Transcriptome analysis revealed sh2 gene mutation leads reduced zein protein accumulation in maize endosperm

Maize plants with a mutation of the shrunken2 ( sh2 ) gene are characterized by a collapsed kernel, a phenotype that is associated with reduced starch synthesis. Zeins are the main storage protein in maize and are encoded by a large gene family. In the sh2 mutant, zein accumulation is significantly lower than that of wild-type maize during the kernel-filling stage. To gain a better understanding of how the sh2 gene mutation affects zein accumulation, we compared the gene expression profiles of the sh2 mutant and wild-type maize by RNA sequencing analysis and quantitative real-time PCR. A total of 4457 differentially expressed genes were identified and the top enriched metabolic processes included genes involved in sugar metabolism, storage protein synthesis, and amino acid metabolism, as well as genes encoding transcription factor family and auxin-binding proteins. Our results indicate that mutation of the sh2 gene in maize endosperm affects the transcript and protein levels of zein genes, whereas little change was observed in the expression level of known zein-regulated genes, such as the endosperm-specific transcription factor Opaque2 ( O2 ), the prolamine-box binding factor, the O2 heterodimerizing proteins ( OHP1 and OHP2 ), and the MADS-box protein ZmMADS47 . We accordingly suspect that zein production might be affected by transcriptional and post-transcriptional regulation through changes in transcription factors and metabolic enzyme expression, rather than by regulation of the genes directly associated with zein biosynthesis. These findings indicate that carbon and nitrogen metabolic pathways are tightly coordinated to ensure appropriate development of the maize endosperm.