2006. Reduction of polar auxin transport in tobacco by the tumorigenic Agrobacterium tumefaciens AK-6b gene. Planta, 223, 237–247.
Kim J I, Ciesielski P N, Donohoe B S, Chapple C, Li X. 2014. Chemically induced conditional rescue of the reduced epidermal fluorescence8 mutant of Arabidopsis reveals rapid restoration of growth and selective turnover of secondary metabolite pools. Plant Physiology, 164, 584–595.
Kuhn B M, Geisler M, Bigler L, Ringli C. 2011. Flavonols accumulate asymmetrically and affect auxin transport in Arabidopsis. Plant Physiology, 156, 585–595.
Kuhn B M, Nodzynski T, Errafi S, Bucher R, Gupta S, Aryal B, Dobrev P, Bigler L, Geisler M, Zazimalova E, Friml J, Ringli C. 2017. Flavonol-induced changes in PIN2 polarity and auxin transport in the Arabidopsis thaliana rol1-2 mutant require phosphatase activity. Scientific Reports, 7, 41906.
Lanot A, Hodge D, Jackson R G, George G L, Elias L, Lim E K, Vaistij F E, Bowles D J. 2006. The glucosyltransferase UGT72E2 is responsible for monolignol 4-O-glucoside production in Arabidopsis thaliana. The Plant Journal, 48, 286–295.
Leple J C, Dauwe R, Morreel K, Storme V, Lapierre C, Pollet B, Naumann A, Kang K Y, Kim H, Ruel K, Lefebvre A, Joseleau J P, Grima-Pettenati J, De Rycke R, Andersson-Gunneras S, Erban A, Fehrle I, Petit-Conil M, Kopka J, Polle A, et al. 2007. Downregulation of cinnamoyl-coenzyme A reductase in poplar: Multiple-level phenotyping reveals effects on cell wall polymer metabolism and structure. Plant Cell, 19, 3669–3691.
Lewis D R, Ramirez M V, Miller N D, Vallabhaneni P, Ray W K, Helm R F, Winkel B S, Muday G K. 2011. Auxin and ethylene induce flavonol accumulation through distinct transcriptional networks. Plant Physiology, 156, 144–164.
Li J, Nagpal P, Vitart V, McMorris T C, Chory J. 1996. A role for brassinosteroids in light-dependent development of Arabidopsis. Science, 272, 398–401.
Li J, Wen J, Lease K A, Doke J T, Tax F E, Walker J C. 2002. BAK1, an Arabidopsis LRR receptor-like protein kinase, interacts with BRI1 and modulates brassinosteroid signaling. Cell, 110, 213–222.
Li X, Bonawitz N D, Weng J K, Chapple C. 2010. The growth reduction associated with repressed lignin biosynthesis in Arabidopsis thaliana is independent of flavonoids. Plant Cell, 22, 1620–1632.
Li Y, Han S, Qi Y. 2023. Advances in structure and function of auxin response factor in plants. Journal of Integrative Plant Biology, 65, 617–632.
Li Y, Kim J I, Pysh L, Chapple C. 2015. Four isoforms of Arabidopsis 4-coumarate:CoA ligase have overlapping yet distinct roles in phenylpropanoid metabolism. Plant Physiology, 169, 2409–2421.
Li Z, Zhang X, Zhao Y, Li Y, Zhang G, Peng Z, Zhang J. 2018. Enhancing auxin accumulation in maize root tips improves root growth and dwarfs plant height. Plant Biotechnology Journal, 16, 86–99.
Liu C, Zheng S, Gui J S, Fu C J, Yu H S, Song D L, Shen J H, Qin P, Liu X M, Han B, Yang Y Z, Li L G. 2018. Shortened basal internodes encodes a gibberellin 2-oxidase and contributes to lodging resistance in rice. Molecular Plant, 11, 288–299.
Lu G W, Coneva V, Casaretto J A, Ying S, Mahmood K, Liu F, Nambara E, Bi Y M, Rothstein S J. 2015. OsPIN5b modulates rice (Oryza sativa) plant architecture and yield by changing auxin homeostasis, transport and distribution. Plant Journal, 83, 913–925
Ma C, Rehman A, Li H G, Zhao Z B, Sun G, Du X M. 2022. Mapping of dwarfing QTL of Ari1327, a semi-dwarf mutant of upland cotton. BMC Plant Biology, 22, 5.
Macmillan C P, Birke H, Bedon F, Pettolino F A. 2013. Lignin deposition in cotton cells - Where is the lignin? Journal of Plant Biochemistry & Physiology, 1, 1000e1106.
Maeda H, Dudareva N. 2012. The shikimate pathway and aromatic amino acid biosynthesis in plants. Annual Review of Plant Biology, 63, 73–105.
Martin S L, Benedict L, Sauder C A, Wei W, da Costa L O, Hall L M, Beckie H J. 2017. Glyphosate resistance reduces kochia fitness: Comparison of segregating resistant and susceptible F2 populations. Plant Science, 261, 69–79.
McKim S M. 2019. How plants grow up. Journal of Integrative Plant Biology, 61, 257–277.
Meyer K. 2003. Secondary products | lignin. In: Thomas B, ed., Encyclopedia of Applied Plant Sciences. Elsevier, Oxford. pp. 1131–1140.
Muro-Villanueva F, Mao X, Chapple C. 2019. Linking phenylpropanoid metabolism, lignin deposition, and plant growth inhibition. Current Opinion in Biotechnology, 56, 202–208.
Nakajima M, Shimada A, Takashi Y, Kim Y C, Park S H, Ueguchi-Tanaka M, Suzuki H, Katoh E, Iuchi S, Kobayashi M, Maeda T, Matsuoka M, Yamaguchi I. 2006. Identification and characterization of Arabidopsis gibberellin receptors. The Plant Journal, 46, 880–889.
Overvoorde P J, Okushima Y, Alonso J M, Chan A, Chang C, Ecker J R, Hughes B, Liu A, Onodera C, Quach H, Smith A, Yu G, Theologis A. 2005. Functional genomic analysis of the AUXIN/INDOLE–3-ACETIC ACID gene family members in Arabidopsis thaliana. Plant Cell, 17, 3282–3300.
Park J E, Park J Y, Kim Y S, Staswick P E, Jeon J, Yun J, Kim S Y, Kim J, Lee Y H, Park C M. 2007. GH3-mediated auxin homeostasis links growth regulation with stress adaptation response in Arabidopsis. Journal of Biological Chemistry, 282, 10036–10046.
Peer W A, Bandyopadhyay A, Blakeslee J J, Makam S N, Chen R J, Masson P H, Murphy A S. 2004. Variation in expression and protein localization of the PIN family of auxin efflux facilitator proteins in flavonoid mutants with altered auxin transport in Arabidopsis thaliana. Plant Cell, 16, 1898–1911.
Peer W A, Murphy A S. 2007. Flavonoids and auxin transport: modulators or regulators? Trends in Plant Science, 12, 556–563.
Peret B, Swarup K, Ferguson A, Seth M, Yang Y, Dhondt S, James N, Casimiro I, Perry P, Syed A, Yang H, Reemmer J, Venison E, Howells C, Perez-Amador M A, Yun J, Alonso J, Beemster G T, Laplaze L, Murphy A, et al. 2012. AUX/LAX genes encode a family of auxin influx transporters that perform distinct functions during Arabidopsis development. Plant Cell, 24, 2874–2885.
Qi H K, Du M W, Meng L, Xie L W, Eneji A E, Xu D Y, Tian X L, Li Z H. 2022. Cotton maturity and responses to harvest aids following chemical topping with mepiquat chloride during bloom period. Journal of Integrative Agriculture, 21, 2577–2587.
Ranocha P, Denance N, Vanholme R, Freydier A, Martinez Y, Hoffmann L, Kohler L, Pouzet C, Renou J P, Sundberg B, Boerjan W, Goffner D. 2010. Walls are thin 1 (WAT1), an Arabidopsis homolog of Medicago truncatula NODULIN21, is a tonoplast-localized protein required for secondary wall formation in fibers. The Plant Journal, 63, 469–483.
Ranocha P, Dima O, Nagy R, Felten J, Corratge-Faillie C, Novak O, Morreel K, Lacombe B, Martinez Y, Pfrunder S, Jin X, Renou J P, Thibaud J B, Ljung K, Fischer U, Martinoia E, Boerjan W, Goffner D. 2013. Arabidopsis WAT1 is a vacuolar auxin transport facilitator required for auxin homoeostasis. Nature Communications, 4, 2625.
Regnault T, Daviere J M, Heintz D, Lange T, Achard P. 2014. The gibberellin biosynthetic genes AtKAO1 and AtKAO2 have overlapping roles throughout Arabidopsis development. The Plant Journal, 80, 462–474.
Rinaldi M A, Liu J, Enders T A, Bartel B, Strader L C. 2012. A gain-of-function mutation in IAA16 confers reduced responses to auxin and abscisic acid and impedes plant growth and fertility. Plant Molecular Biology, 79, 359–373.
Salazar-Cerezo S, Martinez-Montiel N, Garcia-Sanchez J, Perez Y T R, Martinez-Contreras R D. 2018. Gibberellin biosynthesis and metabolism: A convergent route for plants, fungi and bacteria. Microbiology Research, 208, 85–98.
Schilmiller A L, Stout J, Weng J K, Humphreys J, Ruegger M O, Chapple C. 2009. Mutations in the cinnamate 4-hydroxylase gene impact metabolism, growth and development in Arabidopsis. The Plant Journal, 60, 771–782.
Spartz A K, Lee S H, Wenger J P, Gonzalez N, Itoh H, Inzé D, Peer W A, Murphy A S, Overvoorde P J, Gray W M. 2012. The SAUR19 subfamily of SMALL AUXIN UP RNA genes promote cell expansion. The Plant Journal, 70, 978–990.
Sun T, Goodman H M, Ausubel F M. 1992. Cloning the Arabidopsis GA1 locus by genomic subtraction. Plant Cell, 4, 119–128.
Szekeres M, Nemeth K, Koncz-Kalman Z, Mathur J, Kauschmann A, Altmann T, Redei G P, Nagy F, Schell J, Koncz C. 1996. Brassinosteroids rescue the deficiency of CYP90, a cytochrome P450, controlling cell elongation and de-etiolation in Arabidopsis. Cell, 85, 171–182.
Tao Y, Ferrer J L, Ljung K, Pojer F, Hong F X, Long J A, Li L, Moreno J E, Bowman M E, Ivans L J, Cheng Y F, Lim J, Zhao Y D, Ballare C L, Sandberg G, Noel J P, Chory J. 2008. Rapid synthesis of auxin via a new tryptophan-dependent pathway is required for shade avoidance in plants. Cell, 133, 164–176.
Vanholme R, De Meester B, Ralph J, Boerjan W. 2019. Lignin biosynthesis and its integration into metabolism. Current Opinion in Biotechnology, 56, 230–239.
Wang K, Li M, Hakonarson H. 2010. ANNOVAR: Functional annotation of genetic variants from high-throughput sequencing data. Nucleic Acids Research, 38, e164.
Wang S, Chen J, Zhang W, Hu Y, Chang L, Fang L, Wang Q, Lv F, Wu H, Si Z, Chen S, Cai C, Zhu X, Zhou B, Guo W, Zhang T. 2015. Sequence-based ultra-dense genetic and physical maps reveal structural variations of allopolyploid cotton genomes. Genome Biology, 16, 108.
Wang Y, Li J. 2008. Molecular basis of plant architecture. Annual Review of Plant Biology, 59, 253–279.
Weijers D, Wagner D. 2016. Transcriptional responses to the auxin hormone. Annual Review of Plant Biology, 67, 539–574.
Wen X, Chen Z, Yang Z, Wang M, Jin S, Wang G, Zhang L, Wang L, Li J, Saeed S, He S, Wang Z, Wang K, Kong Z, Li F, Zhang X, Chen X, Zhu Y. 2023. A comprehensive overview of cotton genomics, biotechnology and molecular biological studies. Science China (Life Science), 66, 2114–2256.
Xi Y, Yang Y, Yang J, Zhang X, Pan Y, Guo H. 2021. IAA3-mediated repression of PIF proteins coordinates light and auxin signaling in Arabidopsis. PLoS Genetics, 17, e1009384.
Xie M, Muchero W, Bryan A C, Yee K, Guo H B, Zhang J, Tschaplinski T J, Singan V R, Lindquist E, Payyavula R S, Barros-Rios J, Dixon R, Engle N, Sykes R W, Davis M, Jawdy S S, Gunter L E, Thompson O, DiFazio S P, Evans L M, et al. 2018. A 5-enolpyruvylshikimate 3-phosphate synthase functions as a transcriptional repressor in Populus. Plant Cell, 30, 1645–1660.
Yamaguchi S, Sun T, Kawaide H, Kamiya Y. 1998. The GA2 locus of Arabidopsis thaliana encodes ent-kaurene synthase of gibberellin biosynthesis. Plant Physiology, 116, 1271–1278.
Yang Z, Gao C, Zhang Y, Yan Q, Hu W, Yang L, Wang Z, Li F. 2022. Recent progression and future perspectives in cotton genomic breeding. Journal of Integrative Plant Biology, 65, 548–569.
Yang Z, Ge X, Yang Z, Qin W, Sun G, Wang Z, Li Z, Liu J, Wu J, Wang Y, Lu L, Wang P, Mo H, Zhang X, Li F. 2019. Extensive intraspecific gene order and gene structural variations in upland cotton cultivars. Nature Communications, 10, 2989.
Yang Z, Zhang C, Yang X, Liu K, Wu Z, Zhang X, Zheng W, Xun Q, Liu C, Lu L, Yang Z, Qian Y, Xu Z, Li C, Li J, Li F. 2014. PAG1, a cotton brassinosteroid catabolism gene, modulates fiber elongation. New Phytologist, 203, 437–448.
Yanniccari M, Vila-Aiub M, Istilart C, Acciaresi H, Castro A M. 2017. Glyphosate resistance in Perennial Ryegrass (Lolium perenne L.) is associated with a fitness penalty. Weed Science, 64, 71–79.
Yin R H, Han K, Heller W, Albert A, Dobrev P I, Zazimalova E, Schaffner A R. 2014. Kaempferol 3-O-rhamnoside-7-O-rhamnoside is an endogenous flavonol inhibitor of polar auxin transport in Arabidopsis shoots. New Phytologist, 201, 466–475.
Youn J H, Kim T W, Joo S H, Son S H, Roh J, Kim S, Kim T W, Kim S K. 2018. Function and molecular regulation of DWARF1 as a C-24 reductase in brassinosteroid biosynthesis in Arabidopsis. Journal of Experimental Botany, 69, 1873–1886.
Zhang C, Sun J L, Jia Y H, Wang J, Xu Z J, Du X M. 2011. Morphological characters, inheritance and response to exogenous hormones of a cotton super-dwarf mutant of Gossypium hirsutum. Plant Breeding, 130, 67–72.
Zhang X, Hou X, Liu Y, Zheng L, Yi Q, Zhang H, Huang X, Zhang J, Hu Y, Yu G, Liu H, Li Y, Huang H, Zhan F, Chen L, Tang J, Huang Y. 2019. Maize brachytic2 (br2) suppresses the elongation of lower internodes for excessive auxin accumulation in the intercalary meristem region. BMC Plant Biology, 19, 589.
Zhang Y, Zhang Y, Ge X, Yuan Y, Jin Y, Wang Y, Zhao L, Han X, Hu W, Yang L, Gao C, Wei X, Li F, Yang Z. 2023. Genome-wide association analysis reveals a novel pathway mediated by a dual-TIR domain protein for pathogen resistance in cotton. Genome Biology, 24, 111.
Zhao C, Ma J, Zhang Y, Yang S, Feng X, Yan J. 2022. The miR166 mediated regulatory module controls plant height by regulating gibberellic acid biosynthesis and catabolism in soybean. Journal of Integrative Plant Biology, 64, 995–1006.
Zheng Z, Guo Y, Novak O, Chen W, Ljung K, Noel J P, Chory J. 2016. Local auxin metabolism regulates environment-induced hypocotyl elongation. Nature Plants, 2, 16025.
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