
Devkota, K. P., Devkota, M., Rezaei, M. & Oosterbaan, R. Managing salinity for sustainable agricultural production in salt-affected soils of irrigated drylands. Agric. Syst. 198, 103390 (2022).
Koca, Y. O. Effects of different salt concentrations on Quinoa Seedling Quality. Int. J. Second Metab. 4, 20–26 (2017).
Manaa, A. et al. Salinity tolerance of quinoa (Chenopodium quinoa Willd) as assessed by chloroplast ultrastructure and photosynthetic performance. Environ. Exp. Bot. 162, 103–114 (2019).
Graf, B. L. et al. Innovations in health value and functional food development of quinoa (Chenopodium quinoa Willd). Compre Rev. Food Sci. Food Saf. 14, 431–445 (2015).
Cai, Z. Q. & Gao, Q. Comparative physiological and biochemical mechanisms of salt tolerance in five contrasting highland quinoa cultivars. BMC Plant. Biol. 20, 1–15 (2020).
Jarvis, D. E. et al. The genome of Chenopodium quinoa. Nature 542, 307–312 (2017).
Gong, Z. et al. Plant abiotic stress response and nutrient use efficiency. Sci. China Life Sci. 63, 635–674 (2020).
Alshareef, N. O. et al. NAC transcription factors ATAF1 and ANAC055 affect the heat stress response in Arabidopsis. Sci. Rep. 12, 11264 (2022).
Han, Y. et al. Genome-wide identification of AP2/ERF Transcription Factor Family and functional analysis of DcAP2/ERF# 96 Associated with Abiotic stress in Dendrobium catenatum. Int. J. Mol. Sci. 23, 13603 (2022).
Toledo-Ortiz, G., Huq, E. & Quail, P. H. The Arabidopsis basic/helix-loop-helix transcription factor family. Plant. Cell. 15, 1749–1770 (2003).
Dubos, C. et al. MYB transcription factors in Arabidopsis. Trends Plant. sci. 15, 573–581 (2010).
Yang, X., Tuskan, G. A. & Cheng, Z. M. Divergence of the Dof gene families in poplar, Arabidopsis, and rice suggests multiple modes of gene evolution after duplication. Plant. Physiol. 142, 820–830 (2006).
Eulgem, T. & Somssich, I. E. Networks of WRKY transcription factors in defense signaling. Curr. Opin. Plant. Biol. 10, 366–371 (2007).
Feng, K. et al. Advances in AP2/ERF super-family transcription factors in plant. Crit. Rev. Biotechnol. 40, 750–776 (2020).
Yuan, H., Li, L., Cheng, H., Xiao, X. & Cheng, S. Identification of AP2/ERF transcription factors in Ginkgo biloba and the expression analysis of ERF Gene Family under Adversity stresses. Plant. Gene Trait 14, 1–12 (2023).
Nakano, T., Suzuki, K., Fujimura, T. & Shinshi, H. Genome-wide analysis of the ERF gene family in Arabidopsis and rice. Plant. Physiol. 140, 411–432 (2006).
Jofuku, K. D., Den Boer, B., Van Montagu, M. & Okamuro, J. K. Control of Arabidopsis flower and seed development by the homeotic gene APETALA2. Plant. Cell. 6, 1211–1225 (1994).
Riechmann, J. L. & Meyerowitz, E. M. The AP2/EREBP family of plant transcription factors. Biol. Chem. 379, 633–646 (1998).
Sakuma, Y. et al. DNA-binding specificity of the ERF/AP2 domain of Arabidopsis DREBs, transcription factors involved in dehydration-and cold-inducible gene expression. Biochem. Biophys. Res. Commun. 290, 998–1009 (2002).
Zhao, S. P. et al. Genome-wide analysis of the RAV family in soybean and functional identification of GmRAV-03 involvement in salt and drought stresses and exogenous ABA treatment. Front. Plant. Sci. 8, 905 (2017).
Lakhwani, D. et al. Genome-wide analysis of the AP2/ERF family in Musa species reveals divergence and neofunctionalisation during evolution. Sci. Rep. 6, 18878 (2016).
Jiang, F. et al. Mutations in an AP2 transcription factor-like gene affect internode length and leaf shape in maize. PLoS One. 7, e37040 (2012).
Müller, M. & Munné-Bosch, S. Ethylene response factors: a key regulatory hub in hormone and stress signaling. Plant. Physiol. 169, 32–41 (2015).
Sohn, K. H., Lee, S. C., Jung, H. W., Hong, J. K. & Hwang, B. K. Expression and functional roles of the pepper pathogen-induced transcription factor RAV1 in bacterial disease resistance, and drought and salt stress tolerance. Plant. Mol. Biol. 61, 897–915 (2006).
Li, C. W. et al. Tomato RAV transcription factor is a pivotal modulator involved in the AP2/EREBP-mediated defense pathway. Plant. Physiol. 156, 213–227 (2011).
Zhang, G. et al. Overexpression of the soybean GmERF3 gene, an AP2/ERF type transcription factor for increased tolerances to salt, drought, and diseases in transgenic tobacco. J. Exp. Bot. 60, 3781–3796 (2009).
Zhuang, J. et al. A rice OsAP23, functioning as an AP2/ERF transcription factor, reduces salt tolerance in transgenic Arabidopsis. Plant. Mol. Biol. Rep. 31, 1336–1345 (2013).
Kavas, M., Gökdemir, G., Seçgin, Z. & Bakhsh, A. Ectopic expression of common bean ERF transcription factor PvERF35 promotes salt stress tolerance in tobacco. Plant. Biol. 22, 1102–1112 (2020).
Fu, J. et al. Maize transcription factor ZmEREB20 enhanced salt tolerance in transgenic Arabidopsis. Plant. Physiol. Biochem. 159, 257–267 (2021).
Rong, W. et al. The ERF transcription factor Ta ERF 3 promotes tolerance to salt and drought stresses in wheat. Plant. Biotechnol. J. 12, 468–479 (2014).
Yu, Y. et al. Transcriptomic identification of wheat AP2/ERF transcription factors and functional characterization of TaERF-6-3A in response to drought and salinity stresses. Int. J. Mol. Sci. 23, 3272 (2022).
Xie, Z., Nolan, T. M., Jiang, H. & Yin, Y. AP2/ERF transcription factor regulatory networks in hormone and abiotic stress responses in Arabidopsis. Front. Plant. Sci. 10, 228 (2019).
Okamuro, J. K., Caster, B., Villarroel, R., Van Montagu, M. & Jofuku, K. D. The AP2 domain of APETALA2 defines a large new family of DNA binding proteins in Arabidopsis. Proc. Natl. Acad. Sci. 94, 7076–7081 (1997).
Zhuang, J. et al. Genome-wide analysis of the putative AP2/ERF family genes in Vitis vinifera. Sci. Hortic. 123, 73–81 (2009).
Ghorbani, R., Zakipour, Z., Alemzadeh, A. & Razi, H. Genome-wide analysis of AP2/ERF transcription factors family in Brassica napus. Physiol. Mol. Biol. Plants. 26, 1463–1476 (2020).
Li, P. et al. Genome-wide identification and expression analysis of AP2/ERF transcription factors in sugarcane (Saccharum spontaneum L). BMC Genom. 21, 1–17 (2020).
Faraji, S. et al. The AP2/ERF gene family in Triticum durum: genome-wide identification and expression analysis under drought and salinity stresses. Genes 11, 1464 (2020).
Cui, M. et al. Genome-wide identification and expression analysis of AP2/ERF transcription factor related to drought stress in cultivated peanut (Arachis hypogaea L). Front. Genet. 12, 750761 (2021).
Zhang, J., Liao, J., Ling, Q., Xi, Y. & Qian, Y. Genome-wide identification and expression profiling analysis of maize AP2/ERF superfamily genes reveal essential roles in abiotic stress tolerance. BMC Genom. 23, 1–22 (2022).
Xie, H. et al. Combined transcriptomic and metabolomic analyses of high temperature stress response of quinoa seedlings. BMC Plant. Biol. 23, 292 (2023).
Zhang, S. et al. Identification of core genes associated with different phosphorus levels in quinoa seedlings by weighted gene co-expression network analysis. BMC Genom. 24, 399 (2023).
Li, X. et al. Integrated Metabolomic and Transcriptomic Analysis of the Quinoa Seedling response to high relative humidity stress. Biomol 13, 1352 (2023).
Tashi, G. et al. Genome-wide identification and expression analysis of heat shock transcription factor family in Chenopodium quinoa Willd. Agron 8, 103 (2018).
Kumar, S., Stecher, G., Li, M., Knyaz, C. & Tamura, K. MEGA X: molecular evolutionary genetics analysis across computing platforms. Mol. Biol. Evol. 35 (6), 1547–1549 (2018).
Letunic, I. & Bork, P. Interactive tree of life (iTOL) v5: an online tool for phylogenetic tree display and annotation. Nucleic Acids Res. 49, W293–W296 (2021).
Chen, C. et al. TBtools: an integrative toolkit developed for interactive analyses of big biological data. Mol. Plant. 13, 1194–1202 (2020).
Chao, J. et al. MG2C: a user-friendly online tool for drawing genetic maps. Mol. Hortic. 1, 1–4 (2021).
Liu, C. et al. Genome-wide identification and characterization of mungbean CIRCADIAN CLOCK ASSOCIATED 1 like genes reveals an important role of VrCCA1L26 in flowering time regulation. BMC Genom. 23 (1), 374 (2022).
Liu, Y. et al. Genome-wide analysis of the auxin response factor (ARF) gene family in maize (Zea mays). Plant. Growth Regul. 63, 225–234 (2011).
Hurst, L. D. The Ka/Ks ratio: diagnosing the form of sequence evolution. Trends Genet. 18, 486–487 (2002).
Wang, H. et al. Genome-wide identification of the AP2/ERF gene family and functional analysis of GmAP2/ERF144 for drought tolerance in soybean. Front. Plant. Sci. 13, 848766 (2022).
Kanehisa, M., Furumichi, M., Sato, Y., Kawashima, M. & Ishiguro-Watanabe, M. KEGG for taxonomy-based analysis of pathways and genomes. Nucleic Acids Res. 51, 587–592 (2023).
Vita, F. et al. Early responses to salt stress in quinoa genotypes with opposite behavior. Physiol. Plant. 173, 1392–1420 (2021).
Van den Broeck, L. et al. From network to phenotype: the dynamic wiring of an Arabidopsis transcriptional network induced by osmotic stress. Mol. Syst. Biol. 13, 961 (2017).
Sosa-Zuniga, V., Brito, V., Fuentes, F. & Steinfort, U. Phenological growth stages of quinoa (Chenopodium quinoa) based on the BBCH scale. Ann. Appl. Biol. 171, 117–124 (2017).
Zhu, X., Wang, B., Wang, X. & Wei, X. Screening of stable internal reference gene of Quinoa under hormone treatment and abiotic stress. Physiol. Mol. Biol. Plants. 27, 2459–2470 (2021).
Livak, K. J. & Schmittgen, T. D. Analysis of relative gene expression data using real-time quantitative PCR and the 2– ∆∆CT method. Methods 25, 402–408 (2001).
Rashid, M., Guangyuan, H., Guangxiao, Y., Hussain, J. & Xu, Y. AP2/ERF transcription factor in rice: genome-wide canvas and syntenic relationships between monocots and eudicots. Evol. Bioinform. 8, EBO. S9369 (2012).
Agarwal, G. et al. Genome-wide dissection of AP2/ERF and HSP90 gene families in five legumes and expression profiles in chickpea and pigeonpea. Plant. Biotechnol. J. 14, 1563–1577 (2016).
Wang, P. et al. Factors influencing gene family size variation among related species in a plant family, Solanaceae. Genome Biol. Evol. 10, 2596–2613 (2018).
Lee, D. K. et al. Overexpression of the OsERF71 transcription factor alters rice root structure and drought resistance. Plant. Physiol. 172, 575–588 (2016).
Yang, S., Tang, X. F., Ma, N. N., Wang, L. Y. & Meng, Q. W. Heterology expression of the sweet pepper CBF3 gene confers elevated tolerance to chilling stress in transgenic tobacco. J. Plant. Physiol. 168, 1804–1812 (2011).
Song, X. et al. Origination, expansion, evolutionary trajectory, and expression bias of AP2/ERF superfamily in Brassica napus. Front. Plant. Sci. 7, 1186 (2016).
Sun, Z. M., Zhou, M. L., Xiao, X. G., Tang, Y. X. & Wu, Y. M. Overexpression of a Lotus corniculatus AP2/ERF transcription factor gene, LcERF080, enhances tolerance to salt stress in transgenic Arabidopsis. Plant. Biotechnol. Rep. 8, 315–324 (2014).
Magar, M. M., Liu, H. & Yan, G. Genome-wide analysis of AP2/ERF superfamily genes in contrasting wheat genotypes reveals heat stress-related candidate genes. Front. Plant. Sci. 13, 853086 (2022).
Fu, W. Genome-wide identification and characterization of the AP2/ERF Gene Family in Quinoa (Chenopodium quinoa) and their expression profiling during abiotic stress conditions. J. Plant. Growth Regul. 43, 1118–1136 (2024).
Palomino, G., Hernández, L. T. & de la Torres, C. Nuclear genome size and chromosome analysis in Chenopodium quinoa and C. Berlandieri subsp. nuttalliae. Euphytica 164, 221–230 (2008).
Guo, B. et al. Genome-wide analysis of APETALA2/ethylene-responsive factor (AP2/ERF) gene family in barley (Hordeum vulgare L). PLoS One. 11, e0161322 (2016).
Zhang, C. et al. Genome-wide analysis of the AP2/ERF superfamily in peach (Prunus persica). Genet. Mol. Res. 11, 4789–4809 (2012).
Liu, M. et al. Genome-wide investigation of the AP2/ERF gene family in tartary buckwheat (Fagopyum Tataricum). BMC Plant. Biol. 19, 1–19 (2019).
Cui, Y., Deng, X. & Liu, X. Genome-wide analysis and expression profiles of ethylene signal genes and Apetala2/Ethylene-responsive factors in peanut (Arachis hypogaea L). Front. Plant. Sci. 13, 828482 (2022).
Park, S., Shi, A., Meinhardt, L. W. & Mou, B. Genome-wide characterization and evolutionary analysis of the AP2/ERF gene family in lettuce (Lactuca sativa). Sci. Rep. 13, 21990 (2023).
Najafi, S., Sorkheh, K. & Nasernakhaei, F. Characterization of the APETALA2/Ethylene-responsive factor (AP2/ERF) transcription factor family in sunflower. Sci. Rep. 8, 1–16 (2018).
Qian, Z. et al. Genome-wide identification, evolution, and expression analyses of AP2/ERF family transcription factors in Erianthus Fulvus. Int. J. Mol. Sci. 24, 7102 (2023).
Zhou, L. & Yarra, R. Genome-wide identification and characterization of AP2/ERF transcription factor family genes in oil palm under abiotic stress conditions. Int. J. Mol. Sci. 22, 2821 (2021).
Yang, B., Yao, X., Zeng, Y. & Zhang, C. Genome-wide identification, characterization, and expression profiling of AP2/ERF superfamily genes under different development and abiotic stress conditions in pecan (Carya illinoinensis). Int. J. Mol. Sci. 23, 2920 (2022).
Jeffares, D. C., Penkett, C. J. & Bähler, J. Rapidly regulated genes are intron poor. Trends Genet. 24, 375–378 (2008).
Shu, Y., Liu, Y., Zhang, J., Song, L. & Guo, C. Genome-wide analysis of the AP2/ERF superfamily genes and their responses to abiotic stress in Medicago truncatula. Front. Plant. Sci. 6, 1247 (2016).
Licausi, F., Pucciariello, C. & Perata, P. New Role for an old rule: N-end rule‐mediated degradation of Ethylene Responsive factor proteins governs low Oxygen response in plants F. J. Integr. Plant. Biol. 55, 31–39 (2013).
Tiwari, S. B. et al. The EDLL motif: a potent plant transcriptional activation domain from AP2/ERF transcription factors. Plant. J. 70, 855–865 (2012).
Zou, C. et al. A high-quality genome assembly of quinoa provides insights into the molecular basis of salt bladder-based salinity tolerance and the exceptional nutritional value. Cell. Res. 27, 1327–1340 (2017).
Wang, Y., Wang, X. & Paterson, A. H. Genome and gene duplications and gene expression divergence: a view from plants. Ann. N Y Acad. Sci. 1256, 1–14 (2012).
Wang, W., Liu, W. & Wang, B. Identification of CDK gene family and functional analysis of CqCDK15 under drought and salt stress in quinoa. BMC Genom. 24, 461 (2023).
Li, K. et al. Genome-wide identification, phylogenetic analysis, and expression profiles of trihelix transcription factor family genes in quinoa (Chenopodium quinoa Willd.) Under abiotic stress conditions. BMC Genom. 23, 499 (2022).
Zhu, X., Wang, B., Wang, X., Zhang, C. & Wei, X. Genome-wide identification, characterization and expression analysis of the LIM transcription factor family in quinoa. Physiol. Mol. Biol. Plants. 27, 787–800 (2021).
Ma, Z., Hu, L. & Jiang, W. Understanding AP2/ERF Transcription Factor Responses and tolerance to various Abiotic stresses in plants: a Comprehensive Review. Int. J. Mol. Sci. 25, 893 (2024).
Wu, Y. et al. ERF subfamily transcription factors and their function in plant responses to abiotic stresses. Front. Plant. Sci. 13, 1042084 (2022).
Li, F. et al. Genomic identification and comparative expansion analysis of the non-specific lipid transfer protein gene family in Gossypium. Sci. Rep. 6, 38948 (2016).
Wang, J., Mei, J. & Ren, G. Plant microRNAs: biogenesis, homeostasis, and degradation. Front. Plant. Sci. 10, 433008 (2019).
Zhu, Z. F. et al. Isolation and analysis of a novel MYC gene from rice. Yi Chuan Xue bao = Acta Genetica Sinica. 32, 393–398 (2005).
Riaz, M. W. et al. Expansion and molecular characterization of AP2/ERF gene family in wheat (Triticum aestivum L). Front. Genet. 12, 632155 (2021).
Xu, Z. S., Chen, M., Li, L. C. & Ma, Y. Z. Functions and application of the AP2/ERF transcription factor family in crop improvement F. J. Integr. Plant. Biol. 53, 570–585 (2011).
Hu, Y. X., Wang, Y. H., Liu, X. F. & Li, J. Y. Arabidopsis RAV1 is down-regulated by brassinosteroid and may act as a negative regulator during plant development. Cell. Res. 14, 8–15 (2004).
Duan, Y. B. et al. Identification of a regulatory element responsible for salt induction of rice OsRAV2 through ex situ and in situ promoter analysis. Plant. Mol. Biol. 90, 49–62 (2016).
Min, H., Zheng, J. & Wang, J. Maize ZmRAV1 contributes to salt and osmotic stress tolerance in transgenic Arabidopsis. J. Plant. Biol. 57, 28–42 (2014).
Fu, M., Kang, H. K., Son, S. H., Kim, S. K. & Nam, K. H. A subset of Arabidopsis RAV transcription factors modulates drought and salt stress responses independent of ABA. Plant. Cell. Physiol. 55, 1892–1904 (2014).
Sakata, Y., Nakamura, I., Taji, T., Tanaka, S. & Quatrano, R. S. Regulation of the ABA-responsive em promoter by ABI3 in the moss Physcomitrella patens: role of the ABA response element and the RY element. Plant. Signal. Behav. 5, 1061–1066 (2010).
Lee, S. et al. DREB2C interacts with ABF2, a bZIP protein regulating abscisic acid-responsive gene expression, and its overexpression affects abscisic acid sensitivity. Plant. Physiol. 153, 716–727 (2010).
Zhang, Y. et al. Identification of salinity-related genes in ENO2 mutant (eno2–) of Arabidopsis thaliana. J. Integr. Agric. 17, 94–110 (2018).
Olivas, N. H. D. Ecogenomics of Plant Resistance to Biotic and Abiotic Stresses (Wageningen University and Research, 2016).
Ma, S., Gong, Q. & Bohnert, H. J. Dissecting salt stress pathways. J. Exp. Bot. 57, 1097–1107 (2006).
Wang, M. et al. ERF 109 of trifoliate orange (Poncirus trifoliata (L.) Raf.) Contributes to cold tolerance by directly regulating expression of Prx1 involved in antioxidative process. Plant. Biotechnol. J. 17, 1316–1332 (2019).
Bahieldin, A. et al. Ethylene responsive transcription factor ERF109 retards PCD and improves salt tolerance in plant. BMC Plant. Biol. 16, 1–9 (2016).
Bahieldin, A. et al. Multifunctional activities of ERF109 as affected by salt stress in Arabidopsis. Sci. Rep. 8, 6403 (2018).
Sun, S., Liang, X., Chen, H., Hu, L. & Yang, Z. Identification of AP2/ERF Transcription Factor Family Genes and expression patterns in response to Drought stress in Pinus Massoniana. Forests 13, 1430 (2022).
Zhang, Y. et al. Improvement of salt tolerance of Arabidopsis thaliana seedlings inoculated with endophytic Bacillus cereus KP120. Plant. Interact. 17, 884–893 (2022).
Ghorbani, R., Alemzadeh, A. & Razi, H. Microarray analysis of transcriptional responses to salt and drought stress in Arabidopsis thaliana. Heliyon 5, e02614 (2019).
Cao, F. Y. et al. Arabidopsis ETHYLENE RESPONSE FACTOR 8 (ERF8) has dual functions in ABA signaling and immunity. BMC Plant. Biol. 18, 1–16 (2018).
Keshishian, E. A. et al. CYTOKININ RESPONSE FACTOR 2 is involved in modulating the salt stress response. Plant. J. 110, 1097–1110 (2022).
Papon, N. & Courdavault, V. ARResting cytokinin signaling for salt-stress tolerance. Plant. Sci. 314, 111116 (2022).