Computational protocol: QTL mapping of egg albumen quality in egg layers

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Protocol publication

[…] Marker maps were constructed with CRI-MAP [] using procedures TWOPOINT, BUILD, FLIPS and CHROMPIC. QTL analyses were performed using the least squares method via the web-based GridQTL software []. Significance thresholds for QTL analysis were determined empirically by permutation, and confidence intervals were based on bootstrapping. The length of the chromosomes was taken into account when defining the significance thresholds. More information on the models used and how the significance levels and confidence intervals were derived is available in []. Fine-mapping in the F2 population used the same software for the chromosome 7 data, whereas a custom-made regression program [] was applied to the chromosome Z data. The significance levels for the linkage analysis were obtained using a permutation procedure as explained in [].For the commercial Hy-Line, microsatellite marker associations were tested with a non-parametric Kruskal–Wallis test, because the genotyping data comprised a single generation and linkage analysis could not be applied. Let μij be the trait mean for genotype j in marker i, and i = 1,…,3. The total amount of different genotype groups per marker is Ni and depends on the marker, so that j = 1,…,Ni. The null hypothesis to be tested is then H0i: μi1 = μi2 =…= μiNi versus: H1i: μik ≠ μil for at least one pair of genotypes k ≠ l and k, l ≤ Ni.Chromosome Z was analyzed with PLINK []. Data were checked for genotyping quality and Hardy-Weinberg equilibrium (none of the markers were excluded) before analysis. Basic association testing for quantitative traits and adjustment for multiple comparisons were used. […]

Pipeline specifications

Software tools GridQTL, PLINK
Applications WGS analysis, GWAS
Organisms Gallus gallus