Transcriptome profile of Brassica napus seed development

We profiled the gene regulatory landscape of Brassica napus reproductive development using RNA sequencing. Comparative analysis of this nascent allotetraploid across the plant lifecycle revealed the contribution of each subgenome to plant reproduction. Global mRNA profiling across reproductive development revealed lower accumulation of C subgenome transcripts relative to the A subgenome. Subgenome-specific transcriptional networks identified distinct transcription factor families enriched in each of the A and C subgenome in early seed development. Analysis of a tissue specific transcriptome of early seed development revealed transcription factors predicted to be regulators encoded by the A subgenome are expressed primarily in the seed coat whereas regulators encoded by the C subgenome were expressed primarily in the embryo. Whole genome transcription factor networks identified BZIP11 as an essential regulator of early B. napus seed development. Knockdown of BZIP11 using RNA interference resulted in knockdown of predicted target genes, and a reproductive-lethal phenotype. Our data indicate that subgenome bias are characteristic features of the B. napus seed throughout its development, and that such bias might not be universal across the embryo, endosperm, and seed coat of the developing seed. We also find that examining transcriptional networks spanning both the A and C genomes of the whole B. napus seed can identify valuable targets for seed development research. We suggest that-omics level approaches to studying gene regulation in B. napus can benefit from both broad and high-resolution analyses. Overall design: RNA were isolated from ovules, and seeds 7 (GLOB), 10 (HEART), 28 (MG), and 35 (DS) days post fertilization. Three replicates were sequenced for each stage except DS, for which only 2 replicates were sequenced. Samples were sequenced 100bp SE reads on the Illumina HiSeq2500. Reads were trimmed with Trimmomatic 0.36 and aligned with HiSat2 to the DH12075 genome. Counts, normalization, and differential expression were called using Cuffquant and Cuffdiff.