Genome-wide transcriptomic profiles reveal comprehensive insights into flooding-tolerant responses in 3 rice cultivars
Date Issued
2016
Date
2016
Author(s)
Yang, Hung-An
Abstract
Abstract Rice SUB1A-1 (SUBMERGENCE1A-1), a member of group-Vll ethylene response transcription factor (ERF-Vll), is up-regulated during submergence, and it plays an important role in flooding tolerance among rice cultivars. The cultivars that contain the SUB1A-1 allele, including FR13A and Pokkali, display flooding-tolerant phenotype. In contrast, IR29 cultivar, which possesses SUB1A-2 allele, shows flooding-intolerant phenotype. In addition, FR13A and Pokkali both contain SUB1A-1 but display significantly different induction patterns and phenotypes under submergence. During submergence, FR13A stays quiescent to conserve energy and its SUB1A-1 transcription is highly induced. On the contrary, Pokkali continues to grow under submergence, but its SUB1A-1 induction level is much lower than that of FR13A. The genes under SUB1A-1 control are mainly involved in glycolytic pathway, which are also highly induced in Pokkali. Moreover, the ATP level is higher in FR13A and Pokkali than IR29 under submergence. Accordingly these materials provided us a good starting point to look for early hypoxia-tolerant genes, downstream genes of SUB1A-1 and specific hypoxia responsive genes in Pokkali. To characterize the tolerance related genes that respond to early and late hypoxia, we applied genome-wide transcriptomic analysis to FR13A, IR29 and Pokkali under submergence. We identified 53 genes that might be involved in the early flooding tolerance. Four transcription factors and genes related to calcium signaling and MAPK pathways were found in this category. On the other hand, 74 genes that might be under SUB1A-1 control in late hypoxia were identified. The genes were mainly related to carbohydrate metabolism. Interestingly, two ERF transcription factors, ERF66 and ERF67, which are potential targets of the N-end rule regulation, were identified in this group. We further used transient assays to validate the regulation in callus. Our results suggested that SUB1A-1 positively regulated ERF66 and ERF67. In addition, ERF66 and ERF67 might follow the N-end rule to modulate SUB1A-1 expression. This regulatory mechanism may fine-tune hypoxia response in rice. On the other hand, the hypoxia responsive genes that were induced higher in Pokkali were associated with ion channel, DNA replication, expansin and growth regulation. Most of them are GA responsive genes and were similarly expressed in deepwater rice under submergence. In addition, the genes encoding enzymes that catalyze the active form GA to inactive form were expressed at lower levels in Pokkali. We proposed that the GA level might be higher in Pokkali which allowed it to continue growing under submergence and get oxygen from water surface.
Subjects
submergence tolerance
GA response
Type
thesis