Assessment of the genomic prediction accuracy for feed efficiency traits in meat-type chickens

• Published in: PloS one Vol. 12; no. 3; p. e0173620
• Main Authors: Liu, Tianfei, Luo, Chenglong, Wang, Jie, Ma, Jie, Shu, Dingming, Lund, Mogens Sandø, Su, Guosheng, Qu, Hao
• Format: Journal Article
• Language: English
• Published: United States Public Library of Science 09.03.2017; Public Library of Science (PLoS)
• Subjects: Analysis; Animal Feed; Animal husbandry; Animals; Biology and Life Sciences; Body Weight - genetics; Bone morphogenetic proteins; Breast muscle; Breeding; Cattle; Chickens; Chickens - genetics; Chickens - growth & development; Control; Conversion ratio; Correlation; Eating - genetics; Efficiency; Feed conversion; Feed efficiency; Feed utilization efficiency; Female; Food and nutrition; Genomics - methods; Greenhouse effect; Greenhouse gases; Heritability; Livestock breeding; Mathematical models; Meat; Meat - analysis; Medicine and Health Sciences; Model accuracy; Models, Genetic; Models, Statistical; Muscles; Pedigree; Physical growth; Physical Sciences; Polymorphism; Poultry; Poultry industry; Prediction models; Prices and rates; Research and Analysis Methods; Sampling; Single-nucleotide polymorphism; Weaning
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0173620

Feed represents the major cost of chicken production. Selection for improving feed utilization is a feasible way to reduce feed cost and greenhouse gas emissions. The objectives of this study were to investigate the efficiency of genomic prediction for feed conversion ratio (FCR), residual feed intake (RFI), average daily gain (ADG) and average daily feed intake (ADFI) and to assess the impact of selection for feed efficiency traits FCR and RFI on eviscerating percentage (EP), breast muscle percentage (BMP) and leg muscle percentage (LMP) in meat-type chickens. Genomic prediction was assessed using a 4-fold cross-validation for two validation scenarios. The first scenario was a random family sampling validation (CVF), and the second scenario was a random individual sampling validation (CVR). Variance components were estimated based on the genomic relationship built with single nucleotide polymorphism markers. Genomic estimated breeding values (GEBV) were predicted using a genomic best linear unbiased prediction model. The accuracies of GEBV were evaluated in two ways: the correlation between GEBV and corrected phenotypic value divided by the square root of heritability, i.e., the correlation-based accuracy, and model-based theoretical accuracy. Breeding values were also predicted using a conventional pedigree-based best linear unbiased prediction model in order to compare accuracies of genomic and conventional predictions. The heritability estimates of FCR and RFI were 0.29 and 0.50, respectively. The heritability estimates of ADG, ADFI, EP, BMP and LMP ranged from 0.34 to 0.53. In the CVF scenario, the correlation-based accuracy and the theoretical accuracy of genomic prediction for FCR were slightly higher than those for RFI. The correlation-based accuracies for FCR, RFI, ADG and ADFI were 0.360, 0.284, 0.574 and 0.520, respectively, and the model-based theoretical accuracies were 0.420, 0.414, 0.401 and 0.382, respectively. In the CVR scenario, the correlation-based accuracy and the theoretical accuracy of genomic prediction for FCR was lower than RFI, which was different from the CVF scenario. The correlation-based accuracies for FCR, RFI, ADG and ADFI were 0.449, 0.593, 0.581 and 0.627, respectively, and the model-based theoretical accuracies were 0.577, 0.629, 0.631 and 0.638, respectively. The accuracies of genomic predictions were 0.371 and 0.322 higher than the conventional pedigree-based predictions for the CVF and CVR scenarios, respectively. The genetic correlations of FCR with EP, BMP and LMP were -0.427, -0.156 and -0.338, respectively. The correlations between RFI and the three carcass traits were -0.320, -0.404 and -0.353, respectively. These results indicate that RFI and FCR have a moderate accuracy of genomic prediction. Improving RFI and FCR could be favourable for EP, BMP and LMP. Compared with FCR, which can be improved by selection for ADG in typical meat-type chicken breeding programs, selection for RFI could lead to extra improvement in feed efficiency.