GEOapplication/xmlftp://ftp.ncbi.nlm.nih.gov/geo/series/GSE324nnn/GSE324982/primaryOK200TranscriptomicsOryza sativaExpression profiling by high throughput sequencinghttps://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE324982GEOGSEfalseTranscriptional Response of Rice Mesocotyl Elongation to Sowing Depth and Identification of Key Regulatory FactorsRice with longer mesocotyls is beneficial for improving its deep-sowing tolerance, which is important for seedling establishment. 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.2026/05/15GSE324982GSM9589868GSM9589864GSM9589865GSM9589866GSM9589867GSM9589860GSM9589861GSM9589862GSM958986327660324982Oryza sativa[42074500]