Transcriptomic, proteomic, and phosphoproteomic analyses reveal dynamic signaling networks influencing long-grain rice development

The LGS1 (Large grain size 1) gene, also known as GS2/GL2/OsGRF4, is involved in regulating grain size and quality in rice, but the mechanism governing grain size has not been elucidated. We performed transcriptomic, proteomic, and phosphoproteomic analyses of young rice panicles in Samba (a wild-type cultivar with extra-small grain) and NIL-LGS1 (a nearly isogenic line of LGS1 with large grain in the Samba genetic background) at three developmental stages (4–6) to identify internal dynamic functional networks determining grain size that are mediated by LGS1. Differentially expressed proteins formed seven highly functionally correlated clusters. The concordant regulation of multiple functional clusters may be key features of the development of grain length in rice. In stage 5, 16 and 24 phosphorylated proteins were significantly up-regulated and down-regulated, and dynamic phosphorylation events may play accessory roles in determining rice grain size by participating in protein–protein interaction networks. Transcriptomic analysis in stage 5 showed that differentially expressed alternative splicing events and dynamic gene regulatory networks based on 39 transcription factors and their highly correlated target genes might contribute to rice grain development. Integrative multilevel omics analysis suggested that the regulatory network at the transcriptional and posttranscriptional levels could be directly manifested at the translational level, and this analysis also suggested a regulatory mechanism, regulation of protein translation levels, in the biological process that extends from transcript to protein to the development of grain. Functional analysis suggested that biological processes including MAPK signaling, calcium signaling, cell proliferation, cell wall, energy metabolism, hormone pathway, and ubiquitin-proteasome pathway might be involved in LGS1-mediated regulation of grain length. Thus, LGS1-mediated regulation of grain size is affected by dynamic transcriptional, posttranscriptional, translational and posttranslational changes.