A systematic dissection reveals the key genes and mechanisms underlying the natural variation of silique length in rapeseed (Brassica napus L.)

Transcriptomic analysis of two pools of silique walls with extreme length identified a total of 3248 differentially expressed genes (DEGs), which were enriched in several pathways (such as cell wall, cell division, and hormone metabolism etc.) that are associated with cell proliferation/expansion and silique development. The silique walls at 15-days after flowering were sampled from the 12 long- and 11 short-silique accessions and then equally mixed to form two pools, respectively. The RNA extraction, purification, and quantification were performed according to the Plant Mini RNeasy Kit (Qiagen, Shanghai, China). The RNA-seq libraries were prepared using the Illumina TrueSeq RNA Sample Preparation Kit (Illunima Inc., San Diego, USA). The final cDNA libraries were sequenced using the Illumina Hiseq platform, which generated the raw reads. Then, the low-quality, low-complexity, and repetitive raw reads were filtered, and the clean reads that passed quality control were used for subsequent analysis. All reads of each library were mapped to the reference genome of Darmor, and the uniquely mapped reads were selected for transcript quantification. In this study, the false discovery rate (FDR) ≤0.05 and the p-value ≤0.005 were used as a threshold to characterize the differentially expressed genes (DEGs).