Incorporation of Putative Functional Variants in the Ncapg, ARRDC3, PLAG1 and ERGIC1 Genes Improves Accuracies of Genomic Predictions for Growth Traits in Beef Cattle

In beef cattle, body weight is an important trait and optimizing size at various ages is of key economic interest. In our previous study, we identified four large-effect pleiotropic QTLs located on BTA6, 7, 14 and 20 associated with body weights in several beef breeds. Some 96 new functional variants of candidate genes within these and some other QTL regions were selected from the dbSNP and assayed into the new versions of GeneSeek Genomic Profilers (GGP-LD, GGP-UHD and GGP-50K). Some 5,964 Simmental and 2,871 Red Angus animals were genotyped with one of these assays. Some 200 animals of each population were used as the test and the rest for training purposes. Only 9,439 autosomal markers in common between these assays were used in the analyses. We compared accuracies of genomic predictions for birth, weaning and yearling weights fitting 9K, 9K plus 96 functional variants or only 96 functional variants in BayesC0 model using GenSel software. The correlations between estimated molecular breeding values (MBV) and adjusted phenotypes divided by the square root of the trait heritability were used as a measurement of accuracy, which are shown in Table 1. The accuracies of MBV were equal or higher in the model including additional 96 functional variants. Interestingly, genomic predictions were more accurate for yearling weight using only 96 functional variants in both Simmental and Red Angus populations. These functional variants accounted for significant amount of additive genetic variances of body weights in these populations. Some functional variants including rs109570900 encoding p.Ile442Met in NCAPG, rs109901274 encoding p.Tyr182Cys in ARRDC3, rs136369910 encoding g.25019900A>G in PLAG1 and rs43350563 encoding c.322G>A in ERGIC1 were among significantly associated markers with remarkable impact on body weights. Knowledge of such functional variants improves the accuracies of genomic predictions and would create new opportunities for the selection of animals with appropriate body weights for harvest or maternal purposes and could decrease dystocia in beef cattle population.

Table 1 – The accuracies of genomic predictions for birth, weaning and yearling weights using different marker sets.

Breed	Trait	9K	9K plus 96 functional variants	Only 96 functional variants
Simmental	Birth weight	0.60	0.60	0.15
	Weaning weight	0.16	0.16	0.02
	Yearling weight	0.19	0.21	0.40
Red Angus	Birth weight	0.49	0.51	0.47
	Weaning weight	0.23	0.23	0.27
	Yearling weight	0.15	0.19	0.57