Extended Data Fig. 3: Genetic mapping of flesh color intensity in watermelon.

a, Genome-wide ΔSNP-index profile from bulked-segregant analysis (BSA) of an F2 population derived from the cross ‘Ming 58’ (scarlet flesh) x ‘JX2’ (pink flesh). The black curve represents ΔSNP-index values, while red and blue envelopes mark the 95% and 99% confidence thresholds, respectively. b,c, Recombinant-based fine-mapping of the ClFCI1 locus in 141 F2 plants from the ‘Ming 58’ x ‘JX2’ cross (b), and 636 F2 plants from the ‘JLM’ x ‘Cream of Saskatchewan’ (CS) cross (c). Top, fruits of parental lines and F1 hybrids. Scale bars, 10 cm. Middle, QTL curves showing logarithm of odds (LOD) scores using KASP markers between 23 Mb and 26 Mb on chromosome 6. Bottom, graphical genotypes of key recombinant individuals. Pink, red, and scarlet segments denote homozygous ‘JX2’, heterozygous, and homozygous ‘Ming 58’ regions, respectively; pale yellow, orange, and yellow segments denote homozygous ‘CS’, heterozygous, and homozygous ‘JLM’ regions, respectively. d, Relative expression levels of candidate genes in the four parental lines (‘Ming 58’, ‘JX2’, ‘JLM’, and ‘CS’). Error bars indicate the standard deviation of three biological replicates. Different lowercase letters indicate significant differences according to Turkey’s multiple range test (P < 0.05).