Transcriptome analysis reveals potential genes associated with plant height in rice

Plant height (PH) is a complex trait regulated by the environment and multiple genes. PH directly affects crop yield, harvest index, and lodging resistance. From plant dwarf mutants, many genes related to PH have been identified and described. Nonetheless, the molecular mechanism of height regulation in high-culm rice mutants has not been well studied. By using transcriptome and weighted gene co-expression network analysis (WGCNA), we identified the differentially expressed genes (DEGs) between high-culm rice mutants (MUT) and wild-type (WT) and explored the key pathways and potential candidate genes involved in PH regulation. Transcriptome analysis identified a total of 2,184 DEGs, of which 1,317 were identified at the jointing stage and 1,512 were identified at the heading stage. Kyoto Encyclopedia of Genes and Genomes enrichment showed that the enrichment pathways were mainly involved in plant hormone signal transduction, ABC transportation, and steroid hormone biosynthesis. Among these metabolic pathways, LOC_Os05g43910 and LOC_Os01g35030 were auxin (IAA)-related genes, up-regulated in MUT and LOC_Os02g08500 (LEPTO1), LOC_Os11g04720, and LOC_Os12g04500 were cytokinin (CK)-related genes, downregulated in MUT. The WGCNA identified four modules (light cyan, dark grey, grey, and pale turquoise) closely related to PH, and seven key genes were screened from these modules, of which two were up-regulated cell wallrelated genes (LOC_Os01g26174 (OsWAK5), LOC_Os06g05050) in MUT, and one gibberellic acid (GA) gene (LOC_Os06g37364, OsKO2) was also up-regulated. These genes might be closely related to PH regulation. These findings help us better understand the transcriptional regulation of rice plant growth and development and provide a theoretical basis for mapping and cloning the PH regulatory genes.