Genome-wide effect of OSA1 on gene expression. Oryza sativa Japonica Group

To identify differentially expressed genes (DEGs) and associated pathways that may provide a molecular basis for the described OSA1-overexpression (ox) and osa1 mutant phenotypes, we analysed the comprehensive gene expression profiles in the leaves and roots of 4-week-old WT, OSA1-ox (OSA1#2), and osa1-2 mutant plants using RNA sequencing (RNA-seq) analysis. Among the DEGs, 1,373 and 1,124 transcripts were upregulated in the leaves and roots of the OSA1-ox line, and 347 and 3,295 transcripts were downregulated in the leaves and roots of the osa1-2 mutant, respectively. By contrast, 1,895 and 1,304 transcripts were downregulated in the leaves and roots of the OSA1-ox line, and 1,859 and 2,913 transcripts were upregulated in the leaves and roots of the osa1-2 mutant, respectively. Consistent with OSA1 expression levels, we detected 59 and 82 genes in the leaves and roots, respectively, that were upregulated in the OSA1-ox line but downregulated in the osa1-2 mutant. We then performed Gene Ontology (GO) term enrichment analysis of the DEGs upregulated in the OSA1-ox line and downregulated in the osa1-2 mutant to investigate the molecular mechanisms underlying OSA1-mediated biological processes. The results indicated that many biological processes were significantly enriched, including photosynthesis, NH4+ assimilation, glutamate biosynthesis, amino acid metabolism, carbohydrate transmembrane transport, various ion transport, and N utilisation.