Evaluation of non-additive genetic effects on carcass and meat quality traits in Korean Hanwoo cattle using genomic models

Abstract

The traditional genetic evaluation methods generally consider additive genetic effects only and often ignore non-additive (dominance and epistasis) effects that may have contributions in genetic variation of complex traits of livestock species. The available dense single nucleotide polymorphisms (SNPs) panels offer to investigate the potential benefits of including non-additive genetic effects in the genomic evaluation’s models. Data from 16,971 genotyped (Illumina Bovine 50K SNP chip) Korean Hanwoo cattle were used to estimate genetic variance components and prediction accuracy of genomic breeding values (GEBV) for four carcass and meat quality traits: carcass weight (CWT), eye muscle area (EMA), back fat thickness (BFT) and marbling score (MS). Five different genetic models were evaluated through including additive, dominance and epistatic interactions (additive by additive, A×A; additive by dominance, A×D and dominance by dominance, D×D) successively in the models. The estimates of additive genetic variances and narrow sense heritabilities (ha2) were found similar across the evaluated models and traits except when additive interaction (A×A) was included. The dominance variance estimates relative to phenotypic variance ranged from 1.7 to 3.4% for CWT and MS traits, whereas, they were close to zero for EMA and BFT traits. The magnitude of A×A epistatic heritability (haa2) ranged between 14.8 and 27.7% in all traits. However, heritability estimates for A×D and D×D epistatic interactions (had2 and hdd2) were quite low compared to haa2 and were contributed only 0.0 to 9.7% of the total phenotypic variation. In general, broad sense heritability (hG2) estimates were almost twice (ranged between 0.54 and 0.68) the ha2 for all of the investigated traits. The inclusion of dominance effects did not improve the prediction accuracy of GEBV but improved 2.0 to 3.0% when epistatic effects included in the model. More importantly, rank correlation revealed that partitioning of variance components considering dominance and epistatic effects in the model would enable to re-rank of top animals with better prediction of GEBV. The present result suggest that dominance and epistatic effects could be included in the genomic evaluation model for better estimates of variance components and more accurate prediction of GEBV for carcass and meat quality traits in Korean Hanwoo cattle.