BackgroundDespite the great contributions of utilizing heterosis to crop productivity worldwide, the molecular mechanism of heterosis remains largely unexplored. Thus, the present research is focused on the grain number heterosis of a widely used late-cropping indica super hybrid rice combination in China using a high-throughput next-generation RNA-seq strategy.ResultsHere, we obtained 872 million clean reads, and at least one read could maps 27,917 transcripts out of 35,679 annotations. Transcript differential expression analysis revealed a total of 5910 differentially expressed genes (DGHP) between super-hybrid rice Wufengyou T025 (WFYT025) and its parents were identified in the young panicles. Out of the 5910 DGHP, 63.1% had a genetic action mode of over-dominance, 17.3% had a complete-dominance action, 15.6% had a partial-dominance action and 4.0% had an additive action. DGHP were significantly enriched in carotenoid biosynthesis, diterpenoid biosynthesis and plant hormone signal transduction pathways, with the key genes involved in the three pathways being up-regulated in the hybrid. By comparing the DGHP enriched in the KEGG pathway with QTLs associated with grain number, several DGHP were located on the same chromosomal segment with some of these grain number QTLs.ConclusionThrough young panicle development transcriptome analysis, we conclude that the over-dominant effect is probably the major contributor to the grain number heterosis of WFYT025. The DGHP sharing the same location with grain number QTLs could be considered a candidate gene and provide valuable targets for the cloning and functional analysis of these grain number QTLs.Electronic supplementary materialThe online version of this article (10.1186/s12284-018-0229-y) contains supplementary material, which is available to authorized users.
N6-methyladenosine (m6A) is the most prevalent internal modification present in mRNAs of all higher eukaryotes. However, the role of the m6A methylomes in rice is still poorly understood. With the development of MeRIP-seq technique, in-depth identification of mRNAs with m6A modification becomes feasible. We investigated the m6A methylomes in roots of cadmium (Cd) group and compared that with the roots in the control (CK) group by m6A sequencing, in 9311 and Nipponbare (NIP), respectively. The results indicated that Cd leads to altered modification profile in 3,406 differential m6A peaks in 9311, and 2,065 differential m6A peaks in NIP. KEGG pathway analysis of genes with differentially modified m6A peaks indicates that the “phenylalanine”, “tyrosine and tryptophan biosynthesis”, “glycine”, “adherens junctions”, “glycerophospholipid metabolism” and “threonine metabolism” signaling pathways may be associated with abnormal roots development of rice due to exposure to cadmium in 9311. “Arginine”, “proline metabolism”, “glycerolipid”, “protein processing in endoplasmic reticulum”, metabolism pathways were significantly enriched in genes with differentially modified m6A peaks in NIP. Different from that in Arabidopsis, the m6A peak (m6A-modified nucleotide position on mRNAs) distribution exhibits preference toward both the stop codon and 3′UTRs region. These findings provide a resource for plant RNA epi-transcriptomics studies and further enlarge our knowledge on the function of RNA m6A modification in plants.
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