Fig. 1: Identification of major loci for the pointed tip trait using GWAS and BSA.
From: Variation in the fruit development gene POINTED TIP regulates protuberance of tomato fruit tip
a Composition of the 311 tomato accessions. b Percentages of fruit with pointed and non-pointed tips in wild, CER, and BIG accessions. c Schematic diagram of pointed tip and non-pointed tip fruit. θ represents the angle of the distal end of the fruit. d Representative images of fruit with pointed and non-pointed tips. Bars, 2 cm. e Manhattan plot from GWAS on the morphology of the distal end of the fruit. The blue and red dashed lines indicate the Bonferroni-adjusted significant and suggestive thresholds (P = 2.41 × 10−7 and 1.20 × 10−8). The lead SNP (ch05_64012700, P = 7.57 × 10−40) in the PT gene is indicated with a red arrow. f Quantile-quantile plot of expected versus observed P values for GWAS. g Detail plot surrounding the lead SNP (purple rhombus) on chromosome 5. The color of each dot corresponds to the r2 value indicated on the color scale. h Representation of the pairwise r2 values among all polymorphic sites in the genomic region (63.48–64.03 Mb) from g. The haploblocks are represented by inverted triangles. The darkness of the color of each box indicates an r2 value indicated in the color scale. The red star indicates the lead SNP containing haploblock. i Gene structure in the haploblock containing the lead SNP. Blue boxes, black lines, and arrows represent exons, introns, and gene orientation, respectively. The lead SNP is indicated with red under the blue box. j Fruit phenotypes of TS-9, LA4053, and their F1 progeny. k Cells from the distal end of the ripening fruit from TS-9 and LA4053. Three independent experiments were performed. l Distribution of the ΔSNP-index between the fruit with pointed and non-pointed tips. The statistical confidence interval under the null hypothesis of no QTLs is indicated with green (P < 0.05) and blue (P < 0.01) lines. m Details on loci that produce fruit with pointed tips on chromosome 5. Significance windows for the ΔSNP-index above the confidence intervals are indicated with red points and blue shading. Source data underlying Fig. 1b are provided as a Source Data file.
