QTL analysis for the identification of candidate genes controlling phenolic compound accumulation in broccoli (Brassica oleracea L. var. italica)

Quantitative trait loci (QTL) analysis of phenolic compound accumulation was performed in a broccoli mapping population (Brassica oleracea) saturated with single nucleotide polymorphism markers from an Illumina 60K array designed for rapeseed (Brassica napus). In 2 years of analysis in North Carolina and 1 year in Illinois, variation in total phenolic content and antioxidant capacity was associated with 60 QTL. Twenty-three of these loci were identified in at least two analyses (three phenolic/antioxidant assays times 4 years (2009, 2010, 2014, and the mean of the 3 years) making a total of 12 trait-year assays); the two most stable QTL (no. 7 and no. 52) were identified in six and five analyses, respectively. Genome-specific SNP markers were used to identify a priori candidate genes within the QTL marker intervals. Genes involved in the early stages of phenylpropanoid biosynthesis and MYB transcription factors were most heavily represented among the putative candidate genes. The results demonstrate the complexity of the regulatory network involved in phenolic compound accumulation, but highlight potential targets for the development of Brassica vegetables with enhanced phenolic compound profiles.