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

Abstract

Abstract 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+)‐ ATP ase gene orthologous to the transparent testa gene AHA 10 . 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 . CCR 1 was localized in silico near the peak of a corresponding seed fibre QTL , whereas in this case Bna . CAD 2/ CAD 3 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.