1.Hussain M, Farooq S, Hasan W, Ul-Allah S, Tanveer M, Farooq M, Nawaz A. Drought stress in sunflower: physiological effects and its management through breeding and agronomic alternatives. Agricultural Water Management. 2018;201:152–66.
2.Araújo AE, Silva CAD, Azevedo DMP et al. Cultivo do algodão irrigado. Série Documentos, Sistemas de Produção, 3rd, Versão eletrônica, 2003. p. 1678–8710.
3.Pasapula V, Shen GX, Kuppu S, Paez-Valencia J, Mendoza M, Hou P, Chen J, Qiu XY, Zhu LF, Zhang XL, Auld D, Blumwald E, Zhang H, Gaxiola R, Payton P. Expression of an Arabidopsis vacuolar H+-pyrophosphatase gene (AVP1) in cotton improves drought- and salt tolerance and increases fibre yield in the field conditions. Plant Biotechnology Journal. 2011;9:88–99.
4.Hu Y, Li WC, Xu YQ, Li GJ, Liao Y, Fu FL. Differential expression of candidate genes for lignin biosynthesis under drought stress in maize leaves. J Appl Genet. 2009;50:213–23.
5.Geng D, Chen P, Shen X, Zhang Y, Li X, Jiang L, Niu C, Zhang J, Huang X, Ma F, Guan Q. MdMYB88 and MdMYB124 enhance drought tolerance by modulating root vessels and cell walls in apple. Plant Physiol. 2018;178:1296–309.
6.Hu Q, Min L, Yang XY, Jin SX, Zhang L, Li YY, Ma YZ, Qi XW, Li DQ, Liu HB, Lindsey K, Zhu LF, Zhang XL. Laccase GhLac1 modulates broad-spectrum biotic stress tolerance via manipulating phenylpropanoid pathway and jasmonic acid synthesis. Plant Physiol. 2018;176:1808–23.
7.Zhang K, Cui H, Cao S, Yan L, Li M, Sun Y. Overexpression of CrCOMT from Carex rigescens increases salt stress and modulates melatonin synthesis in Arabidopsis thaliana. Plant Cell Reports. 2019; https://doi.org/10.1007/s00299–019–02461–7.
8.Ehlting JR, Büttner DB, Wang Q, Douglas CJ, Somssich IE, Kombrink E. Three 4-coumarate:coenzyme a ligases in arabidopsis thaliana, represent two evolutionarily divergent classes in angiosperms. Plant J. 1999;19:9–20.
9. Vogt T. Phenylpropanoid biosynthesis. Mol Plant. 2010;3:2–20.
10.Lavhale SG, Kalunke RM, Giri1Structural AP. functional and evolutionary diversity of 4‑coumarate-CoA ligase in plants. Planta. 2018;248:1063–78.
11.Costa MA, Bedger DL, Moinuddin SGA et al. Characterization in vitro and in vivo of the putativemultigene 4-coumarate: CoA ligase network in Arabidopsis: syringyl lignin and sinapate/sinapyl alcohol derivative formation. Phytochemistry. 2005;66:2072–91.
12. Gui JS, Shen JH, Li LG. Functional Characterization of Evolutionarily Divergent 4-Coumarate: Coenzyme A Ligases in Rice. Plant Physiology. 2011;157:574–86.
13.Sun HY, Li Y, Feng SQ, Zou WH, Guo K, Fan CF, Si SL, Peng LC. Analysis of five rice 4-coumarate: coenzyme A ligase enzyme activity and stress response for potential roles in lignin and favonoid biosynthesis in rice. Biochem Biophys Res Commun. 2013;430:1151–6.
14.Uhlmann A, Ebel J. Molecular cloning and expression of 4-coumarate:Coenzyme a ligase, an enzyme involved in the resistance response of soybean (Glycine max L.) against pathogen attack. Plant Physiol. 1993;102:1147–56.
15.Shi R, Sun YH, Li Q, Heber S, Sederoff R, Chiang VL. Towards a systems approach for lignin biosynthesis in Populus trichocarpa: transcript abundance and specificity of the monolignol biosynthetic genes. Plant Cell Physiol. 2010;51:144–63.
16.Souza CA, Barbazuk B, Ralph SG, Bohlmann J, Hamberger B, Douglas CJ. Genome-wideanalysis of a land plant-specific acyl:coenzyme A synthetase (ACS) gene family in Arabidopsis, poplar, rice and Physcomitrella. New Phytol. 2008;179:987–1003.
17.Hu WJ, Kawaoka A, Tsai CJ, Lung J, Osakabe K, Ebinuma H, Chiang VL. Compartmentalized expression of two structurally and functionally distinct 4-coumarate:coa ligase genes in aspen (populus tremuloides). P Natl Acad Sci USA. 1998;95:5407–12.
18.Raes J, Rohde A, Christensen JH, VandePeer Y, Boerjan W. Genome-wide characterization of the lignification toolbox in Arabidopsis. Plant Physiol. 2003;133:1051–71.
19.Zhang CH, Ma T, Luo WC, Xu JM, Liu JQ, Wan DS. Identification of 4CL Genes in Desert Poplars and Their Changes in Expression in Response to Salt Stress. Genes. 2015;6:901–17.
20. Naik P, Wang JP, Sederof R et al. Assessing the impact of the 4CL enzyme complex on the robustness of monolignol biosynthesis using metabolic pathway analysis. PLoS One. 2018;13:e0193896.
21.Li Y, Kim JI, Pysh L, Chapple C. Four isoforms of arabidopsis thaliana 4-coumarate: coa ligase (4cl) have overlapping yet distinct roles in phenylpropanoid metabolism. Plant Physiol. 2014;169:2409–15.
22.Gao S, Yu HN, Xu RX, Cheng AX, Lou HX. Cloning and functional characterization of a 4-coumarate CoA ligase from liverwort Plagi ochasma appendiculatum. Phytochemistry. 2015;111:48–58.
23.Di P, Hu YS, Xuan HJ, Xiao Y, Chen JF, Zhang L, Chen WS. Characterisation and the expression profile of 4-coumarate:coa ligase (Ii4CL) from hairy roots of isatis indigotica. Afr J Pharm Pharmaco. 2012;6:2166–75.
24.Chen XH, Wang HT, Li XY, Ma K, Zhan YG, Zeng FS. Molecular cloning and functional analysis of 4-Coumarate:CoA ligase 4(4CL-like 1) from Fraxinus mandshurica and its role in abiotic stress tolerance and cell wall synthesis. BMC Plant Biology. 2019;19:231–47.
25.Cannon SB, Mitr A, Baumgarten A, Young ND, May G. The roles of segmental and tandem gene duplication in the evolution of large gene families in Arabidopsis thaliana. BMC Plant Biol. 2004;4:10–20.
26.Lescot M, Déhais P, Thijs G, Marchal K, Moreau Y, Yves VDP, Pieree R, Stephane R. Plantcare, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Res. 2002;30:325–7.
27.Zhang T, Hu Y, Jiang W, Fang L, Chen ZJ. Sequencing of allotetraploid cotton (gossypium hirsutum L. acc. TM–1) provides a resource for fiber improvement. Nat Biotechnol. 2015;33:531–7.
28.Rao GD, Pan X, Xu F, Zhang YZ, Cao S, Jiang XG, Lu H. Divergent and overlapping function of five 4-Coumarate: coenzyme A ligases from Populus tomentosa. Plant Mol Biol Rep. 2015;33:841–54.
29.Lindermayr C, Möllers B, Fliegmann J, Uhlmann A, Lottspeich F, Meimberg H, Ebel J. Divergent members of a soybean (glycine max l.) 4-coumarate:coenzyme a ligase gene family. Eur J Biochem. 2002;269:1304–15.
30.Hamberger B, Hahlbrock K. The 4-coumarate:coa ligase gene family in arabidopsis thaliana comprises one rare, sinapate-activating and three commonly occurring isoenzymes. P Natl Acad Sci USA. 2004;101:2209–14.
31.Chen HC, Song J, Williams CM, Shuford CM, Liu J, Wang JP, Li Q, Shi R, Gokce E, Ducoste J, Muddiman DC, Sederoff RR, Chiang VL. Monolignol pathway 4-coumaric acid:coenzyme a ligases in populus trichocarpa: novel specificity, metabolic regulation, and simulation of coenzyme a ligation fluxes. Plant Physiol. 2013;161:1501–16.
32.Choudhary EK, Choi B, Cho BK Kim JB, Park SU, Natarajan S, Lim HS, Bael H. Regulation of 4CL, encoding 4-coumarate: coenzyme A ligase, expression in kenaf under diverse stress conditions. Plant Omics J. 2013;6:254–62.
33.Sutela S, Hahl T, Tiimonen H, Aronen T, Ylioja T, Laakso T, Saranpää P, Chiang V, Julkunen-Tiitto R, Häggman H. Phenolic compounds and expression of 4CL genes in silver birch clones and Pt4CL1a lines. Plos One. 2014;9:e114434.
34.Lee D, Douglas CJ. Two divergent members of a tobacco 4-Coumarate: coenzyme A ligase (4CL) gene family (cDNA structure, gene inheritance and expression, and properties of recombinant proteins). Plant Physiol. 1996;112:193–205.
35. Shinde BA, Dholakia BB, Hussain K Panda S, Meir S, Rogachev I, Aharoni A, Giri AP, Kamble AC. Dynamic metabolic reprogramming of steroidal glycol-alkaloid and phenylpropanoid biosynthesis may impart early blight resistance in wild tomato (Solanum arcanum Peralta). Plant Mol Biol. 2017;95:411–23.
36.Ehlting J, Shin JJ, Douglas CJ. Identification of 4-coumarate:coenzyme A ligase (4CL) substrate recognition domains. Plant J. 2001;27:455–65.
37.Schneider K, Hövel K, Witzel K, Hamberger B, Schomburg D, Kombrink E, Stuible H-P. The substrate specificity-determining amino acid code of 4-coumarate:CoA ligase. Proc Natl Acad Sci USA. 2003;100:8601–6.
38.Rose AB. Intron-mediated regulation of gene expression. Curr Top Microbiol Immunol. 2008;326:277–90.
39.Xu G, Guo C, Shan H, Kong H. Divergence of duplicate genes in exon-intron structure. Proc Nat Acad Sci USA. 2012;109:1187–92.
40.Zhao P, Wang DD, Wang RQ, Kong NN, Zhang C, Yang CH, Wu WT, Ma HL, Chen Q. Genome-wide analysis of the potato Hsp20 gene family: identification, genomic organization and expression profiles in response to heat stress. BMC Genomics. 2018;19:61–73.
41.Xu J, Xu XY, Tian LL, Wang GL, Zhang XY, Guo WZ. Discovery and identification of candidate genes from the chitinase gene family for Verticillium dahliae resistance in cotton. Scientific Reports. 2016; 6:29022.
42.Liu Z, Ge XY, Yang ZR, Zhang CJ, Zhao G, Chen EY, Liu J, Zhang XY, Li FG. Genome-wide identification and characterization of SnRK2gene family in cotton (Gossypium hirsutumL.). BMC Genetics. 2017;18:54–68.
43.Turner JG, Ellis C, Devoto A. The jasmonate signal pathway. Plant Cell. 2002;14:S153–S164.
44.Browse J and Howe GA. New weapons and a rapid response against insect attack. Plant Physiol. 2008;146:832–8.
45.Xu WR, Yu YH, Ding JH, Hua ZY, Wang YJ. Characterization of a novel stilbene synthase promoter involved in pathogen and stress inducible expression from Chinese wild Vitis pseudoreticulata. Planta. 2010;231:475–87.
46.Li W, Cui X, Meng ZL, Huang XH, Xie Q, Wu H, Jin HL, Zhang DB, Liang WQ. Transcriptional regulation of Arabidopsis MIR168a and ARGONAUTE1 homeostasis in abscisic acid and abiotic stress responses. Plant Physiol. 2012;158:1279–92.
47.Hossain MA, Bhattacharjee S, Armin S-M, Qian PP, Xin W, Li HY, Burritt DJ, Fujita M, Tran LSP. Hydrogen peroxide priming modulates abiotic oxidative stress tolerance: insights from ROS detoxification and scavenging. Front Plant Sci. 2015;6:420–39.
48.Jain G, Gould KS. Are betalain pigments the functional homologues of anthocyanins in plants? Environ Exp Bot. 2015;119:48–53.
49.Parkhi V, Kumar V, Sunilkumar G, Campbell LM, Singh NK, Rathore KS. Expression of apoplastically secreted tobacco osmotin in cotton confers drought tolerance. Mol Breed. 2009;23:625–39.
50.Sharma P, Jha AB, Dubey RS, Pessarakli M. Reactive oxygen species, oxidative damage, and antioxidative defense mechanism in plants under stressful conditions. J Exp Bot. 2012;12:1–26.
51.Ullah A, Sun H, Hakim YX, Zhang X. A novel cotton WRKY gene, GhWRKY6-like, improves salt tolerance by activating the ABA signaling pathway and scavenging of reactive oxygen species. Physiol Plant. 2018;162:439–54.
52.Comas LH, Becker SR, Cruz VMV, Byrne PF, Dierig DA. Root traits contributing to plant productivity under drought. Front Plant Sci, 2013;4:442–58.
53.Xiong L, Wang RG, Mao G, Koczan JM. Identification of drought tolerance determinants by genetic analysis of root response to drought stress and abscisic acid. Plant Physiol. 2006;142:1065–74.
54.Montillet JL, Leonhardt N, Mondy S, Tranchimand S, Rumeau D, Boudsocq M, Garcia AV, Douki T, Bigeard J, Laurie’re C, Chevalier A, Castresana C, Hirt H. An abscisic acid-independent oxylipin pathway controls stomata closure and immune defense in Arabidopsis. PLoS Biol. 2013;11:e1001513.
55.Rowe JH, Topping JF, Liu J, Lindsey K. Abscisic acid regulates root growth under osmotic stress conditions via an interacting hormonal network with cytokinin, ethylene and auxin. New Phytol. 2016;211:225–39.
56.Skriver K, Mundy J. Gene expression in response to abscisic acid and osmotic stress. Plant Cell. 1990;2:503–12.
57.Chandler PM, Robertson M. Gene expression regulated by abscisic acid and its relation to stress tolerance. Annu. Rev. Plant Physiol. Plant Mol Biol. 1994;45:113–41.
58.Leung J, Giraudat J. Abscisic acid signal transduction. Annu Rev Plant Physiol Plant Mol Biol. 1998;49:199–222.
59.Penning BW, Hunter CT, Tayengwa R, Eveland AL, Dugard CK, Olek AT, Vermerris W, Koch KE, McCarty DR, Davis MF, Thomas SR, McCann MC, Carpita NC. Genetic resources for maize cell wall biology. Plant Physiol. 2009;151:1703–28.
60.Campbell M, Sederoff R. Variation in lignin content and composition (mechanisms of control and implications for the genetic improvement of plants). Plant Physiol. 1996;110:3–13.
61.Vance C, And TK, Sherwood R. Lignification as a mechanism of disease resistance. Annu Rev Phytopathol. 2003;18:259–88.
62.Lin CY, Wang JP, Li QZ, Chen HC, Liu J, Loziuk P, Song J. 4-Coumaroyl and caffeoyl shikimic acids inhibit 4-coumaric acid: coenzyme a ligases and modulate metabolic flux for 3-hydroxylation in monolignol biosynthesis of Populus trichocarpa. Mol Plant. 2015;8:176–87.
63.Li WQ, Zhang MJ, Gan PF, Qiao L, Yang SQ, Miao H, Wang GF, Zhang MM, Liu WT, Li HF, Shi CH, Chen KM. CLD1/SRL1 modulates leaf rolling by affecting cell wall formation, epidermis integrity and water homeostasis in rice. Plant J. 2017;92:904–23.
64.Jordan R. Structural changes and associated reduction of hydraulic conductance in roots of Sorghum bicolor L. following exposure to water deficit. Plant Physiol. 1992;99:203–12.
65.Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR. The pfam protein families database. Nucleic Acids Res. 2014;42:222–30.
66.Finn RD, Clements J, Eddy SR. Hmmer web server: interactive sequence similarity searching. Nucleic Acids Res. 2011;39:29–37.
67.Aron MB, Myra KD, Noreen RG, Shennan L, Farideh C, Lewis YG. Cdd: ncbi’s conserved domain database. Nucleic Acids Res. 2015;43:D222.
68.Letunic I, Bork P. 20 years of the smart protein domain annotation resource. Nucleic Acids Res. 2018;46:D493–D496.
69.Gasteiger E, Hoogland C, Gattiker A, Duvaud S, Wilkins MR, Appel RD, Bairoch A. Protein Identification and Analysis Tools on the ExPASy Server. In: Walker J.M, editor. The Proteomics Protocols Handbook. Totowa:New Jersey; 2005. p. 571–607.
70.Guo AY, Zhu QH, Chen X, Luo JC. GSDS: a gene structure display server. Hereditas. 2007;29:1023–26.
71.Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, Ren JY, Li WW, Noble WS. MEME Suite: tools for motif discovery and searching. Nucleic Acids Res. 2009;37:W202–W208.
72. Thompson JD, Gibson TJ, Plewniak F, Jeanmougin F, Higgins DG. The CLUSTAL_X
windows interface: flexible strategies for multiple sequence alignment aided by quality analysis tools. Nucleic Acids Res. 1997;25:4876–82.
73.Tamura K, Stecher G, Peterson D, Filipski A, Kumar S. Mega6: molecular evolutionary genetics analysis version 6.0. Mol Biol Evol. 2013;30:2725–9.
74.Chen CJ, Xia R, Chen H, He YH. TBtools, a Toolkit for Biologists integrating various HTS-data handling tools with a user-friendly interface. BioRxiv. 2018;http://doi.org/10.1101/289660.
75.Holub EB. The arms race is ancient history in arabidopsis, the wildflower. Nat Rev Genet. 2001;2:516–27.
76.Wang YP, Tang HB, Debarry JD, Tan X, Li JP, Wang XY, Lee TH, Jin HZ, Marler B, Guo H, Kissinger JC, Paterson AH. MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity. Nucleic Acids Research. 2012;40:e49.
77.Wang D, Zhang Y, Zhang Y, Zhu J, Yu J. KaKs_Calculator 2.0: a toolkit incorporating gamma-series methods and sliding window strategies. Genom Proteom Bioinf. 2010;8:77–80.
78.Clough SJ, Bent AF. Floral dip: a simplifed method for Agrobacterium-mediated transformat of Arabidopsis thaliana. Plant J. 1998;16:735–43.
79.Xiong XP, Sun SC, Li YJ, Zhang XY, Sun J, Xue F. The cotton WRKY transcription factor GhWRKY70 negatively regulates the defense response against Verticillium dahliae. The Crop Journal. 2019;7:393–402.
80.Porra RJ, Thompson WA, Kriedemann PE. Determination of accurate extinction coefficients and simultaneous equations for assaying chlorophylls a and b extracted with four different solvents:verification of the concentration of chlorophyll standards by atomic absorption spectroscopy. Biochimica et Biophysica Acta. 1989;975:384–94.
81.Lefebvre V, North H, Frey A, Sotta B, Seo M, Okamoto M, Nambara E, Marion-Poll A. Functional analysis of Arabidopsis NCED6 and NCED9 genes indicates that ABA synthesized in the endosperm is involved in the induction of seed dormancy. Plant J. 2006;45:309–19.
82.Sade N, Vinocur BJ, Diber A, Shatil A, Ronen G, Nissan H, Wallach R, Karchi H, Moshelion M. Improving plant stress tolerance and yield production: is the tonoplast aquaporin SlTIP2; 2 a key to isohydric to anisohydric conversion?. New Phytol. 2009;181:651–61.
83.Geisler M, Nadeau J, Sack FD. Oriented asymmetric divisions that generate the stomatal spacing pattern in arabidopsis are disrupted by the too many mouths mutation. Plant Cell. 2000;12:2075–86.
84.Morrison I. A semi-micro method for the determination of lignin and its use in predicting the digestibility of forage crops. J Sci Food Agric. 1972;23:455–63.
85.Pomar F, Merino F, Barceló AR. O–4-Linked coniferyl and sinapyl aldehydes in lignifying cell walls are the main targets of the Wiesner (phloroglucinol-HCl) reaction. Protoplasma. 2002;220:17–28.