SummaryAn updated platform was developed to underpin association genetics studies in the polyploid crop species Brassica napus (oilseed rape). Based on 1.92 × 1012 bases of leaf mRNAseq data, functional genotypes, comprising 355 536 single‐nucleotide polymorphism markers and transcript abundance were scored across a genetic diversity panel of 383 accessions using a transcriptome reference comprising 116 098 ordered coding DNA sequence (CDS) gene models. The use of the platform for Associative Transcriptomics was first tested by analysing the genetic architecture of variation in seed erucic acid content, as high‐erucic rapeseed oil is highly valued for a variety of applications in industry. Known loci were identified, along with a previously undetected minor‐effect locus. The platform was then used to analyse variation for the relative proportions of tocopherol (vitamin E) forms in seeds, and the validity of the most significant markers was assessed using a take‐one‐out approach. Furthermore, the analysis implicated expression variation of the gene Bo2g050970.1, an orthologue of VTE4 (which encodes a γ‐tocopherol methyl transferase converting γ‐tocopherol into α‐tocopherol) associated with the observed trait variation. The establishment of the first full‐scale Associative Transcriptomics platform for B. napus enables rapid progress to be made towards an understanding of the genetic architecture of trait variation in this important species, and provides an exemplar for other crops.

Intake of flavanols, a subgroup of dietary polyphenols present in many fruits and vegetables, may be associated with health benefits, particularly with reducing the risk of coronary diseases. Cocoa and chocolate products are rich in flavanol monomers, oligomers, and polymers (procyanidins). This study used normal phase HPLC to detect, identify, and quantify epicatechin, catechin, total monomers, procyanidin oligomers and polymers in 14 commercially available chocolate bars. In addition, methylxanthines (theobromine and caffeine) were also quantified. Nonfat cocoa solids (NFCS) were determined both gravimetrically and by calculation from theobromine contents. The flavanol levels of 12 commonly consumed brands of dark chocolate have been quantified and correlated with % theobromine and % NFCS. Epicatechin comprised the largest fraction of total chocolate flavonoids, with the remainder being catechin and procyanidins. Calculated NFCS did not reflect epicatechin (R(2) = 0.41) or total flavanol contents (R(2) = 0.49). Epicatechin (R(2) = 0.96) was a reliable marker of total flavanols, catechin (R(2) = 0.67) to a lesser extent. All dark chocolate tested contained higher levels of total flavanols (93.5-651.1 mg of epicatechin equiv/100 g of product) than a milk or a white "chocolate" (40.6 and 0.0 mg of epicatechin equiv/100 g, respectively). The amount and integrity of procyanidins often suffer in the manufacturing of chocolate, chiefly due to oxidation and alkalinization. In this study, the labeled cocoa content of the chocolate did not always reflect analyzed levels of flavonoids. Increasingly, high % NFCS is being used commercially to reflect chocolate quality. If the flavanol content of chocolate is accepted to be a key determinant of health benefits, then continued monitoring of flavanol levels in commercially available chocolate products may be essential for consumer assurance.

The diverse biological activities of glucosinolate (GSL) hydrolysis products play significant biological and economical roles in the defense system and nutritional qualities of Brassica napus (oilseed rape). Yet, genomic-based study of the B. napus GSL regulatory mechanisms are scarce due to the complexity of working with polyploid species. To address these challenges, we used transcriptome-based GWAS approach, Associative Transcriptomics (AT), across a diversity panel of 288 B. napus genotypes to uncover the underlying genetic basis controlling quantitative variation of GSLs in B. napus vegetative tissues. Single nucleotide polymorphism (SNP) markers and gene expression markers (GEMs) associations identify orthologues of MYB28/HAG1 (AT5G61420), specifically the copies on chromosome A9 and C2, to be the key regulators of aliphatic GSL variation in leaves. We show that the positive correlation observed between aliphatic GSLs in seed and leaf is due to the amount synthesized, as controlled by Bna.HAG1.A9 and Bna.HAG1.C2, rather than by variation in the transport processes. In addition, AT and differential expression analysis in root tissues implicate an orthologue of MYB29/HAG3 (AT5G07690), Bna.HAG3.A3, as controlling root aromatic GSL variation. Based on the root expression data we also propose Bna.MAM3.A3 to have a role in controlling phenylalanine chain elongation for aromatic GSL biosynthesis. This work uncovers a regulator of homophenylalanine-derived aromatic GSLs and implicates the shared biosynthetic pathways between aliphatic and aromatic GSLs.

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