Capturing Clues to Complex Trait Control: Variation Among Flowering Genes in Brassica napus

Flowering, the transition from the vegetative to the generative phase, is a decisive time point in a plant’s lifecycle. Flowering is controlled by a complex network of transcription factors, photoreceptors, enzymes and miRNAs. In recent years, several studies gave rise to the hypothesis that this network is also strongly involved in the regulation of other important lifecycle processes like germination, seed development and even heterosis for developmental and yield-related traits. A confirmation of this link would make these loci even more interesting candidates for crop breeding, beyond their present implementation for adaptation to temperature and day-length-dependent factors.

To investigate the potential role of flowering regulators as global controllers of agronomically important trait variation, we set up a workflow for targeted deep sequencing in the allopolyploid crop species Brassica napus. Initially, four genetically and phenologically diverse genotypes including a winter oilseed rape, a winter fodder rape, a spring oilseed rape (all B. napus ssp. napus) and a swede (B. napus ssp. napobrassica) were successfully enriched for Illumina sequencing using a SureSelect sequence capture protocol (Agilent). The oligonucleotide sequences for targeted enrichment were obtained from the diploid progenitors of B. napus, B. rapa and B. oleracea. Sequencing of the initial panel revealed a broad range of genetic variation in the targeted genes, including SNPs, InDels, copy number variation and presence-absence variation.  Based on these results we optimized the oligonucleotide pool for sequence capture in 300 genotypes of a B. napus diversity set and 200 doubled-haploid lines of a genetic mapping population, segregating for diverse agronomic and flowering-related traits. This will enable associations of sequence variants to extensive trait data from growth chamber, greenhouse and field studies.