Sweetpotato (Ipomoea batatas [L.] Lam) is an important starch crop that ensures food and nutrition security in the era of climate change. Sweetpotato is tolerant to environmental stresses such as drought, high temperature, and high salt, and therefore, is well adapted to marginal lands; however, it is relatively vulnerable to flooding stress, which severely reduces its yield and commercial value. To understand the flooding stress response of sweetpotato, we performed comparative transcriptome analysis of the leaves of two sweetpotato cultivars with contrasting flooding stress tolerance levels: Yeonjami (YJM; flooding tolerant) and Jeonmi (JM; flooding sensitive). Both cultivars were partially submerged in water for 0, 0.5, and 3 days. RNA-seq data of both cultivars revealed 14,229 differentially expressed genes (DEGs), which were categorized into seven clusters and six groups, based on the expression pattern of co-expressed DEGs and expression duration of DEGs, respectively. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses showed that DEGs of distinguishing functions between the two cultivars were involved in plant hormone signaling, carbohydrate transport, and mitogen-activated protein kinase (MAPK) signaling. Based on these results, we predict that YJM promotes adventitious growth, whereas JM exhibits shoot elongation under flooding stress. The expression levels of several key candidate genes involved in flooding tolerance correlated well with the comparative transcriptomics data. Overall, this study provides further insights into the molecular mechanism of flooding stress response in sweetpotato, and reveals candidate genes that could be used for developing new flooding tolerant sweetpotato cultivars.

甘薯（Ipomoea batatas[L.] Lam）是重要的淀粉作物，可确保气候变化时代的粮食和营养安全。甘薯能忍受干旱，高温和高盐等环境压力，因此非常适合边缘土地。但是，它相对容易遭受洪水压力，从而严重降低了产量和商业价值。为了了解甘薯的淹水胁迫响应，我们对两个甘薯品种的叶片进行了转录组比较分析，两个品种具有不同的淹水胁迫耐性水平：Yeonjami（YJM；耐水）和Jeonmi（JM；对水浸敏感）。两个品种都部分浸没在水中0、0.5和3天。两个品种的RNA-seq数据均显示14,229个差异表达基因（DEG），根据共表达的DEG的表达模式和DEG的表达持续时间，将其分为七个簇和六个组。基因本体论（GO）和《京都基因与基因组百科全书》（KEGG）富集分析表明，两个品种之间的区别功能DEG参与植物激素信号传导，碳水化合物转运和丝裂原活化蛋白激酶（MAPK）信号传导。基于这些结果，我们预测YJM促进不定形生长，而JM在洪水胁迫下表现出枝条伸长。泛洪耐受性涉及的几个关键候选基因的表达水平与比较转录组学数据相关性很好。总体而言，这项研究提供了对甘薯中水淹胁迫响应的分子机制的进一步见解，