Flavonoid differences between near-isogenic lines of yellow- and brown-seeded Brassica carinata were used to identify a genetic block in seed coat and seedling leaf pigment biosynthesis. Seed coat pigment in the brown-seeded line consisted of proanthocyanidins (condensed tannins), while anthocyanin was absent. Dihydroquercetin, dihydrokaempferol, quercetin and kaempferol accumulated only in the mature seed coat of the yellow-seeded line, indicating dihydroflavonol reductase (DFR) as an element of genetic control in pigment biosynthesis. DFR transcripts from the developing seed coat in the yellow-seeded line were absent or less abundant at 5-30 days after pollination compared to transcript levels in the brown-seeded line. Seedling leaves of the yellow-seeded line exhibited reduced expression of DFR and contained less anthocyanin compared to the respective tissues from plants of the brown-seeded line when grown at 25/20 degrees C (day/night). Cooler (18/15 degrees C) growing temperatures affected seedling leaf pigmentation, mature seed coat colouration and DFR expression in the yellow-seeded line. Comparable brown-seeded line tissues were unaffected by these temperature changes. These results are suggestive of a temperature-sensitive regulator of DFR in the yellow-seeded line of Brassica carinata which ultimately affects the formation of pigments in the seedling leaves and in the mature seed coats.