Comparative transcriptome analysis reveals the molecular mechanism of heterosis on waterlogging tolerance in Chrysanthemum indicum

Abstract Background Heterosis breeding is one of the most important breeding methods of chrysanthemum. Currently, the genetic mechanism of heterosis for waterlogging tolerance in chrysanthemum is still unclear. This study analyzed the expression profiles and potential heterosis-related genes of two hybrid lines and their parents with extreme differences in waterlogging tolerance under control and waterlogging stress conditions using RNA-seq. Results A population of 140 F 1 progeny derived from Chrysanthemum indicum (Nanchang) (waterlogging-tolerant) and Chrysanthemum indicum (Nanjing) (waterlogging-sensitive) was used to characterize the extent of genetic variation for seven waterlogging tolerance related traits across two years. Lines 98 and 95 respectively showing positive and negative overdominance heterosis for the waterlogging tolerance traits together with their parents were used for RNA-seq under control and waterlogging stress conditions. The results showed line 98 exhibited the maximum number of differentially expressed genes (DEGs). Gene ontology (GO) enrichment analysis revealed multiple stress-related biological processes for the common up-regulated genes. Line 98 had a significant increase in non-additive genes under waterlogging stress, with the transgressive up-regulation and paternal-expression dominance patterns being the major gene expression profiles, further, GO analysis identified 55 and 95 genes overlapped with the up-regulated genes shared by two parents in terms of response to stress and response to stimulus, respectively. A total of 6,640 genes displayed maternal-expression dominance patterns were observed in line 95. In addition, 16 candidate genes including SAP12 , DOX1 , and ERF017 potentially responsible for the formation of waterlogging tolerance heterosis of line 98 were highlighted. Conclusion The current study gives a comprehensive overview of the root transcriptomes at F 1 hybrids and their parents, and provides novel insights into the molecular mechanism of heterosis and the response to waterlogging stress in chrysanthemum.