Capsanthin, the main carotenoid of red pepper fruits, is beneficial for human health. To breed pepper ( L.) with high capsanthin content by marker-assisted selection, we constructed a linkage map of doubled-haploid (DH) lines derived from a cross of two pure lines of ('S3586' × 'Kyoto-Manganji No. 2'). The map, designated as the SM-DH map, consisted of 15 linkage groups and the total map distance was 1403.8 cM. Mapping of quantitative trait loci (QTLs) for capsanthin content detected one QTL on linkage group (LG) 13 at 90 days after flowering (DAF) and one on LG 15 at 45 DAF; they were designated and , respectively. explained 17.0% of phenotypic variance and explained 16.1%. We grouped DH lines according to the genotypes of markers adjacent to and on both sides. The DH lines with the alleles of both QTLs derived from 'S3586' showed higher capsanthin content at 45 and 90 DAF than the other lines. This is the first identification of QTLs for capsanthin content in any plant species. The data obtained here will be useful in marker-assisted selection for pepper breeding for high capsanthin content.
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