Waterlogging is a hazardous natural occurrence to constrain maize production in the high rainfall area in modern agriculture. Thus, there is need to use maize cultivars with desirable resistance to waterlogging stress to mitigate the threat. In this study, Comparative physiological and transcriptomic analysis of tropical and temperate maize lines was performed to reveal the molecular mechanisms underlying maize tolerance to waterlogging. Physiological parameter analysis showed that the tropical line “Suwan-2” sustained relatively lower peroxidase (POD), superoxide dismutase (SOD), and malondialdehyde (MDA), but higher chlorophyll, soluble carbohydrate, and soluble protein contents, as compared to the temperate line “Cim-3” under waterlogging stress. Chlorophyll fluorescence parameters Fv/Fo and Fv/Fm declined consistently and were significant higher in the tropical maize line than the temperate maize line under waterlogging stress. RNA sequencing experiments yielded 21,348 differentially expressed genes (DEGs). Among these, three sets of waterlogging-responsive DEGs were detected, including 314 specific to “Cim-3”, 1186 shared between the two lines subjected to waterlogging stress, and 259 overlapping DEGs between the two lines in control conditions. The gene ontology terms cellular process, metabolic process, plant hormone signal transduction, and catalytic activity were highly enriched in the tropical maize line “Suwan-2”. Crucial waterlogging-responsive genes in “Suwan-2” were related to transcription factor modulation, cellular redox homeostasis maintenance, plant hormone biosynthesis regulation, and metabolic process. These findings offer insight into the mechanisms underlying the waterlogging tolerance of tropical maize.

涝渍是现代农业高雨区玉米生产的一种危险自然现象。因此，需要使用对涝胁迫具有理想抗性的玉米品种来减轻威胁。在这项研究中，对热带和温带玉米品系进行了比较生理学和转录组学分析，以揭示玉米耐涝的分子机制。生理参数分析表明，与温带相比，热带线“苏湾2号”的过氧化物酶（POD）、超氧化物歧化酶（SOD）和丙二醛（MDA）含量相对较低，但叶绿素、可溶性碳水化合物和可溶性蛋白质含量较高。 “Cim-3”线在涝渍胁迫下。叶绿素荧光参数Fv/Fo和频率/频率在涝渍胁迫下，热带玉米品系的显着高于温带玉米品系。RNA 测序实验产生了 21,348 个差异表达基因 (DEG)。其中检测到3组内涝响应DEG，其中“Cim-3”特有的314个，受涝胁迫的两条线共有1186条，控制条件下两条线之间重叠的DEG有259条。细胞过程、代谢过程、植物激素信号转导和催化活性等基因本体术语在热带玉米品系“Suwan-2”中高度丰富。“Suwan-2”中关键的涝渍反应基因与转录因子调节、细胞氧化还原稳态维持、植物激素生物合成调节和代谢过程有关。