Yellow seed is a desirable quality trait of the Brassica oilseed species.Yellow sarson is a valuable yellow seed material in the Brassica rapa.As such, it was used to create several artificial synthesis yellow-seeded Brassica napus because yellow seed colour dose not naturally occur in that species.Several seed coat color genes have been mapped in the Brassica species during the past years, but the molecular mechanism has not been elucidated.Here, a seed coat colour gene, which is located on A9 of the B.rapa, was identified by the map-based cloning.A blast analysis with the Arabidopsis genome showed that there are 22 Arabidopsis genes in this region from at4g09820 to at4g10620, and the functional complementation exhibited a phenotype reversion to the Arabidopsis tt8 mutant and yellow-seeded plant.These results suggest that the candidate gene was TRANSPARENT TESTA8 (TT8) homolog.BrTT8 not only affected the accumulation of pigment in the seed coat, but also regulated the development of its endothelium.Allele sequence analyses revealed a large insertion in yellow sarson with features of a new class of transposable elements, Helitron.In addition, no mRNA was detected in the yellow-seeded line.These data indicated that the natural transposon may have caused the loss of function of BrTT8.BrTT8 encodes a basic/helix-loop-helix (bHLH) protein that shares a high degree of similarily with other bHLH proteins in the Brassica.Further expression analyses also revealed the involvement of BrTT8 in controlling the late biosynthetic genes (LBGs) of the flavonoid pathway.