Veraverbeke WS, Delcour JA. Wheat protein composition and properties of wheat glutenin in relation to breadmaking functionality. Crit Rev Food Sci Nutr. 2002;42(3):179–208. https://doi.org/10.1080/10408690290825510.
Article
CAS
PubMed
Google Scholar
Shiferaw B, Smale M, Braun HJ, Duveiller E, Reynolds M, Muricho G. Crops that feed the world 10. Past successes and future challenges to the role played by wheat in global food security. Food Security. 2013;5(3):291–317. https://doi.org/10.1007/s12571-013-0263-y.
Article
Google Scholar
Rajaram S. Prospects and promise of wheat breeding in the 21st century. Euphytica. 2001;119(1–2):3–15. https://doi.org/10.1023/A:1017538304429.
Article
Google Scholar
Zadražnik T, Hollung K, Egge-Jacobsen W, Meglič V, Šuštar-Vozlič J. Differential proteomic analysis of drought stress response in leaves of common bean (Phaseolus vulgaris L.). J Proteome. 2013;78:254–72. https://doi.org/10.1016/j.jprot.2012.09.021.
Article
CAS
Google Scholar
Tricker PJ, ElHabti A, Schmidt J, Fleury D. The physiological and genetic basis of combined drought and heat tolerance in wheat. J Exp Bot. 2018;69(13):3195–210. https://doi.org/10.1093/jxb/ery081.
Article
CAS
PubMed
Google Scholar
Hanin M, Ebel C, Ngom M, Laplaze L, Masmoudi K. New insights on plant salt tolerance mechanisms and their potential use for breeding. Front Plant Sci. 2016;7:1787.
Article
Google Scholar
Zheng Y, Xu X, Li Z, Yang X, Zhang C, Li F, et al. Differential responses of grain yield and quality to salinity between contrasting winter wheat cultivars. Seed Sci Biotechnol. 2009;3(2):40–3.
Google Scholar
Tuteja N. Mechanisms of high salinity tolerance in plants. Methods Enzymol. 2007;428:419–38. https://doi.org/10.1016/S0076-6879(07)28024-3.
Article
CAS
PubMed
Google Scholar
Gupta B, Huang B. Mechanism of salinity tolerance in plants: physiological, biochemical, and molecular characterization. Int J Genomics. 2014;2014(1):701596.
PubMed
PubMed Central
Google Scholar
Aprile A, Sabella E, Francia E, Milc J, Ronga D, Pecchioni N, et al. Combined effect of cadmium and Lead on durum wheat. Int J Mol Sci. 2019;20(23):5891. https://doi.org/10.3390/ijms20235891.
Article
CAS
PubMed Central
Google Scholar
Rizwan M, Ali S, Zia Ur Rehman M, Rinklebe J, DCW T, Bashir A, et al. Cadmium phytoremediation potential of Brassica crop species: A review. Sci Total Environ. 2018;631–632:1175–91.
Article
Google Scholar
Chen D, Chen D, Xue R, Long J, Lin X, Lin Y, et al. Effects of boron, silicon and their interactions on cadmium accumulation and toxicity in rice plants. J Hazard Mater. 2019;367:447–55. https://doi.org/10.1016/j.jhazmat.2018.12.111.
Article
CAS
PubMed
Google Scholar
Breddam K. Serine carboxy peptidases. A review. Carlsberg Res Commun. 1986;51(2):83–128. https://doi.org/10.1007/BF02907561.
Article
CAS
Google Scholar
Mortensen UH, Olesen K, Breddam K. Carboxypeptidase C including carboxypeptidase Y. Handbook Proteolytic Enzymes. 2013:3408–12. https://doi.org/10.1016/B978-0-12-382219-2.00753-5.
Milkowski C, Strack D. Serine carboxypeptidase-like acyltransferases. Phytochemistry. 2004;65(5):517–24. https://doi.org/10.1016/j.phytochem.2003.12.018.
Article
CAS
PubMed
Google Scholar
Ollis DL, Cheah E, Cygler M, Dijkstra B, Frolow F, Franken SM, et al. The alpha/beta hydrolase fold. Protein Eng. 1992;5(3):197–211. https://doi.org/10.1093/protein/5.3.197.
Article
CAS
PubMed
Google Scholar
Holmquist M. Alpha/Beta-hydrolase fold enzymes: structures, functions and mechanisms. Curr Protein Pept Sci. 2000;1(2):209–35. https://doi.org/10.2174/1389203003381405.
Article
CAS
PubMed
Google Scholar
Fricker LD, Leiter EH. Peptides, enzymes and obesity: new insights from a ‘dead’ enzyme. Trends Biochem Sci. 1999;24(10):390–3. https://doi.org/10.1016/S0968-0004(99)01448-6.
Article
CAS
PubMed
Google Scholar
Liao DI, Remington SJ. Structure of wheat serine carboxypeptidase II at 3.5-a resolution. A new class of serine proteinase. J Biol Chem. 1990;265(12):6528–31. https://doi.org/10.1016/S0021-9258(19)39176-8.
Article
CAS
PubMed
Google Scholar
Fraser CM, Rider LW, Chapple C. An expression and bioinformatics analysis of the Arabidopsis serine carboxypeptidase-like gene family. Plant Physiol. 2005;138(2):1136–48. https://doi.org/10.1104/pp.104.057950.
Article
CAS
PubMed
PubMed Central
Google Scholar
Agarwal V, Tikhonov A, Metlitskaya A, Severinov K, Nair SK. Structure and function of a serine carboxypeptidase adapted for degradation of the protein synthesis antibiotic microcin C7. Proc Natl Acad Sci U S A. 2012;109(12):4425–30. https://doi.org/10.1073/pnas.1114224109.
Article
PubMed
PubMed Central
Google Scholar
Vendrell J, Avilés FX. Carboxypeptidases. Proteases New Perspect. 1999:13–34. https://doi.org/10.1007/978-3-0348-8737-3_2.
Bamforth CW, Martin HL, Wainwright T. A role for carboxypeptidase in the solubilization of barley β-glucan. J I Brewing. 1979;85(6):334–8. https://doi.org/10.1002/j.2050-0416.1979.tb03937.x.
Article
CAS
Google Scholar
Bradley D. Isolation and characterization of a gene encoding a carboxypeptidase Y-like protein from Arabidopsis thaliana. Plant Physiol. 1992;98(4):1526–9. https://doi.org/10.1104/pp.98.4.1526.
Article
CAS
PubMed
PubMed Central
Google Scholar
Walker-Simmons M, Ryan CA. Isolation and properties of carboxypeptidase from leaves of wounded tomato plants. Phytochemistry. 1980;19(1):43–7. https://doi.org/10.1016/0031-9422(80)85010-2.
Article
CAS
Google Scholar
Washio K, Ishikawa K. Organ-specific and hormone-dependent expression of genes for serine carboxypeptidases during development and following germination of rice grains. Plant Physiol. 1994;105(4):1275–80. https://doi.org/10.1104/pp.105.4.1275.
Article
CAS
PubMed
PubMed Central
Google Scholar
Moura DS, Bergey DR, Ryan CA. Characterization and localization of a wound-inducible type I serine-carboxypeptidase from leaves of tomato plants (Lycopersicon esculentum mill.). Planta. 2001;212(2):222–30. https://doi.org/10.1007/s004250000380.
Article
CAS
PubMed
Google Scholar
Liu H, Wang X, Zhang H, Yang Y, Ge X, Song F. A rice serine carboxypeptidase-like gene OsBISCPL1 is involved in regulation of defense responses against biotic and oxidative stress. Gene. 2008;420(1):57–65. https://doi.org/10.1016/j.gene.2008.05.006.
Article
CAS
PubMed
Google Scholar
Shirley AM, McMichael CM, Chapple C. The sng2 mutant of Arabidopsis is defective in the gene encoding the serine carboxypeptidase-like protein sinapoylglucose:choline sinapoyltransferase. Plant J. 2001;28(1):83–94. https://doi.org/10.1046/j.1365-313X.2001.01123.x.
Article
CAS
PubMed
Google Scholar
Lehfeldt C, Shirley AM, Meyer K, Ruegger MO, Cusumano JC, Viitanen PV, et al. Cloning of the SNG1 gene of Arabidopsis reveals a role for a serine carboxypeptidase-like protein as an acyltransferase in secondary metabolism. Plant Cell. 2000;12(8):1295–306. https://doi.org/10.1105/tpc.12.8.1295.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lorenzen M, Racicot V, Strack D, Chapple C. Sinapic acid ester metabolism in wild type and a sinapoylglucose-accumulating mutant of arabidopsis. Plant Physiol. 1996;112(4):1625–30. https://doi.org/10.1104/pp.112.4.1625.
Article
CAS
PubMed
PubMed Central
Google Scholar
Peyrot C, Mention MM, Brunissen F, Allais F. Sinapic acid esters: Octinoxate substitutes combining suitable UV protection and antioxidant activity. Antioxidants (Basel). 2020;9(9):782. https://doi.org/10.3390/antiox9090782.
Article
CAS
Google Scholar
Christie PJ, Alfenito MR, Walbot V. Impact of low-temperature stress on general phenylpropanoid and anthocyanin pathways: enhancement of transcript abundance and anthocyanin pigmentation in maize seedlings. Planta. 1994;194(4):541–9. https://doi.org/10.1007/BF00714468.
Article
CAS
Google Scholar
Garriga M, Retamales JB, Romero-Bravo S, Caligari PD, Lobos GA. Chlorophyll, anthocyanin, and gas exchange changes assessed by spectroradiometry in Fragaria chiloensis under salt stress. J Integr Plant Biol. 2014;56(5):505–15. https://doi.org/10.1111/jipb.12193.
Article
CAS
PubMed
Google Scholar
Kovinich N, Kayanja G, Chanoca A, Riedl K, Otegui MS, Grotewold E. Not all anthocyanins are born equal: distinct patterns induced by stress in Arabidopsis. Planta. 2014;240(5):931–40. https://doi.org/10.1007/s00425-014-2079-1.
Article
CAS
PubMed
PubMed Central
Google Scholar
Miki S, Wada KC, Takeno K. A possible role of an anthocyanin filter in low-intensity light stress-induced flowering in Perilla frutescens var. crispa. J Plant Physiol. 2015;175:157–62. https://doi.org/10.1016/j.jplph.2014.12.002.
Article
CAS
PubMed
Google Scholar
Peng M, Hudson D, Schofield A, Tsao R, Yang R, Gu H, et al. Adaptation of Arabidopsis to nitrogen limitation involves induction of anthocyanin synthesis which is controlled by the NLA gene. J Exp Bot. 2008;59(11):2933–44. https://doi.org/10.1093/jxb/ern148.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang Y, Zheng S, Liu Z, Wang L, Bi Y. Both HY5 and HYH are necessary regulators for low temperature-induced anthocyanin accumulation in Arabidopsis seedlings. J Plant Physiol. 2011;168(4):367–74. https://doi.org/10.1016/j.jplph.2010.07.025.
Article
CAS
PubMed
Google Scholar
Olsen KM, Lea US, Slimestad R, Verheul M, Lillo C. Differential expression of four Arabidopsis PAL genes; PAL1 and PAL2 have functional specialization in abiotic environmental-triggered flavonoid synthesis. J Plant Physiol. 2008;165(14):1491–9. https://doi.org/10.1016/j.jplph.2007.11.005.
Article
CAS
PubMed
Google Scholar
Pourcel L, Irani NG, Koo AJ, Bohorquez-Restrepo A, Howe GA, Grotewold E. A chemical complementation approach reveals genes and interactions of flavonoids with other pathways. Plant J. 2013;74(3):383–97. https://doi.org/10.1111/tpj.12129.
Article
CAS
PubMed
Google Scholar
Marko D, Puppel N, Tjaden Z, Jakobs S, Pahlke G. The substitution pattern of anthocyanidins affects different cellular signaling cascades regulating cell proliferation. Mol Nutr Food Res. 2004;48(4):318–25. https://doi.org/10.1002/mnfr.200400034.
Article
CAS
PubMed
Google Scholar
Hughes NM, Carpenter KL, Keidel TS, Miller CN, Waters MN, Smith WK. Photosynthetic costs and benefits of abaxial versus adaxial anthocyanins in Colocasia esculenta ‘Mojito’. Planta. 2014;240(5):971–81. https://doi.org/10.1007/s00425-014-2090-6.
Article
CAS
PubMed
Google Scholar
Tattini M, Landi M, Brunetti C, Giordano C, Remorini D, Gould KS, et al. Epidermal coumaroyl anthocyanins protect sweet basil against excess light stress: multiple consequences of light attenuation. Physiol Plant. 2014;152(3):585–98. https://doi.org/10.1111/ppl.12201.
Article
CAS
PubMed
Google Scholar
Gould K, McKelvie J, Markham K. Do anthocyanins function as antioxidants in leaves? Imaging of H2O2 in red and green leaves after mechanical injury. Plant Cell Environ. 2002;25(10):1261–9. https://doi.org/10.1046/j.1365-3040.2002.00905.x.
Article
CAS
Google Scholar
Nakabayashi R, Yonekura-Sakakibara K, Urano K, Suzuki M, Yamada Y, Nishizawa T, et al. Enhancement of oxidative and drought tolerance in Arabidopsis by overaccumulation of antioxidant flavonoids. Plant J. 2014;77(3):367–79. https://doi.org/10.1111/tpj.12388.
Article
CAS
PubMed
Google Scholar
Fraser CM, Thompson MG, Shirley AM, Ralph J, Schoenherr JA, Sinlapadech T, et al. Related Arabidopsis serine carboxypeptidase-like sinapoylglucose acyltransferases display distinct but overlapping substrate specificities. Plant Physiol. 2007;144(4):1986–99. https://doi.org/10.1104/pp.107.098970.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ren Z, Qiu F, Wang Y, Yu W, Liu C, Sun Y, et al. Network analysis of transcriptome and LC-MS reveals a possible biosynthesis pathway of anthocyanins in Dendrobium officinale. Biomed Res Int. 2020;2020:6512895.
PubMed
PubMed Central
Google Scholar
Dal Degan F, Rocher A, Cameron-Mills V, von Wettstein D. The expression of serine carboxypeptidases during maturation and germination of the barley grain. Proc Natl Acad Sci U S A. 1994;91(17):8209–13. https://doi.org/10.1073/pnas.91.17.8209.
Article
CAS
PubMed
PubMed Central
Google Scholar
Li J, Lease KA, Tax FE, Walker JC. BRS1, a serine carboxypeptidase, regulates BRI1 signaling in Arabidopsis thaliana. Proc Natl Acad Sci U S A. 2001;98(10):5916–21. https://doi.org/10.1073/pnas.091065998.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wolf AE, Dietz KJ, Schröder P. Degradation of glutathione S-conjugates by a carboxypeptidase in the plant vacuole. FEBS Lett. 1996;384(1):31–4. https://doi.org/10.1016/0014-5793(96)00272-4.
Article
CAS
PubMed
Google Scholar
Potokina E, Prasad M, Malysheva L, Röder MS, Graner A. Expression genetics and haplotype analysis reveal cis regulation of serine carboxypeptidase I (Cxp1), a candidate gene for malting quality in barley (Hordeum vulgare L.). Funct Integr Genomics. 2006;6(1):25–35. https://doi.org/10.1007/s10142-005-0008-x.
Article
CAS
PubMed
Google Scholar
Feng Y, Yu C. Genome-wide comparative study of rice and Arabidopsis serine carboxypeptidase-like protein families. J Zhejiang Univ. 2009;35(1):1–15.
Google Scholar
Zhu D, Chu W, Wang Y, Yan H, Chen Z, Xiang Y. Genome-wide identification, classification and expression analysis of the serine carboxypeptidase-like protein family in poplar. Physiol Plant. 2018;162(3):333–52. https://doi.org/10.1111/ppl.12642.
Article
CAS
PubMed
Google Scholar
Ahmad MZ, Li P, She G, Xia E, Benedito VA, Wan XC, et al. Genome-wide analysis of serine carboxypeptidase-like acyltransferase gene family for evolution and characterization of enzymes involved in the biosynthesis of Galloylated Catechins in the tea plant (Camellia sinensis). Front Plant Sci. 2020;11:848. https://doi.org/10.3389/fpls.2020.00848.
Article
PubMed
PubMed Central
Google Scholar
Sharopova N. Plant simple sequence repeats: distribution, variation, and effects on gene expression. Genome. 2008;51(2):79–90. https://doi.org/10.1139/G07-110.
Article
CAS
PubMed
Google Scholar
Zhang L, Zuo K, Zhang F, Cao Y, Wang J, Zhang Y, et al. Conservation of noncoding microsatellites in plants: implication for gene regulation. BMC Genomics. 2006;7(1):323. https://doi.org/10.1186/1471-2164-7-323.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dai X, Zhuang Z, Zhao PX. psRNATarget: a plant small RNA target analysis server (2017 release). Nucleic Acids Res. 2018 Jul 2;46(W1):W49–54. https://doi.org/10.1093/nar/gky316.
Article
CAS
PubMed
PubMed Central
Google Scholar
Han R, Jian C, Lv J, Yan Y, Chi Q, Li Z, et al. Identification and characterization of microRNAs in the flag leaf and developing seed of wheat (Triticum aestivum L.). BMC Genomics. 2014;15:289.
Article
Google Scholar
Yao Y, Guo G, Ni Z, Sunkar R, Du J, Zhu JK, et al. Cloning and characterization of microRNAs from wheat (Triticum aestivum L.). Genome Biol. 2007;8(6):R96.
Article
Google Scholar
Zhang J. Evolution by gene duplication: an update. Trends Ecol Evol. 2003;18(6):292–8. https://doi.org/10.1016/S0169-5347(03)00033-8.
Article
Google Scholar
Sukumari Nath V, Kumar Mishra A, Kumar A, Matoušek J, Jakše J. Revisiting the Role of Transcription Factors in Coordinating the Defense Response Against Citrus Bark Cracking Viroid Infection in Commercial Hop (Humulus lupulus L.). Viruses. 2019;11(5):419.
Article
Google Scholar
Maren E, Veatch-Blohm. Principles of Plant Genetics and Breeding. Crop Sci. 2007;47(4):1763.
Article
Google Scholar
Gill SS, Tuteja N. Reactive oxygen species and antioxidant machinery in abiotic stress tolerance in crop plants. Plant Physiol Biochem. 2010;48(12):909–30. https://doi.org/10.1016/j.plaphy.2010.08.016.
Article
CAS
PubMed
Google Scholar
Székely G, Abrahám E, Cséplo A, Rigó G, Zsigmond L, Csiszár J, et al. Duplicated P5CS genes of Arabidopsis play distinct roles in stress regulation and developmental control of proline biosynthesis. Plant J. 2008;53(1):11–28. https://doi.org/10.1111/j.1365-313X.2007.03318.x.
Article
CAS
PubMed
Google Scholar
Zhu JK. Abiotic stress signaling and responses in plants. Cell. 2016;167(2):313–24. https://doi.org/10.1016/j.cell.2016.08.029.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bolser DM, Staines DM, Perry E, Kersey PJ. Ensembl plants: integrating tools for visualizing, mining, and analyzing plant genomic data. Methods Mol Biol. 2017;1533:1–31. https://doi.org/10.1007/978-1-4939-6658-5_1.
Article
CAS
PubMed
Google Scholar
Finn RD, Bateman A, Clements J, Coggill P, Eberhardt RY, Eddy SR, et al. Pfam: the protein families database. Nucleic Acids Res. 2014;42(Database issue):D222–30. https://doi.org/10.1093/nar/gkt1223.
Article
CAS
PubMed
Google Scholar
Coggill P, Finn RD, Bateman A. Identifying protein domains with the Pfam database. Curr Protoc Bioinformatics. 2008;2:2–5.
Google Scholar
Finn RD, Clements J, Eddy SR. HMMER web server: interactive sequence similarity searching. Nucleic Acids Res. 2011;39(suppl):W29–37. https://doi.org/10.1093/nar/gkr367.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rao KP, Richa T, Kumar K, Raghuram B, Sinha AK. In silico analysis reveals 75 members of mitogen-activated protein kinase kinase kinase gene family in rice. DNA Res. 2010;17(3):139–53. https://doi.org/10.1093/dnares/dsq011.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang M, Yue H, Feng K, Deng P, Song W, Nie X. Genome-wide identification, phylogeny and expressional profiles of mitogen activated protein kinase kinase kinase (MAPKKK) gene family in bread wheat (Triticum aestivum L.). BMC Genomics. 2016;17(1):668.
Article
Google Scholar
Yang M, Derbyshire MK, Yamashita RA, Marchler-Bauer A. NCBI's conserved domain database and tools for protein domain analysis. Curr Protoc Bioinformatics. 2020;69(1):e90. https://doi.org/10.1002/cpbi.90.
Article
CAS
PubMed
PubMed Central
Google Scholar
Schultz J, Milpetz F, Bork P, Ponting CP. SMART, a simple modular architecture research tool: identification of signaling domains. Proc Natl Acad Sci U S A. 1998;95(11):5857–64. https://doi.org/10.1073/pnas.95.11.5857.
Article
CAS
PubMed
PubMed Central
Google Scholar
Artimo P, Jonnalagedda M, Arnold K, Baratin D, Csardi G, de Castro E, et al. ExPASy: SIB bioinformatics resource portal. Nucleic Acids Res. 2012;40(W1):W597–603. https://doi.org/10.1093/nar/gks400.
Article
CAS
PubMed
PubMed Central
Google Scholar
Larkin MA, Blackshields G, Brown NP, Chenna R, McGettigan PA, McWilliam H, et al. Clustal W and Clustal X version 2.0. Bioinformatics. 2007;23(21):2947–8. https://doi.org/10.1093/bioinformatics/btm404.
Article
CAS
PubMed
Google Scholar
Price MN, Dehal PS, Arkin AP. FastTree 2--approximately maximum-likelihood trees for large alignments. PLoS One. 2010;5(3):e9490. https://doi.org/10.1371/journal.pone.0009490.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jones DT, Taylor WR, Thornton JM. The rapid generation of mutation data matrices from protein sequences. Comput Appl Biosci. 1992;8(3):275–82. https://doi.org/10.1093/bioinformatics/8.3.275.
Article
CAS
PubMed
Google Scholar
Stamatakis A. Phylogenetic models of rate heterogeneity: a high performance computing perspective. Proceedings 20th IEEE International Parallel & Distributed Processing Symposium. 2006. https://doi.org/10.1109/IPDPS.2006.1639535.
Shimodaira H, Hasegawa M. Multiple comparisons of log-likelihoods with applications to phylogenetic inference. Mol Biol Evol. 1999;16(8):1114–6. https://doi.org/10.1093/oxfordjournals.molbev.a026201.
Article
CAS
Google Scholar
Voorrips RE. MapChart: software for the graphical presentation of linkage maps and QTLs. J Hered. 2002;93(1):77–8. https://doi.org/10.1093/jhered/93.1.77.
Article
CAS
PubMed
Google Scholar
Schilling S, Kennedy A, Pan S, Jermiin LS, Melzer R. Genome-wide analysis of MIKC-type MADS-box genes in wheat: pervasive duplications, functional conservation and putative neofunctionalization. New Phytol. 2020;225(1):511–29. https://doi.org/10.1111/nph.16122.
Article
CAS
PubMed
Google Scholar
Fan K, Yuan S, Chen J, Chen Y, Li Z, Lin W, et al. Molecular evolution and lineage-specific expansion of the PP2C family in Zea mays. Planta. 2019;250(5):1521–38. https://doi.org/10.1007/s00425-019-03243-x.
Article
CAS
PubMed
Google Scholar
Kong X, Lv W, Zhang D, Jiang S, Zhang S, Li D. Genome-wide identification and analysis of expression profiles of maize mitogen-activated protein kinase kinase kinase. PLoS One. 2013;8(2):e57714. https://doi.org/10.1371/journal.pone.0057714.
Article
CAS
PubMed
PubMed Central
Google Scholar
Gu Z, Cavalcanti A, Chen FC, Bouman P, Li WH. Extent of gene duplication in the genomes of Drosophila, nematode, and yeast. Mol Biol Evol. 2002;19(3):256–62. https://doi.org/10.1093/oxfordjournals.molbev.a004079.
Article
CAS
PubMed
Google Scholar
Krzywinski M, Schein J, Birol I, Connors J, Gascoyne R, Horsman D, et al. Circos: an information aesthetic for comparative genomics. Genome Res. 2009;19(9):1639–45. https://doi.org/10.1101/gr.092759.109.
Article
CAS
PubMed
PubMed Central
Google Scholar
Chen C, Chen H, Zhang Y, Thomas HR, Frank MH, He Y, et al. TBtools: an integrative toolkit developed for interactive analyses of big biological data. Mol Plant. 2020;13(8):1194–202. https://doi.org/10.1016/j.molp.2020.06.009.
Article
CAS
PubMed
Google Scholar
Hurst LD. The Ka/Ks ratio: diagnosing the form of sequence evolution. Trends Genet. 2002;18(9):486–7. https://doi.org/10.1016/S0168-9525(02)02722-1.
Article
PubMed
Google Scholar
Bailey TL, Boden M, Buske FA, Frith M, Grant CE, Clementi L, et al. MEME SUITE: tools for motif discovery and searching. Nucleic Acids Res. 2009;37(Web Server):W202–8. https://doi.org/10.1093/nar/gkp335.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lescot M, Déhais P, Thijs G, Marchal K, Moreau Y, Van de Peer Y, et al. 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(1):325–7. https://doi.org/10.1093/nar/30.1.325.
Article
CAS
PubMed
PubMed Central
Google Scholar
Beier S, Thiel T, Münch T, Scholz U, Mascher M. MISA-web: a web server for microsatellite prediction. Bioinformatics. 2017;33(16):2583–5. https://doi.org/10.1093/bioinformatics/btx198.
Article
CAS
PubMed
PubMed Central
Google Scholar
Untergasser A, Cutcutache I, Koressaar T, Ye J, Faircloth BC, Remm M, et al. Primer3--new capabilities and interfaces. Nucleic Acids Res. 2012;40(15):e115. https://doi.org/10.1093/nar/gks596.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rotmistrovsky K, Jang W, Schuler GD. A web server for performing electronic PCR. Nucleic Acids Res. 2004;32:108–12.
Article
Google Scholar
Kumar A, Sharma M, Gahlaut V, Nagaraju M, Chaudhary S, Kumar A, et al. Genome-wide identification, characterization, and expression profiling of SPX gene family in wheat. Int J Biol Macromol. 2019;140:17–32. https://doi.org/10.1016/j.ijbiomac.2019.08.105.
Article
CAS
PubMed
Google Scholar
Kozomara A, Griffiths-Jones S. miRBase: annotating high confidence microRNAs using deep sequencing data. Nucleic Acids Res. 2014;42(Database issue):D68–73. https://doi.org/10.1093/nar/gkt1181.
Article
CAS
PubMed
Google Scholar
Borrill P, Ramirez-Gonzalez R, Uauy C. expVIP: a customizable RNA-seq data analysis and visualization platform. Plant Physiol. 2016;170(4):2172–86. https://doi.org/10.1104/pp.15.01667.
Article
CAS
PubMed
PubMed Central
Google Scholar
Wang R, Ma J, Zhang Q, Wu C, Zhao H, Wu Y, et al. Genome-wide identification and expression profiling of glutathione transferase gene family under multiple stresses and hormone treatments in wheat (Triticum aestivum L.). BMC Genomics. 2019;20(1):986.
Article
CAS
Google Scholar
Zhang XZ, Zheng WJ, Cao XY, Cui XY, Zhao SP, Yu TF, et al. Genomic analysis of stress associated proteins in soybean and the role of GmSAP16 in abiotic stress responses in Arabidopsis and soybean. Front Plant Sci. 2019;10:1453. https://doi.org/10.3389/fpls.2019.01453.
Article
PubMed
PubMed Central
Google Scholar
Clough SJ, Bent AF. Floral dip: a simplified method for agrobacterium-mediated transformation of Arabidopsis thaliana. Plant J. 1998;16(6):735–43. https://doi.org/10.1046/j.1365-313x.1998.00343.x.
Article
CAS
PubMed
Google Scholar
Udvardi MK, Czechowski T, Scheible WR. Eleven golden rules of quantitative RT-PCR. Plant Cell. 2008;20(7):1736–7. https://doi.org/10.1105/tpc.108.061143.
Article
CAS
PubMed
PubMed Central
Google Scholar