Van Treuren R, Coquin P, Lohwasser U. Genetic resources collections of leafy vegetables (lettuce, spinach, chicory, artichoke, asparagus, lamb’s lettuce, rhubarb and rocket salad): composition and gaps. Genet Resour Crop Evol. 2012;59(6):981–97. https://doi.org/10.1007/s10722-011-9738-x.
Article
Google Scholar
Koh E, Charoenprasert S, Mitchell AE. Effect of organic and conventional cropping systems on ascorbic acid, vitamin C, flavonoids, nitrate, and oxalate in 27 varieties of spinach (Spinacia oleracea L.). J Agric Food Chem. 2012;60(12):3144–50. https://doi.org/10.1021/jf300051f.
Article
CAS
PubMed
Google Scholar
Food F: Agriculture Organization of the United Nations Statistical Databases. 2016. Diponível em: http//faostat fao org/site/339 default aspx Acesso em 2018, 25.
van Treuren R, Hoekstra R, van Hintum TJ. Inventory and prioritization for the conservation of crop wild relatives in the Netherlands under climate change. Biol Conserv. 2017;216:123–39. https://doi.org/10.1016/j.biocon.2017.10.003.
Article
Google Scholar
van Treuren R, de Groot L, Hisoriev H, Khassanov F, Farzaliyev V, Melyan G, et al. Acquisition and regeneration of Spinacia turkestanica Iljin and S. tetrandra Steven ex M. Bieb. To improve a spinach gene bank collection. Genet Resour Crop Evol. 2020;67(3):549–59. https://doi.org/10.1007/s10722-019-00792-8.
Article
Google Scholar
Cho LH, Yoon J, An G. The control of flowering time by environmental factors. Plant J. 2017;90(4):708–19. https://doi.org/10.1111/tpj.13461.
Article
CAS
PubMed
Google Scholar
Chen C, Huang W, Hou K, Wu W. Bolting, an important process in plant development, two types in plants. J Plant Biol. 2019;62(3):161–9. https://doi.org/10.1007/s12374-018-0408-9.
Article
CAS
Google Scholar
Arif M, Jatoi SA, Rafique T, Ghafoor A. Genetic divergence in indigenous spinach genetic resources for agronomic performance and implication of multivariate analyses for future selection criteria. J Sci Technol Dev. 2013;32(1):7–15.
Google Scholar
Chitwood J, Shi A, Mou B, Evans M, Clark J, Motes D, et al. Population structure and association analysis of bolting, plant height, and leaf erectness in spinach. HortScience. 2016;51(5):481–6. https://doi.org/10.21273/HORTSCI.51.5.481.
Article
CAS
Google Scholar
Ma J, Shi A, Mou B, Evans M, Clark JR, Motes D, et al. Association mapping of leaf traits in spinach (Spinacia oleracea L.). Plant Breed. 2016;135(3):399–404. https://doi.org/10.1111/pbr.12369.
Article
CAS
Google Scholar
Piñeiro M, Gómez-Mena C, Schaffer R, Martínez-Zapater JM, Coupland G. EARLY BOLTING IN SHORT DAYS is related to chromatin remodeling factors and regulates flowering in Arabidopsis by repressing FT. Plant Cell. 2003;15(7):1552–62. https://doi.org/10.1105/tpc.012153.
Article
CAS
PubMed
PubMed Central
Google Scholar
Lee Y-S, An G. Regulation of flowering time in rice. J Plant Biol. 2015;58(6):353–60. https://doi.org/10.1007/s12374-015-0425-x.
Article
CAS
Google Scholar
Alter P, Bircheneder S, Zhou L-Z, Schlüter U, Gahrtz M, Sonnewald U, et al. Flowering time-regulated genes in maize include the transcription factor ZmMADS1. Plant Physiol. 2016;172(1):389–404. https://doi.org/10.1104/pp.16.00285.
Article
CAS
PubMed
PubMed Central
Google Scholar
Leijten W, Koes R, Roobeek I, Frugis G. Translating flowering time from Arabidopsis thaliana to Brassicaceae and Asteraceae crop species. Plants. 2018;7(4):111. https://doi.org/10.3390/plants7040111.
Article
CAS
PubMed Central
Google Scholar
de Dios EA, Delaye L, Simpson J. Transcriptome analysis of bolting in A. tequilana reveals roles for florigen, MADS, fructans and gibberellins. BMC Genomics. 2019;20(1):473.
Article
Google Scholar
Nie S, Li C, Xu L, Wang Y, Huang D, Muleke EM, et al. De novo transcriptome analysis in radish (Raphanus sativus L.) and identification of critical genes involved in bolting and flowering. BMC Genomics. 2016;17(1):389.
Article
PubMed
PubMed Central
Google Scholar
Ou CG, Mao JH, Liu LJ, Li CJ, Ren HF, Zhao ZW, et al. Characterising genes associated with flowering time in carrot (Daucus carota L.) using transcriptome analysis. Plant Biol. 2017;19(2):286–97. https://doi.org/10.1111/plb.12519.
Article
CAS
PubMed
Google Scholar
Han Y, Chen Z, Lv S, Ning K, Ji X, Liu X, et al. MADS-box genes and gibberellins regulate bolting in Lettuce (Lactuca sativa L.). Front Plant Sci. 2016;7:1889.
PubMed
PubMed Central
Google Scholar
Ito S, Song YH, Josephson-Day AR, Miller RJ, Breton G, Olmstead RG, et al. FLOWERING BHLH transcriptional activators control expression of the photoperiodic flowering regulator CONSTANS in Arabidopsis. Proc Natl Acad Sci. 2012;109(9):3582–7. https://doi.org/10.1073/pnas.1118876109.
Article
PubMed
PubMed Central
Google Scholar
Wang Y, Liu W, Xu L, Wang Y, Chen Y, Luo X, et al. Development of SNP markers based on transcriptome sequences and their application in germplasm identification in radish (Raphanus sativus L.). Mol Breed. 2017;37(3):26.
Article
Google Scholar
Searle I, He Y, Turck F, Vincent C, Fornara F, Kröber S, et al. The transcription factor FLC confers a flowering response to vernalization by repressing meristem competence and systemic signaling in Arabidopsis. Genes Dev. 2006;20(7):898–912. https://doi.org/10.1101/gad.373506.
Article
CAS
PubMed
PubMed Central
Google Scholar
Deng W, Ying H, Helliwell CA, Taylor JM, Peacock WJ, Dennis ES. FLOWERING LOCUS C (FLC) regulates development pathways throughout the life cycle of Arabidopsis. Proc Natl Acad Sci. 2011;108(16):6680–5. https://doi.org/10.1073/pnas.1103175108.
Article
PubMed
PubMed Central
Google Scholar
Preston JC, Hileman L. Functional evolution in the plant SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE (SPL) gene family. Front Plant Sci. 2013;4:80.
PubMed
PubMed Central
Google Scholar
Winter CM, Yamaguchi N, Wu MF, Wagner D. Transcriptional programs regulated by both LEAFY and APETALA1 at the time of flower formation. Physiol Plant. 2015;155(1):55–73. https://doi.org/10.1111/ppl.12357.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang Z, Wang P, Li Y, Ma L, Li L, Yang R, et al. Global transcriptome analysis and identification of the flowering regulatory genes expressed in leaves of Lagerstroemia indica. DNA Cell Biol. 2014;33(10):680–8. https://doi.org/10.1089/dna.2014.2469.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ness RW, Siol M, Barrett SC. De novo sequence assembly and characterization of the floral transcriptome in cross-and self-fertilizing plants. BMC Genomics. 2011;12(1):298. https://doi.org/10.1186/1471-2164-12-298.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhang Z, Wang P, Li Y, Ma L, Li L, Yang R, et al. Global Transcriptome analysis and identification of the flowering regulatory genes expressed in leaves of Lagerstroemia indica. DNA Cell Biol. 2014;33(10):680–8. https://doi.org/10.1089/dna.2014.2469.
Article
CAS
PubMed
PubMed Central
Google Scholar
Xu C, Jiao C, Sun H, Cai X, Wang X, Ge C, et al. Draft genome of spinach and transcriptome diversity of 120 Spinacia accessions. Nat Commun. 2017;8(1):1–10.
Article
Google Scholar
Collins K, Zhao K, Jiao C, Xu C, Cai X, Wang X, et al. SpinachBase: a central portal for spinach genomics. Database. 2019;2019. https://doi.org/10.1093/database/baz072.
Abolghasemi R, Haghighi M, Etemadi N, Soorni A, Jafari P. Screening of some native and foreign accessions of spinach for spring culture in Isfahan. Iran Agric Res. 2019;38(1):87–99.
Google Scholar
Yu D, Hu Y, Wang H, Pan J, Li Y, Lou D. The DELLA-CONSTANS transcription factor cascade integrates gibberelic acid and photoperiod signaling to regulate flowering. Plant Physiol. 2016.
Berg IA, Kockelkorn D, Ramos-Vera WH, Say RF, Zarzycki J, Hügler M, et al. Autotrophic carbon fixation in archaea. Nat Rev Microbiol. 2010;8(6):447–60. https://doi.org/10.1038/nrmicro2365.
Article
CAS
PubMed
Google Scholar
Lv G-Y, Guo X-G, Xie L-P, Xie C-G, Zhang X-H, Yang Y, et al. Molecular characterization, gene evolution, and expression analysis of the fructose-1, 6-bisphosphate aldolase (FBA) gene family in wheat (Triticum aestivum L.). Front Plant Sci. 2017;8:1030.
Article
PubMed
PubMed Central
Google Scholar
Furbank RT, Taylor WC. Regulation of photosynthesis in C3 and C4 plants: a molecular approach. Plant Cell. 1995;7(7):797–807. https://doi.org/10.2307/3870037.
Article
CAS
PubMed
PubMed Central
Google Scholar
Raines CA. The Calvin cycle revisited. Photosynth Res. 2003;75(1):1–10. https://doi.org/10.1023/A:1022421515027.
Article
CAS
PubMed
Google Scholar
Uematsu K, Suzuki N, Iwamae T, Inui M, Yukawa H. Increased fructose 1, 6-bisphosphate aldolase in plastids enhances growth and photosynthesis of tobacco plants. J Exp Bot. 2012;63(8):3001–9. https://doi.org/10.1093/jxb/ers004.
Article
CAS
PubMed
Google Scholar
van Dijken AJ, Schluepmann H, Smeekens SC. Arabidopsis trehalose-6-phosphate synthase 1 is essential for normal vegetative growth and transition to flowering. Plant Physiol. 2004;135(2):969–77. https://doi.org/10.1104/pp.104.039743.
Article
PubMed
PubMed Central
Google Scholar
Wahl V, Ponnu J, Schlereth A, Arrivault S, Langenecker T, Franke A, et al. Regulation of flowering by trehalose-6-phosphate signaling in Arabidopsis thaliana. Science. 2013;339(6120):704–7. https://doi.org/10.1126/science.1230406.
Article
CAS
PubMed
Google Scholar
Dai Y, Zhang S, Sun X, Li G, Yuan L, Li F, et al. Comparative Transcriptome analysis of gene expression and regulatory characteristics associated with different Vernalization periods in Brassica rapa. Genes. 2020;11(4):392. https://doi.org/10.3390/genes11040392.
Article
CAS
PubMed Central
Google Scholar
Wang X, Fan S, Song M, Pang C, Wei H, Yu J, et al. Upland cotton gene GhFPF1 confers promotion of flowering time and shade-avoidance responses in Arabidopsis thaliana. PLoS One. 2014;9(3):e91869. https://doi.org/10.1371/journal.pone.0091869.
Article
CAS
PubMed
PubMed Central
Google Scholar
Sawa M, Nusinow DA, Kay SA, Imaizumi T. FKF1 and GIGANTEA complex formation is required for day-length measurement in Arabidopsis. Science. 2007;318(5848):261–5. https://doi.org/10.1126/science.1146994.
Article
CAS
PubMed
PubMed Central
Google Scholar
Dalchau N, Baek SJ, Briggs HM, Robertson FC, Dodd AN, Gardner MJ, et al. The circadian oscillator gene GIGANTEA mediates a long-term response of the Arabidopsis thaliana circadian clock to sucrose. Proc Natl Acad Sci. 2011;108(12):5104–9. https://doi.org/10.1073/pnas.1015452108.
Article
PubMed
PubMed Central
Google Scholar
Brandoli C, Petri C, Egea-Cortines M, Weiss J. Gigantea: uncovering new functions in flower development. Genes. 2020;11(10):1142. https://doi.org/10.3390/genes11101142.
Article
CAS
PubMed Central
Google Scholar
Zhao XY, Liu MS, Li JR, Guan CM, Zhang XS. The wheat TaGI1, involved in photoperiodic flowering, encodesan Arabidopsis GI ortholog. Plant Mol Biol. 2005;58(1):53–64. https://doi.org/10.1007/s11103-005-4162-2.
Article
CAS
PubMed
Google Scholar
Zakhrabekova S, Gough SP, Braumann I, Müller AH, Lundqvist J, Ahmann K, et al. Induced mutations in circadian clock regulator mat-a facilitated short-season adaptation and range extension in cultivated barley. Proc Natl Acad Sci. 2012;109(11):4326–31. https://doi.org/10.1073/pnas.1113009109.
Article
PubMed
PubMed Central
Google Scholar
Yu J-W, Rubio V, Lee N-Y, Bai S, Lee S-Y, Kim S-S, et al. COP1 and ELF3 control circadian function and photoperiodic flowering by regulating GI stability. Mol Cell. 2008;32(5):617–30. https://doi.org/10.1016/j.molcel.2008.09.026.
Article
CAS
PubMed
PubMed Central
Google Scholar
Nelson DC, Lasswell J, Rogg LE, Cohen MA, Bartel B. FKF1, a clock-controlled gene that regulates the transition to flowering in Arabidopsis. Cell. 2000;101(3):331–40. https://doi.org/10.1016/S0092-8674(00)80842-9.
Article
CAS
PubMed
Google Scholar
Imaizumi T, Tran HG, Swartz TE, Briggs WR, Kay SA. FKF1 is essential for photoperiodic-specific light signalling in Arabidopsis. Nature. 2003;426(6964):302–6. https://doi.org/10.1038/nature02090.
Article
CAS
PubMed
Google Scholar
Kim S-G, Kim S-Y, Park C-M. A membrane-associated NAC transcription factor regulates salt-responsive flowering via FLOWERING LOCUS T in Arabidopsis. Planta. 2007;226(3):647–54. https://doi.org/10.1007/s00425-007-0513-3.
Article
CAS
PubMed
Google Scholar
Reeves PH, Ellis CM, Ploense SE, Wu M-F, Yadav V, Tholl D, et al. A regulatory network for coordinated flower maturation. PLoS Genet. 2012;8(2):e1002506. https://doi.org/10.1371/journal.pgen.1002506.
Article
CAS
PubMed
PubMed Central
Google Scholar
Ning Y-Q, Ma Z-Y, Huang H-W, Mo H, Zhao T-T, Li L, et al. Two novel NAC transcription factors regulate gene expression and flowering time by associating with the histone demethylase JMJ14. Nucleic Acids Res. 2015;43(3):1469–84. https://doi.org/10.1093/nar/gku1382.
Article
CAS
PubMed
PubMed Central
Google Scholar
Kim J, Kim D-S, Park S, Lee H-E, Ahn Y-K, Kim JH, et al. Development of a high-throughput SNP marker set by transcriptome sequencing to accelerate genetic background selection in Brassica rapa. Hortic Environ Biotechnol. 2016;57(3):280–90. https://doi.org/10.1007/s13580-016-1036-2.
Article
CAS
Google Scholar
Richter R, Bastakis E, Schwechheimer C. Cross-repressive interactions between SOC1 and the GATAs GNC and GNL/CGA1 in the control of greening, cold tolerance, and flowering time in Arabidopsis. Plant Physiol. 2013;162(4):1992–2004. https://doi.org/10.1104/pp.113.219238.
Article
CAS
PubMed
PubMed Central
Google Scholar
Zhu L, Liu D, Li Y, Li N. Functional phosphoproteomic analysis reveals that a serine-62-phosphorylated isoform of ethylene response factor110 is involved in Arabidopsis bolting. Plant Physiol. 2013;161(2):904–17. https://doi.org/10.1104/pp.112.204487.
Article
CAS
PubMed
Google Scholar
Jiang W, Zhang X, Song X, Yang J, Pang Y. Genome-wide identification and characterization of APETALA2/ethylene-responsive element Binding factor superfamily genes in soybean seed development. Front Plant Sci. 2020;11:1348.
Google Scholar
Zhu Q-H, Helliwell CA. Regulation of flowering time and floral patterning by miR172. J Exp Bot. 2011;62(2):487–95. https://doi.org/10.1093/jxb/erq295.
Article
CAS
PubMed
Google Scholar
Ning K, Han Y, Chen Z, Luo C, Wang S, Zhang W, et al. Genome-wide analysis of MADS-box family genes during flower development in lettuce. Plant Cell Environ. 2019;42(6):1868–81. https://doi.org/10.1111/pce.13523.
Article
CAS
PubMed
Google Scholar
Schilling S, Pan S, Kennedy A, Melzer R. MADS-box genes and crop domestication: the jack of all traits. UK: Oxford University Press; 2018.
Google Scholar
Yoo SK, Wu X, Lee JS, Ahn JH. AGAMOUS-LIKE 6 is a floral promoter that negatively regulates the FLC/MAF clade genes and positively regulates FT in Arabidopsis. Plant J. 2011;65(1):62–76. https://doi.org/10.1111/j.1365-313X.2010.04402.x.
Article
CAS
PubMed
Google Scholar
Manivannan A, Kim J-H, Yang E-Y, Ahn Y-K, Lee E-S, Choi S, et al. Next-generation sequencing approaches in genome-wide discovery of single nucleotide polymorphism markers associated with pungency and disease resistance in pepper. Biomed Res Int. 2018;2018:1–7. https://doi.org/10.1155/2018/5646213.
Article
CAS
Google Scholar
Kim J, Manivannan A, Kim D-S, Lee E-S, Lee H-E. Transcriptome sequencing assisted discovery and computational analysis of novel SNPs associated with flowering in Raphanus sativus in-bred lines for marker-assisted backcross breeding. Horticulture Res. 2019;6(1):1–12.
Article
Google Scholar
Dobin A, Davis CA, Schlesinger F, Drenkow J, Zaleski C, Jha S, et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics. 2013;29(1):15–21. https://doi.org/10.1093/bioinformatics/bts635.
Article
CAS
PubMed
Google Scholar
Pertea M, Pertea GM, Antonescu CM, Chang T-C, Mendell JT, Salzberg SL. StringTie enables improved reconstruction of a transcriptome from RNA-seq reads. Nat Biotechnol. 2015;33(3):290–5. https://doi.org/10.1038/nbt.3122.
Article
CAS
PubMed
PubMed Central
Google Scholar
Jiménez-Jacinto V, Sanchez-Flores A, Vega-Alvarado L. Integrative differential expression analysis for multiple experiments (IDEAMEX): a web server tool for integrated rna-seq data analysis. Front Genet. 2019;10:279. https://doi.org/10.3389/fgene.2019.00279.
Article
CAS
PubMed
PubMed Central
Google Scholar
Anders S, Huber W. Differential expression analysis for sequence count data. Nat Precedings. 2010:1–1.
Love MI, Huber W, Anders S. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biol. 2014;15(12):550. https://doi.org/10.1186/s13059-014-0550-8.
Article
CAS
PubMed
PubMed Central
Google Scholar
Tarazona S, García-Alcalde F, Dopazo J, Ferrer A, Conesa A. Differential expression in RNA-seq: a matter of depth. Genome Res. 2011;21(12):2213–23. https://doi.org/10.1101/gr.124321.111.
Article
CAS
PubMed
PubMed Central
Google Scholar
Bindea G, Mlecnik B, Hackl H, Charoentong P, Tosolini M, Kirilovsky A, et al. ClueGO: a Cytoscape plug-in to decipher functionally grouped gene ontology and pathway annotation networks. Bioinformatics. 2009;25(8):1091–3. https://doi.org/10.1093/bioinformatics/btp101.
Article
CAS
PubMed
PubMed Central
Google Scholar
Shannon P, Markiel A, Ozier O, Baliga NS, Wang JT, Ramage D, et al. Cytoscape: a software environment for integrated models of biomolecular interaction networks. Genome Res. 2003;13(11):2498–504. https://doi.org/10.1101/gr.1239303.
Article
CAS
PubMed
PubMed Central
Google Scholar
Rao X, Huang X, Zhou Z, Lin X. An improvement of the 2ˆ (−delta delta CT) method for quantitative real-time polymerase chain reaction data analysis. Biostatistics Bioinformatics Biomathematics. 2013;3(3):71.
PubMed
Google Scholar
Brouard J-S, Schenkel F, Marete A, Bissonnette N. The GATK joint genotyping workflow is appropriate for calling variants in RNA-seq experiments. J Anim Sci Biotechno. 2019;10(1):44. https://doi.org/10.1186/s40104-019-0359-0.
Article
CAS
Google Scholar
Li H, Handsaker B, Wysoker A, Fennell T, Ruan J, Homer N, et al. The sequence alignment/map format and SAMtools. Bioinformatics. 2009;25(16):2078–9. https://doi.org/10.1093/bioinformatics/btp352.
Article
CAS
PubMed
PubMed Central
Google Scholar
Danecek P, Auton A, Abecasis G, Albers CA, Banks E, DePristo MA, et al. The variant call format and VCFtools. Bioinformatics. 2011;27(15):2156–8. https://doi.org/10.1093/bioinformatics/btr330.
Article
CAS
PubMed
PubMed Central
Google Scholar
Cingolani P, Platts A, Wang LL, Coon M, Nguyen T, Wang L, et al. A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff: SNPs in the genome of Drosophila melanogaster strain w1118; iso-2; iso-3. Fly. 2012;6(2):80–92. https://doi.org/10.4161/fly.19695.
Article
CAS
PubMed
PubMed Central
Google Scholar