Whole genomic prediction of growth and carcass traits in a Chinese quality chicken population.

By incorporating high-density markers into breeding value prediction models, the whole genomic prediction (WGP) method can effectively accelerate genetic improvement in livestock breeding. However, the performance of WGP varies across species and populations and is affected by the underlying genetic architecture. In particular, very little is known about the performance of WGP for many chicken breeds. Here we estimate the genetic parameters and evaluate the performance of WGP for 18 growth and carcass traits in a Chinese quality chicken population. In total, 435 chickens were systematically phenotyped and genotyped using a 600K genotyping array. Two variance component estimation scenarios, 3 breeding value prediction methods, and 2 validation procedures were compared. The results showed that the heritability of these 18 traits was medium to high (ranging from 0.28 to 0.60) and that deviations existed between the heritability estimated from pedigrees and markers. Compared with conventional breeding methods, WGP could potentially increase the selection accuracy by 20% or more depending on the prediction model used, the trait under consideration, and the genetic connectedness between the training and validation individuals. Our results showed the potential of implementing genomic selection in small breeding herds.