Fig. 3: Analysis of a major QTL for phylloxera resistance.

a Quantitative Trait Locus (QTL) scans, controlling for genomic background via the leave-one-chromosome-out method for % phylloxera gall incidence. This experiment was conducted once at a single time point. Since the phenotype is non-normal, we determine the significance of QTL peaks via 10,000 permutations. The full genome and a close-up visualization of chromosome 16 are presented along the physical position (Mb: megabases) of the ‘Oaxaca’ genome assembly. The 95% confidence interval surrounding the QTL peak is shaded. b As evidenced by very high LOD scores for a 140-genotype population, there is an extremely strong haplotype structure at the peak QTL (between the vertical white bars), where all but two individuals that inherited the ‘Mahan’ haplotype from ‘Lakota’ have no evidence of phylloxera galls (gray horizontal bars in the plot to the right), while all individuals with >50% phylloxera gall incidence retained the ‘Major’ haplotype at the QTL peak region (brown horizontal bars indicate % incidence). c To define candidate genes, we queried the pan-genome within the physical bounds (base pairs, bp) of the QTL interval. All unique genes in this interval were projected onto the alternative haplotype; those contigs where >50% of the projected genes were derived from the candidate interval were extracted and aligned to the primary haplotype. Orthologous genes between the two haplotypes are connected by a solid line, the thickness of which is scaled by % identity between the two protein sequences. Presence–absence variant (PAV) genes without a projected ortholog are represented by open circles. Homologs of the genes in the interval were queried in model systems and qualified by whether annotations indicated a disease-related function or a leucine-rich repeat (LRR) motif. Finally, the haplotypes were coded by whether they were derived from the ‘Mahan’ or ‘Major’ parents of ‘Lakota’. Source data underlying c are provided as a Source Data file. Raw data associated with a, b can be found in Supplementary Data 5.