Computational protocol: A Sexual Ornament in Chickens Is Affected by Pleiotropic Alleles at HAO1 and BMP2, Selected during Domestication

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Protocol publication

[…] DNA preparation for both crosses was performed by Agowa GmbH (Berlin, Germany), using standard salt extraction. A total number of 347 SNPs and 20 microsatellite markers were used for the OS cross, with the marker map generated using Crimap , covering ∼2535 cM, with an average marker spacing of ∼7.5 cM. For the F8L13 cross, 652 SNP markers were used to generate a map of length ∼8760 cM, with an average marker spacing of ∼15 cM. QTL analysis was performed using QTL Express (http://qtlcap.ed.ac.uk), qxpak v2.16 and R/Qtl for the standard interval mapping and epistatic analyses. Interval mapping was performed using additive and additive+dominance models. Batch and sex were always included in the model as a fixed effect, whilst bodyweight at slaughter was included as a covariate. To account for a particular QTL varying between the sexes, a sex-interaction analysis was also performed. […]

Pipeline specifications

Software tools QxPak, R/qtl
Applications WGS analysis, GWAS
Organisms Gallus gallus