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.

水稻（水稻）的主要种子贮藏蛋白由谷蛋白，谷醇溶蛋白和球蛋白组成。我们先前产生了四种球蛋白水平降低的SSP -RNAi系（Glb -RNAi）。谷醇溶蛋白（Pro -RNAi）; 谷醇溶蛋白和球蛋白（PGb -RNAi）; 以及谷蛋白，谷醇溶蛋白和球蛋白（GPGb -RNAi）。为了鉴定与SSP缺失相关的基因和分子事件，我们在这四个SSP中分析了种子转录本的水平-种子发育期间的RNAi系。我们鉴定出2951个差异表达基因（DEG），其相对于野生型（cv。Ilmi）的倍数变化≥2或≤− 2。基因本体论（GO）分析表明，大多数DEG与功能类别“转录调控，DNA依赖性”，“ RNA代谢过程调控”和“整合至膜”相关。京都市基因与基因组百科全书（KEGG）分析表明，DEG还具有“新陈代谢”，“折叠，分类和降解”以及“运输和分解代谢”的功能。我们确定了105个转录因子（TF）基因，并且在我们的DEG列表中属于25个TF基因家族。具体来说，预期会影响SSP的表达相关基因，锌指蛋白，碱性螺旋-环-螺旋蛋白008和MYB转录因子55 / 61L等TF基因的表达降低，C2H2型锌指蛋白，碱性螺旋的表达水平降低RNA-Seq数据和实时定量PCR可增加-loop-helix蛋白073和锌指蛋白。此外，在四个SSP- RNAi系中证实脂质转移蛋白的表达水平降低。这些结果提供了有关SSPs相关基因对种子发育的影响的重要信息。