Fig. 5: Missing heritability, genetic correlations and genomic predictions of agronomic traits.

a, The heritability of 29 traits contributed by genomic SVs and SNPs. The contributions from SNP and SV were distinguished. b, The genetic correlations among 29 traits. FDR (Benjamini–Hochberg) corrected. c, The genotypes of the gene Vitvi011368 and SSC in each group. Top, schematic diagram of a deletion in the region including the gene Vitvi011368. Bottom, SSC2 values in each group with different genotypes (center line, median; box limits, first and third quartiles; whiskers, 1.5× interquartile range). The sample sizes, from left to right, are [6, 50, 54], [6, 40, 61] and [10, 42, 50]. Statistical significance was determined using two-sided Student’s t-tests. d, GWAS result and LD analysis of the BL2 locus, which contained a candidate gene, Vitvi018414. Differences in BL between populations and genotypes were estimated (center line, median; box limits, first and third quartiles; whiskers, 1.5× interquartile range). The sample sizes, from left to right, are [38, 70], [12, 96] and [103, 3]. Statistical significance was determined using two-sided Student’s t-tests. e, Linear regression analysis for phenotype prediction between SSC2 values and values predicted by LDpred2-auto. The confidence interval (CI) is shown by gray shading. The smoothed line represents a linear regression fit of the actual data, and the shading represents the CI. Sample size n = 29. f, Linear regression analysis for phenotype prediction between BL values and predicted values by lassoum2. The significance of the linear relationship between variables was evaluated through Pearson correlation coefficients. The smoothed line represents a linear regression fit of the actual data, and the shading represents the CI. Sample size n = 29. °Bx, degrees Brix; NS, nonsignificant.