Genomic evaluation of carcass traits of Korean beef cattle Hanwoo using a single-step marker effect model

Abstract

Hanwoo beef cattle are well known for the flavor and tenderness of their meat. Genetic improvement programs have been extremely successful over the last 40 years. Recently, genomic selection was initiated in Hanwoo to enhance genetic progress. Routine genomic evaluation based on the single-step breeding value model was implemented in 2020 for all economically important traits. In this study, we tested a single-step marker effect model for the genomic evaluation of four carcass traits, namely, carcass weight, eye muscle area, backfat thickness, and marbling score. In total, 8,023,666 animals with carcass records were jointly evaluated, including 29,965 genotyped animals. To assess the prediction stability of the single-step model, carcass data from the last four years were removed in a forward validation study. The estimated genomic breeding values (GEBV) of the validation animals and other animals were compared between the truncated and full evaluations. A parallel conventional best linear unbiased prediction (BLUP) evaluation with either the full or the truncated dataset was also conducted for comparison with the single-step model. The estimates of the marker effect from the truncated evaluation were highly correlated with those from the full evaluation, ranging from 0.88–0.92. The regression coefficients of the estimates of the marker effect for the full and truncated evaluations were close to their expected value of 1, indicating unbiased estimates for all carcass traits. Estimates of the marker effect revealed three chromosomal regions (chromosomes 4, 6, and 14) harboring the major genes for carcass weight in Hanwoo. For validation of cows or steers, the single-step model had a much higher R2 value for the linear regression model than the conventional BLUP model. Based on the regression intercept and slope of the validation, the single-step evaluation was neither inflated nor deflated. For genotyped animals, the estimated GEBV from the full and truncated evaluations were more correlated than the estimated breeding values from the two conventional BLUP evaluations. The single-step model provided a more accurate and stable evaluation over time.

Wagyu Feeder Check: A genomic-based tool to identify performance differences of Australian Wagyu and Wagyu crossed cattle

“…Unlike the recent work of Reverter et al (2023) with 3766 purebred Angus steers plus 2124 Angus-based commercial steers, in the present study we did not observe a tendency for over-dispersion (or inflation) of GEBV for CWT or MARB. Similarly, the recent work by Koo et al (2023) exploring the quality of the genomic evaluation of Korean Hanwoo cattle based on a large number of genotyped cows, steers and young animals applied the LR method to confirm a slight negative bias (GEBV overestimation) for all traits and animal groups, but a slight positive bias (GEBV underestimation) for CEMA and MARB in steers. However, their estimates of bias did not deviate significantly from zero.…”

A transcriptomic analysis of skeletal muscle tissues reveals promising candidate genes and pathways accountable for different daily weight gain in Hanwoo cattle

“…Most earlier studies employed GWAS-based methods to analyze the genetic basis of carcass traits, revealing several genomic regions containing QTLs associated with carcass weight in diverse cattle breed 7 , 9 , 10 . However, the investigation of carcass traits in Hanwoo cattle through transcriptomic studies, employing RNA sequencing for functional evaluation of pivotal candidate genes, is still in a dynamic phase and requires more comprehensive analyses.…”