Candidate genes associated with capsule dehiscence and endocarp thickness based on genome-wide association study analysis. a Phenotypic difference between dehiscent and indehiscent fruit. b Statistical analysis of the correlation between capsule dehiscence (CD) and endocarp thickness (ET). c Manhattan plots for CD and ET in the full population. The horizontal red line represents the significance threshold (−log10P > 6). The arrowhead indicates the peak signal containing the candidate pleiotropic genes. d, e Local Manhattan plot (top) and linkage disequilibrium heat map (bottom) for genes associated with both CD and ET. The candidate region lies between the red dashed lines. The arrowhead indicates the three nonsynonymous single-nucleotide polymorphisms (SNPs) located in the pleiotropic gene that is co-associated with CD and ET. f Expression of LOC8272207 during the development of the fruit rind in two varieties with different phenotypes, namely, S1015 (thicker endocarp and easier dehiscence) and S1396 (thinner endocarp and more difficult dehiscence), determined by quantitative reverse transcription PCR (*P < 0.05, **P < 0.01, two-tailed t test, three independent biological replicates). Bars donate standard deviation. g Analysis of pericarp composition. The cellulose and lignin contents in the fruit rinds of the S1015 and S1396 plants were measured. Ara, Gal, Glu, and Xyl are abbreviations for arabinose, galactose, glucose, and xylose, respectively. Bars donate standard deviation. h Lignin staining of longitudinal sections of castor fruits at different stages of development. The upper and lower five sections represent the five developmental stages of s1015 and s1396 fruits, respectively. The white arrowhead indicates the differences in endocarps. i The upper part shows the gene structure, and green and black rectangles indicate exons and introns, respectively; the lower box plots are for the two common nonsynonymous SNPs associated with two traits located in the candidate pleiotropic gene LOC8282207. The center line indicates the median; the box limits are the upper and lower quartiles, respectively; the whiskers extend to data <1.5 times the interquartile range; and the dots are outliers (**P < 0.005, ****P < 0.00005, ns indicates no significance, Kruskal–Wallis test; n indicates the number of accessions with the same genotype). Source data of d–g are provided as a Source Data file