Fig. 2

Chromosomal distribution of DNA sequence variant-trait associations for fresh-market tomato yields. The positions of significant common genome-wide association (GWA) signals (derived from both the filtered SNP set and regularization SNP set) are indicated by the symbols of corresponding traits (Y, the total yield; XY, the yield of extra-large-sized fruit; SY, the yield of any fruit smaller than medium size; RY, the yield of red-colored fruit regardless of size). Mapping IDs are indicated immediately below to the right of the symbol of GWA. Black and blue rectangles on chromosomes 2 (Ch2) and 12 (Ch12) highlight the significant common association signals that fall within the intervals of linkage mapping in this study. Numbers with dashed horizontal lines indicate estimated genetic positions (cM) of association signals based on the fresh-market tomato genetic map. The approximate intervals of previously mapped fruit size (weight) loci with a prefix FW are depicted using gray vertical lines. For each chromosome, SNP density (the range of the Y-axis 0 to 400 SNPs per 10-kbp) and nucleotide diversity (π) (the range of the Y-axis 0 to 0.08) plots are provided. A detailed dataset of this figure with the Manhattan plots of SNPs associated with traits and the quantile-quantile plots for association mapping can be found in Additional files 5, 6, and 7