FIGURE 5.

QTL mapping results for seed coat color in the R500 × L58 AI‐RIL population. (a) The R/qtl program was used to identify a major QTL on chromosome A09 for seed coat color that accounts for ~37% of the phenotypic variation in the population. Underlying this QTL is the TT8 locus that has been shown to be responsible for seed coat color in another yellow‐seeded B. rapa (Li et al., 2012). A second major QTL for seed coat color that accounts for ~32% of the phenotypic variation in the population was identified on chromosome A03. Underlying this QTL is the candidate gene PAP2. Horizontal line indicates significance threshold. (b) Cartoon of the R500 and L58 TT8 alleles, with exons indicated by boxes (5′ and 3′ UTRs are filled with gray and coding sequences filled with black) and introns indicated by horizontal lines. Two single nucleotide polymorphisms resulting in amino acid substitutions are indicated, as is the site of insertion of a Helitron transposable element into the second intron of the R500 TT8 sequence. (c) Cartoon of the R500 and L58 PAP2(A03) alleles, with exons indicated by boxes (5′ and 3′ UTRs are filled with gray and coding sequences filled with black) and introns indicated by horizontal lines. SNPs resulting in amino acid substitutions are indicated, although it is not known whether any of these substitutions affect PAP2 activity.