Transcriptome profiling of transgenic rice seeds lacking seed storage proteins (globulin, prolamin, and glutelin) by RNA-Seq analysis

Major seed storage proteins in rice ( Oryza sativa ) are composed of glutelin, prolamin, and globulin. We previously generated four SSP -RNAi lines with reduced levels of globulin ( Glb -RNAi); prolamin ( Pro -RNAi); prolamin and globulin ( PGb -RNAi); and glutelin, prolamin, and globulin ( GPGb -RNAi). To identify the genes and molecular events associated with SSP deletion, we profiled the levels of seed transcripts in these four SSP -RNAi lines during seed development. We identified 2951 differentially expressed genes (DEGs) with a fold change of ≥ 2 or ≤ − 2 relative to the wild type (cv. Ilmi). Gene ontology (GO) analysis showed that most DEGs were associated with the functional categories “regulation of transcription, DNA-dependent”, “regulation of RNA metabolic process”, and “integral to membrane”. Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis demonstrated that the DEGs also functioned in “metabolism”, “folding, sorting and degradation”, and “transport and catabolism”. We identified 105 transcription factor (TF) genes and belonging to 25 TF gene families in our list of DEGs. Specifically, which are expected to affect expression of SSP -related genes, the expressions of TF genes, such as zinc finger protein, basic helix–loop–helix protein 008, and MYB transcription factor 55/61L, were decreased, and the expression levels of C2H2 -type zinc finger protein, basic helix–loop–helix protein 073, and zinc finger protein were increased by RNA-Seq data and real-time quantitative PCR. Furthermore, it was confirmed in four SSP -RNAi lines that the expression levels of lipid transfer proteins were reduced. These results provide important information about the effect of SSPs -related genes on seed development.