Genome-wide association study of durations in zones of an aviary for laying hens

Identifying how birds interact with their environment and selecting birds that are more suitable for specific housing systems could be beneficial for commercial egg production. Previous research has indicated heritability in behavior traits such as duration spent in different zones of an aviary barn, however, the underlying genetic mechanisms affecting aviary usage remain unknown. The objectives of this study were to further explore durations in different zones of an aviary through identifying potential candidate genes associated with these behaviors, to provide insight into the biological processes involved with laying hen behavior and to offer potential candidate genes for selection. Using tracking data and genotypes from 1098 white line pure line crosses (Hendrix Genetics), a genome wide association study (GWAS) was performed. From tracking data, durations spent in each of five designated zones of a semi-commercial aviary (wintergarden, litter, lower tier, nestbox tier, and upper tier) across days 4 to 290 in a production barn were investigated. Hens were genotyped with a proprietary 60K SNP array. After data filtering, 252,154 days of records were used, where phenotypes were recorded as average time spent in a specific zone over the days 4-290, 4-50, 51-100, 101-150, 151-200, and 251-250 of production. Analysis was carried out using a univariate mixed linear model with number of visits to the zone and pen number fitted as fixed effects, the top two principal components fitted as covariates, and the polygenic effects fitted as random. Of the duration in the five zones, 13 significant SNPs were identified across the different periods using chromosome-wise Bonferroni corrections (α = 0.05). The significant SNPs were mapped to within 100,000 base pairs of 64 genes, 22 of which were previously annotated, with several related to feeding behavior, movement, and immune function. The findings of this study suggest that behavioral traits within an aviary could be used to provide important insight into hens' health and performance within their housing system, but further validation is needed.