Dissection of a major QTL for seed colour and fibre content in Brassica napus reveals colocalization with candidate genes for phenylpropanoid biosynthesis and flavonoid deposition

A major quantitative trait locus (QTL) influencing seed fibre and colour in Brassica napus was dissected by marker saturation in a doubled haploid (DH) population from the black-seeded oilseed rape line 'Express 617' crossed with a yellow-seeded B. napus line, '1012-98'. The marker at the peak of a sub-QTL with a strong effect on both seed colour and acid detergent lignin content lay only 4 kb away from a Brassica (H+)-ATPase gene orthologous to the transparent testa gene AHA10. Near the peak of a second sub-QTL, we mapped a copy of the key phenylpropanoid biosynthesis gene cinnamyl alcohol dehydrogenase, while another key phenylpropanoid biosynthesis gene, cinnamoyl co-a reductase 1, was found nearby. In a cross between 'Express 617' and another dark-seeded parent, 'V8', Bna.CCR1 was localized in silico near the peak of a corresponding seed fibre QTL, whereas in this case Bna. CAD2/CAD3 lay nearby. Re-sequencing of the two phenylpropanoid genes via next-generation amplicon sequencing revealed intragenic rearrangements and functionally relevant allelic variation in the three parents.