Transcriptome Profiling of Two Hybrid Rice Provides Insights Into the Genetic Basis of Heterosis.

Abstract BackgroundHeterosis is a phenomenon that hybrids show superior performance over their parents. The successful utilization of heterosis has greatly improved rice productivity, but the molecular basis of heterosis remains largely unclear. ResultsHere, the transcriptomes of young panicles and leaves of the two widely grown two-line super hybrid rice varieties (Jing-Liang-You-Hua-Zhan (JLYHZ) and Long-Liang-You-Hua-Zhan (LLYHZ)) and their parents were analyzed by RNA-seq. Transcriptome profiling of hybrid revealed 1,778 ~ 9,404 differentially expressed genes (DEGs) in two tissues, which were identified compared with their parents. GO and KEGG enrichment analysis showed that the pathways significantly enriched in both tissues of two hybrids were related to yield and resistance, like circadian rhythm (GO:0007623), response to water deprivation (GO:0009414), photosynthetic genes (osa00196). Allele-specific expression genes (ASEGs) were also identified in hybrids. These ASEGs were most significantly enriched in ionotropic glutamate receptor signaling pathway, which was hypothesized to be potential amino acid sensors in plants. Moreover, the ASEGs were also differentially expressed between parents. The number of variations in ASEGs is higher than expected, especially for large effect variations. These DEGs and ASEGs are the potential reasons for the formation of heterosis in the two combinations. ConclusionsOur results provide a comprehensive understanding of the heterosis of two-line super hybrid rice and facilitate the exploitation of heterosis in hybrid rice breeding with high yield heterosis.