Transcriptional Response of Rice Mesocotyl Elongation to Sowing Depth and Identification of Key Regulatory Factors

Here, we performed transcriptome analysis of the elongating mesocotyl in response to three different sowing depths (3 cm, 5 cm, 7 cm) using japonica rice cultivar Zhengdao 209 to identify the pivotal genes regulating rice mesocotyl elongation. A total of 60 common differentially expressed genes (DEGs) were detected among three comparison groups.

GO and KEGG enrichment analysis revealed that these DEGs were primarily involved in phenylpropanoid biosynthesis, MAPK signaling pathway-plant, and diterpenoid biosynthesis. Weighted gene co-expression network analysis (WGCNA) and hierarchical clustering analysis (HCA) further confirmed the key pathways associated with mesocotyl elongation. This study identifies candidate genes governing rice mesocotyl length and provides novel insights into the molecular regulatory mechanisms underlying mesocotyl elongation in rice.