Fig. 3: An overview of pSVs.
a, Histogram of the number of pSV r2 ranks (0–300) that are above the SNP-based median r2 value for common pSVs. b, Top, Manhattan plot of SNP (with ~11.5 million SNPs obtained from DNA deep resequencing (~20×) of 521 diverse lines) and pSV genome-wide association studies for oil concentration. The red line represents the candidate gene encoding the ENR. Bottom left, the expression of ENR is positively correlated with oil concentration. Bottom right, divergence of oil concentrations between different alleles of the lead pSV. n = 86 for B73 allele; n = 7 for SK allele. c, A 36,320-bp insertion in SK contains three expressed genes not present at the syntenic ___location in B73. d, A 29-bp SV in the 5′ untranslated region (UTR) was a cis eQTL of Zm00015a006294, and could be the causal variant reducing gene expression. The break points of this SV are shown. TSS, transcription start site. n = 75 for B73 allele; n = 129 for SK allele. In b and d, the lower and upper box edges correspond to the first and third quartiles (the twenty-fifth and seventy-fifth percentiles); the horizontal line indicates the median value; and the lower and upper whiskers correspond to the smallest value at most 1.5× IQR and the largest value no further than 1.5× IQR (where IQR is the inter-quartile range, or distance between the first and third quartiles).
