RNA-seq profiling the transcriptome of secondary seed dormancy in canola (Brassica napus L.)

Secondary seed dormancy (SSD) is responsible for volunteer plants in canola fields, which causes a series of problems in canola production and serves as an important trait for the environmental safety assessment of transgenic canola. A canola cultivar with strong SSD was used to establish insight into seed transcriptomes in its secondarily dormant seeds and control seeds without dormancy by RNA-seq analysis, aiming to determine the molecular ecological characterizations of SSD. A dataset (more than 4 Gb) of valid sequences was obtained from each sample, which was combined to carry out the de novo assembling. The assembled sequences consisted of 314,261 fragments with length > 100 bp, including 29,740 long transcripts of length a parts per thousand yen 500 bp. Functional annotation indicated that 1,641 long transcripts could be categorized into 24 cluster of orthologous groups of proteins (COGs) and 16,515 transcripts were linked to 2,648 gene ontology (GO) terms. There were 452 long transcripts with significantly different expression identified by a threshold of > 2-fold expression change (P < 0.001) between samples, among which 343 transcripts were unambiguously homologous to Arabidopsis genes. The plant hormones abscisic acid and gibberellins were known as the pivotal regulators of seed dormancy and germination. Although genes responsible for either biosynthesis or signaling of each hormone could be widely verified from the SSD transcriptome, theirs expression evidences failed to correlate with the induction of SSD. Based on the enriched terms of gene ontology and KEGG orthology, as well as the expression models of candidate genes of SSD, we proposed that fatty acid metabolism might implicate in SSD in canola. The information reported here may play a significant role in further understanding of environmental safety assessment of SSD in transgenic canola.