Abstract:

Branch angle is a key trait in plant architecture that influences planting density and the efficiency of mechanical harvesting in rapeseed. A moderately compact plant structure promotes higher planting density and reduces harvesting losses. In this study, we used two rapeseed accessions with significant differences in branch angle and performed strand-specific RNA-seq on young branches at the bolting stage. The analysis identified 6305 differentially expressed genes (DEGs) between the two accessions, including homologs of branch angle-related genes such as FUL, SGR5, SGR6, SGR9, AXR1, ARG1, PIN1, and PIN5. Gene Ontology (GO) enrichment analysis highlighted pathways related to the synthesis and metabolism of tryptophan, auxin, and phosphatidylinositol, all of which are associated with gravity response. Based on the transcriptome data, we identified 4467 actively expressed long non-coding RNAs (lncRNAs) in the branches, including 3460 lincRNAs, 778 lncNATs, and 229 ilncRNAs. Of these, 50.3% contained transposon sequences, with Gypsy and Copia family LTR retrotransposons being the predominant insertion types. Moreover, 1713 lncRNAs were found to be differentially expressed between the two accessions. When comparing the locations of these lncRNAs with 50 known branch angle-associated loci, 37 differentially expressed lncRNAs were located within the confidence intervals of 26 associated loci. Expression correlation analysis, using a total of 103 branch transcriptome datasets (including those from this study and publicly available data), identified 17,782 lncRNA-gene targeting relationships, involving 1003 lncRNAs and 4592 genes. These target genes included homologs of known branch angle regulators such as LAZY1, SGR5, FUL1, and WRKY40. This study provides insights into the role of lncRNAs in regulating branch angles in rapeseed, laying a foundation for future research into the molecular mechanisms governing plant architecture.

Key words: Brassica napus L., plant architecture, branch angle, lncRNA, transcriptome