Fig. 3: Quantitative trait locus for anthracnose resistance.
From: Chromosome evolution and the genetic basis of agronomically important traits in greater yam
a Exemplars of the yam anthracnose disease (YAD) field assessment severity rating scale (scored 1–5) used at IITA in Ibadan, Nigeria. b Genome-wide QTL association scan for YAD resistance in the TDa1402 genetic population (n = 53 biologically independent samples) for the year 2017. A statistically significant association (corrected p = 1.69 × 10−4) was found on chromosome 5, at 23.3 Mb. Per-locus Wald statistic-based logistic regression significance values (gray line) were corrected for multiple testing (black line) via max(T) adjustment with 1 × 106 permutations. The minimum significance threshold (α = 0.05) is represented with a cyan horizontal line. c Effect plot for the peak locus on chromosome 5 at 23.3 Mb, the genotypes (X-axis) of which explain 48.2% of the observed phenotypic variance (i.e., narrow-sense heritability, h2), suggests that an increased dose of the ‘A’ allele is associated with lower severity of YAD. Centerline and whisker plots, and their corresponding statistics (X-axis), represent the mean ± 95% confidence intervals. d Plot showing the strength of linkage disequilibrium (LD) between the peak marker (cyan diamond) and other loci (black points) in chromosome 5. LD was calculated as Pearson’s correlation (r) between alleles. Source data are provided as a Source Data file.
