For these populations with multiple genes contributing large effects to a trait, a strategy of low depth re-sequencing of F 2 individuals followed by QTL-Seq analysis with the free combination of sample groups is proposed. BrMYBL2.1 is a negative regulator of anthocyanin biosynthesis, while BrEG元.2-previously located by linkage mapping-is a positive regulator. A ~100-bp insertion was found in the third exon of gene BrMYBL2.1 in Zicaitai. Furthermore, the draft genomes of the two parents (Zicaitai and Caixin) were assembled and utilized to search for mutations in candidate genes. This was further supported by the data simulation of an in silico F 2 population that QTL-Seq and linkage analysis can locate different major loci. This indicates that there are two major genetic factors that plays different roles in regulating anthocyanin enrichment in Zicaitai. The results showed that the QTL-Seq and linkage analysis located different major loci. Here, quantitative trait locus (QTL)-Seq was performed with two sample groups from the F 2 population: one exhibiting an intense purple phenotype and the other showed a completely green phenotype. parachinensis) and it shows clear segregation of the purple phenotype (i.e., variation in anthocyanin enrichment). We constructed an F 2 population of Zicaitai and “Caixin” ( Brassica rapa ssp.
purpurea “Zicaitai” is rich in anthocyanins. Anthocyanins have strong antioxidant activity and are believed to be healthy for human beings.