DNA was isolated from whole red blood cells from various lines and crosses of broiler chickens. DNA was genotyped using Axiom genome-wide chicken array and cel files were analyzed using Axiom Analysis Suite Software (version 3.0.1) with Gallus gallus 5.0 using the software's Best Practices for agricultural animals. The results were exported (Genotyping_Data-3-21-2018.vcf) for all genotype calls and text file of all SNPs with >= 97% call rate rate was also produced for filtering the VCF file (ALL_SNPSs_with_Call_Rate_97_Plus_3-21-2018).
Overall design
Commercial broiler chickens (all males) from a cross (BCD) between three commercial broiler pure lines were sampled at 29 days of age from the field in the Delmarva region of the United States and transferred into individual cages for feed efficiency measurement. Line B and C chickens were all males from a high breast meat yield purebred line of broiler breeder chickens raised on the floor, in pens of 300, by Heritage Breeders in the Delmarva region of the United States.
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