First, we examined SNPs obtained from the National Human Genome Research Institute (NHGRI) GWAS catalogue and included 14 traits, including traits associated with β-cell dysfunction such as diabetes, changed insulin and glucose levels.
A series of regression analyses including traits and rates their interactions with environmental and ontogenetic stages supported the relationships between traits and vital rates expected from the expectations from tree physiology.
All the 39 target genes/QTL were associated with two or more measured traits including traits not previously reported.
The other age-related trait category includes traits conventionally associated with aging, such as telomere length and inflammation, as well as related age-associated diseases including rheumatoid arthritis and age-related macular degeneration.
They pose, however, some limitations derived from (i) potential trait multicollinearity, (ii) biases introduced by failure to include traits that covary with fitness, (iii) deviations of response variables from multivariate normality assumed for hypothesis testing, and (iv) failure to consider environmental factors that may induce spurious correlations [ 9].
This included traits from the published literature, along with fatty acid quality QTLs, published for the first time here.
The results show the importance of including index traits with high genetic value that are independent of other traits, and they could be useful in breeding programs simultaneously considering production and reproduction traits with nearly zero correlations between them.
Specifically, 83 CNVRs partially or completely overlap with 143 QTLs, and these QTLs are involved in many important traits in chickens, including growth traits, carcass traits, meat quality traits, reproductive traits, and disease-related traits.
To ensure that we did not downwardly bias the detection of pleiotropy (Hill and Zhang 2012a, b), we included all traits with nonzero estimates of variance (3385) in our analyses of mutational covariance, irrespective of statistical confidence in the estimate of mutational variance for these individual traits.
