Comparative Transcriptome Analysis of Waterlogging-Sensitive and Waterlogging-Tolerant Chrysanthemum morifolium Cultivars under Waterlogging Stress and Reoxygenation Conditions

Waterlogging stress is among the most severe abiotic stressors in the breeding and the production of Chrysanthemum morifolium. However, the mechanism underlying the response to waterlogging and post-waterlogging reoxygenation in C. morifolium remains unknown. In this study, we compared the differences between the transcriptomes of two chrysanthemum cultivars, i.e., the waterlogging-tolerant cultivar Nannongxuefeng and the waterlogging-sensitive cultivar Qinglu, by performing RNA-seq to elucidate the possible mechanism of waterlogging and reoxygenation in C. morifolium. Nannongxuefeng had a higher ethylene production under the waterlogging and reoxygenation conditions. Furthermore, the expression of transcription factors and genes that are involved in the hormone response, N-end rule pathway and ROS signaling significantly differed between the two cultivars. Nannongxuefeng and Qinglu significantly differed in their response to waterlogging and reoxygenation, providing a deeper understanding of the mechanism underlying the response to waterlogging and guidance for the breeding of C. morifolium.