Alam A, Al Arif Jahan A, Bari M S, Khandokar L, Mahmud M H, Junaid M, Chowdhury M S, Khan M F, Seidel V, Haque M A. 2023. Allium vegetables: Traditional uses, phytoconstituents, and beneficial effects in inflammation and cancer. Critical Reviews in Food Science and Nutrition, 63, 6580–6614.

An X H, Tian Y, Chen K Q, Liu X J, Liu D D, Xie X B, Cheng C G, Cong P H, Hao Y J. 2015. MdMYB9 and MdMYB11 are involved in the regulation of the JA-induced biosynthesis of anthocyanin and proanthocyanidin in apples. Plant and Cell Physiology, 56, 650–662.

Asemani Y, Zamani N, Bayat M, Amirghofran Z. 2019. Allium vegetables for possible future of cancer treatment. Phytotherapy Research, 33, 3019–3039.

Chen Y, Dubois M, Vermeersch M, Inzé D, Vanhaeren H. 2021. Distinct cellular strategies determine sensitivity to mild drought of Arabidopsis natural accessions. Plant Physiology, 186, 1171–1185.

Cui J, Li X, Gan Q, Lu Z, Du Y, Noor I, Wang L, Liu S, Jin B. 2024. Flavonoids mitigate nanoplastic stress in Ginkgo biloba. Plant, Cell & Environment, 48, 1790–1811.

Dias M C, Pinto D C, Silva A M. 2021. Plant flavonoids: Chemical characteristics and biological activity. Molecules, 26, 5377.

Duggal P, Gillanders E M, Holmes T N, Bailey-Wilson J E. 2008. Establishing an adjusted p-value threshold to control the family-wide type 1 error in genome wide association studies. BMC Genomics, 9, 1–8.

Eysholdt-Derzsó E, Sauter M. 2019. Hypoxia and the group VII ethylene response transcription factor HRE2 promote adventitious root elongation in Arabidopsis. Plant Biology, 21, 103–108.

Fàbregas N, Fernie A R. 2019. The metabolic response to drought. Journal of Experimental Botany, 70, 1077–1085.

Gani U, Nautiyal A K, Kundan M, Rout B, Pandey A, Misra P. 2022. Two homeologous MATE transporter genes, NtMATE21 and NtMATE22, are involved in the modulation of plant growth and flavonol transport in Nicotiana tabacum. Journal of Experimental Botany, 73, 6186–6206.

Goyal K, Kaur K, Kaur G. 2020. Foliar treatment of potassium nitrate modulates the fermentative and sucrose metabolizing pathways in contrasting maize genotypes under water logging stress. Physiology and Molecular Biology of Plants, 26, 899–906.

Harb A, Krishnan A, Ambavaram M M, Pereira A. 2010. Molecular and physiological analysis of drought stress in Arabidopsis reveals early responses leading to acclimation in plant growth. Plant Physiology, 154, 1254–1271.

Hong B, Zhou B, Zhao D, Liao L, Chang T, Wu X, Wu J, Yao M, Chen H, Mao J. 2024. Yield, cell structure and physiological and biochemical characteristics of rapeseed under waterlogging stress. BMC Plant Biology, 24, 941.

Kang H M, Sul J H, Service S K, Zaitlen N A, Kong S Y, Freimer N B, Sabatti C, Eskin E. 2010. Variance component model to account for sample structure in genome-wide association studies. Nature Genetics, 42, 348–354.

Kumar L, Futschik M E. 2007. Mfuzz: A software package for soft clustering of microarray data. Bioinformation, 2, 5.

Li C, Wu J, Hu K D, Wei S W, Sun H Y, Hu L Y, Han Z, Yao G F, Zhang H. 2020. PyWRKY26 and PybHLH3 cotargeted the PyMYB114 promoter to regulate anthocyanin biosynthesis and transport in red-skinned pears. Horticulture Research, 7, 37.

Li Q Q, Zhou S D, He X J, Yu Y, Zhang Y C, Wei X Q. 2010. Phylogeny and biogeography of Allium (Amaryllidaceae: Allieae) based on nuclear ribosomal internal transcribed spacer and chloroplast rps16 sequences, focusing on the inclusion of species endemic to China. Annals of Botany, 106, 709–733.

Liang G, Wang H, Gou H, Li M, Cheng Y, Zeng B, Mao J, Chen B. 2024. Overexpression of VaBAM3 from Vitis amurensis enhances seedling cold tolerance by promoting soluble sugar accumulation and reactive oxygen scavenging. Plant Cell Reports, 43, 1–18.

Liang R, Tan L, Guo X, Lou S, Dan X, Han Y, Zeng C, Zhang H, Yang K, Chen L. 2025. Allelic variation in the promoter of WRKY22 enhances humid adaptation of Arabidopsis thaliana. Molecular Plant, 18, 42–58.

Liao N, Hu Z, Miao J, Hu X, Lyu X, Fang H, Zhou Y M, Mahmoud A, Deng G, Meng Y Q. 2022. Chromosome-level genome assembly of bunching onion illuminates genome evolution and flavor formation in Allium crops. Nature Communications, 13, 6690.

Liu B, Jiang Y, Tang H, Tong S, Lou S, Shao C, Zhang J, Song Y, Chen N, Bi H. 2021. The ubiquitin E3 ligase SR1 modulates the submergence response by degrading phosphorylated WRKY33 in Arabidopsis. The Plant Cell, 33, 1771–1789.

Love M I, Huber W, Anders S. 2014. Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 15, 1–21.

Lu H, Wang M, Li W, Chen Z, Li S, Yi Z, Zhang Y. 2023. Superior antioxidant capacity and auxin production promote seedling formation of rice seeds under submergence stress. Agronomy, 13, 171.

Marinova K, Pourcel L, Weder B, Schwarz M, Barron D, Routaboul J M, Debeaujon I, Klein M. 2007. The Arabidopsis MATE transporter TT12 acts as a vacuolar flavonoid/H+-antiporter active in proanthocyanidin-accumulating cells of the seed coat. The Plant Cell, 19, 2023–2038.

Nicolas P, Shinozaki Y, Powell A, Philippe G, Snyder S I, Bao K, Zheng Y, Xu Y, Courtney L, Vrebalov J. 2022. Spatiotemporal dynamics of the tomato fruit transcriptome under prolonged water stress. Plant Physiology, 190, 2557–2578.

Niu M X, Feng C H, He F, Zhang H, Bao Y, Liu S J, Liu X, Su Y, Liu C, Wang H L. 2024. The miR6445‐NAC029 module regulates drought tolerance by regulating the expression of glutathione S‐transferase U23 and reactive oxygen species scavenging in Populus. New Phytologist, 242, 2043–2058.

Peláez-Vico M Á, Sinha R, Induri S P, Lyu Z, Venigalla S D, Vasireddy D, Singh P, Immadi M S, Pascual L S, Shostak B. 2023. Integrative phenotypic-transcriptomic analysis of soybean plants subjected to multifactorial stress combination. bioRxiv, 2023. 08.15.553447.

Pinheiro S S, de Morais Cardoso L, Anunciação P C, de Menezes C B, Queiroz V A V, Martino H S D, Della Lucia C M, Sant’Ana H M P. 2021. Water stress increased the flavonoid content in tannin-free sorghum grains. Journal of Food Composition and Analysis, 100, 103892.

Rahman M M, Chakraborty T K, Al Mamun A, Kiaya V. 2023. Land- and water-based adaptive farming practices to cope with waterlogging in variably elevated homesteads. Sustainability, 15, 2087.

Renziehausen T, Frings S, Schmidt‐Schippers R. 2024. ‘Against all floods’: Plant adaptation to flooding stress and combined abiotic stresses. The Plant Journal, 117, 1836–1855.

Rymaszewski W, Vile D, Bediee A, Dauzat M, Luchaire N, Kamrowska D, Granier C, Hennig J. 2017. Stress-related gene expression reflects morphophysiological responses to water deficit. Plant Physiology, 174, 1913–1930.

Schenke D, Utami H P, Zhou Z, Gallegos M T, Cai D. 2019. Suppression of UV-B stress induced flavonoids by biotic stress: Is there reciprocal crosstalk? Plant Physiology and Biochemistry, 134, 53–63.

Shomali A, Das S, Arif N, Sarraf M, Zahra N, Yadav V, Aliniaeifard S, Chauhan D K, Hasanuzzaman M. 2022. Diverse physiological roles of flavonoids in plant environmental stress responses and tolerance. Plants, 11, 3158.

Skirycz A, Vandenbroucke K, Clauw P, Maleux K, De Meyer B, Dhondt S, Pucci A, Gonzalez N, Hoeberichts F, Tognetti V B. 2011. Survival and growth of Arabidopsis plants given limited water are not equal. Nature Biotechnology, 29, 212–214.

Sun B, Meng W, Yin W, Niu M, Liu D, Liu J, Zhang X, Dong N, Yang Y, Li X. 2024. Vital contribution of brassinosteroids to hypoxia-stimulated coleoptile elongation in submerged rice. The Crop Journal, 12, 1379–1390.

Sun Y, Wang C, Chen H Y, Ruan H. 2020. Response of plants to water stress: A meta-analysis. Frontiers in Plant Science, 11, 978.

Tanaka Y, Sasaki N, Ohmiya A. 2008. Biosynthesis of plant pigments: Anthocyanins, betalains and carotenoids. The Plant Journal, 54, 733–749.

Tang H, Bi H, Liu B, Lou S, Song Y, Tong S, Chen N, Jiang Y, Liu J, Liu H. 2021. WRKY33 interacts with WRKY12 protein to up‐regulate RAP2.2 during submergence induced hypoxia response in Arabidopsis thaliana. New Phytologist, 229, 106–125.

Waadt R, Seller C A, Hsu P K, Takahashi Y, Munemasa S, Schroeder J I. 2022. Plant hormone regulation of abiotic stress responses. Nature Reviews Molecular Cell Biology, 23, 680–694.

Wang H, Liu X, Yang P, Wu R, Wang S, He S, Zhou Q. 2022. Potassium application promote cotton acclimation to soil waterlogging stress by regulating endogenous protective enzymes activities and hormones contents. Plant Physiology and Biochemistry, 185, 336–343.

Wang S, Chen K, Zhang J, Wang J, Li H, Yang X, Shi Q. 2022. Genome-wide characterization of MATE family members in Cucumis melo L. and their expression profiles in response to abiotic and biotic stress. Horticultural Plant Journal, 8, 474–488.

Yang P, Yuan Y, Yan C, Jia Y, You Q, Da L, Lou A, Lv B, Zhang Z, Liu Y. 2024. AlliumDB: A central portal for comparative and functional genomics in Allium. Horticulture Research, 11, uhad285.

Yin W, Wang X, Liu H, Wang Y, van Nocker S, Tu M, Fang J, Guo J, Li Z, Wang X. 2022. Overexpression of VqWRKY31 enhances powdery mildew resistance in grapevine by promoting salicylic acid signaling and specific metabolite synthesis. Horticulture Research, 9, uhab064.

Yu G, Wang L G, Han Y, He Q Y. 2012. clusterProfiler: An R package for comparing biological themes among gene clusters. Omics: A Journal of Integrative Biology, 16, 284–287.

Zhang B, Yang H J, Qu D, Zhu Z Z, Yang Y Z, Zhao Z Y. 2022. The MdBBX22–miR858–MdMYB9/11/12 module regulates proanthocyanidin biosynthesis in apple peel. Plant Biotechnology Journal, 20, 1683–1700.

Zhang K, Chen X, Yuan P, Song C, Song S, Jiao J, Wang M, Hao P, Zheng X, Bai T. 2023. Comparative physiological and transcriptome analysis reveals potential pathways and specific genes involved in waterlogging tolerance in apple rootstocks. International Journal of Molecular Sciences, 24, 9298.

Zhang L, Wang L, Fang Y, Gao Y, Yang S, Su J, Ni J, Teng Y, Bai S. 2024. Phosphorylated transcription factor PuHB40 mediates ROS-dependent anthocyanin biosynthesis in pear exposed to high light. The Plant Cell, 36, 3562–3583.

Zhang Y, Liang T, Dong H. 2024. Melatonin enhances waterlogging tolerance of field-grown cotton through quiescence adaptation and compensatory growth strategies. Field Crops Research, 306, 109217.

Zhao X, Zhong Y, Shi J, Zhou W. 2021. 24-Epibrassinolide confers tolerance against deep-seeding stress in Zea mays L. coleoptile development by phytohormones signaling transduction and their interaction network. Plant Signaling & Behavior, 16, 1963583.

Zou Q J, Wang T, Guo Q S, Xiao Y M, Wu L W. 2018. Cloning and expression analysis of F3’H and quantification of downstream products in Chrysanthemum morifolium under flooding stress. China Journal of Chinese Materia Medica, 43, 52–57.