Fig. 6

Structural variation in BrPIN3.3 is associated with B. rapa heading morphotype domestication. a The distribution of haplotypes in the BrPIN3.3 gene region in 524 genomes. The numerical suffix denotes a gene’s location on the subgenome LF, MF1, or MF2. Homozygous sites of AA, CC, GG, and TT are filled using different colors as described in the figure, while missing loci (NN) and heterozygous loci (Hetero) are not filled with color. b The distribution of one of the BrPIN3.3 genotypes in 524 accessions. Accessions with a 279 bp deletion in BrPIN3.3 are marked using blue stars. c Micro-synteny analysis between the two genotypes of BrPIN3.3. RNA-seq reads of different accessions were collected and mapped onto the two genotypes. d The genotype of the structural variation in the BrPIN3.3 gene region in 524 accessions. CC indicates that the genotype in the corresponding accession was consistent with the reference genome, and GG indicates that the genotype in the accession was different from the reference genome. e The expression level in TPM of BrPIN3.3 in 44 heading and 42 non-heading accessions. CC (Chinese cabbage) and others represent heading and non-heading types, respectively. f XP-EHH values are normalized as z-scores for B. rapa on A07. A 200-kb sliding window with an increment of 5 kb was used to calculate these normalized XP-EHH values. Each point represents a value in a 200-kb window, and the horizontal dashed line presents the empirical threshold of α = 0.01 (z = 2.33). The arrow indicates the location of the BrPIN3.3 gene