Multi-Trait Single-Step GBLUP Improves Accuracy of Genomic Prediction for Carcass Traits Using Yearling Weight and Ultrasound Traits in Hanwoo

Mehrban, Hossein; Naserkheil, Masoumeh; Lee, Deukhwan; Ibáñez‐Escriche, Noelia

doi:10.3389/fgene.2021.692356

Cited by 13 publications

(11 citation statements)

References 55 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…These findings were also in concordance with those reported by Mehrban et al [ 14 ], who applied the LR method to evaluate carcass traits in Hanwoo cattle using four evaluation models and showed that using genomic information and additional phenotypic information from highly genetically correlated traits is a suitable tool to improve the prediction accuracy.…”

Section: Discussionsupporting

confidence: 91%

“…Consistent with our results, several previous studies have proved the superiority of ssGBLUP over traditional BLUP approaches in various livestock since it was proposed [ 7 , 18 , 32 , 33 , 42 , 43 , 44 , 45 , 46 , 47 , 48 , 49 , 50 ]. Moreover, in Hanwoo cattle studies, the accuracies obtained from single-step models were found to be higher than those from pedigree-based and multi-step methods for carcass traits [ 11 , 12 , 13 , 14 , 15 , 51 ] and body measurement traits [ 16 ].…”

Section: Discussionmentioning

confidence: 99%

“…Single-step genomic BLUP provides the most comprehensive information for genomic evaluation where the phenotypes of genotyped and non-genotyped individuals, pedigree, and genotype data can be considered simultaneously in one step. Several studies have reported that the use of ssGBLUP improves genomic prediction accuracy relative to pedigree-based BLUP or genomic BLUP (GBLUP) for carcass traits [ 11 , 12 , 13 , 14 , 15 ] and linear body measurements in Hanwoo cattle [ 16 ], as well as in other beef cattle [ 17 , 18 , 19 ]. Nonetheless, utilizing primal cut traits to further increase the accuracy of genomic prediction in breeding programs of Hanwoo cattle has not yet been investigated.…”

Section: Introductionmentioning

confidence: 99%

See 2 more Smart Citations

Evaluation of Genome-Enabled Prediction for Carcass Primal Cut Yields Using Single-Step Genomic Best Linear Unbiased Prediction in Hanwoo Cattle

Naserkheil

Mehrban

Lee

et al. 2021

Genes

Self Cite

View full text Add to dashboard Cite

There is a growing interest worldwide in genetically selecting high-value cut carcass weights, which allows for increased profitability in the beef cattle industry. Primal cut yields have been proposed as a potential indicator of cutability and overall carcass merit, and it is worthwhile to assess the prediction accuracies of genomic selection for these traits. This study was performed to compare the prediction accuracy obtained from a conventional pedigree-based BLUP (PBLUP) and a single-step genomic BLUP (ssGBLUP) method for 10 primal cut traits—bottom round, brisket, chuck, flank, rib, shank, sirloin, striploin, tenderloin, and top round—in Hanwoo cattle with the estimators of the linear regression method. The dataset comprised 3467 phenotypic observations for the studied traits and 3745 genotyped individuals with 43,987 single-nucleotide polymorphisms. In the partial dataset, the accuracies ranged from 0.22 to 0.30 and from 0.37 to 0.54 as evaluated using the PBLUP and ssGBLUP models, respectively. The accuracies of PBLUP and ssGBLUP with the whole dataset varied from 0.45 to 0.75 (average 0.62) and from 0.52 to 0.83 (average 0.71), respectively. The results demonstrate that ssGBLUP performed better than PBLUP averaged over the 10 traits, in terms of prediction accuracy, regardless of considering a partial or whole dataset. Moreover, ssGBLUP generally showed less biased prediction and a value of dispersion closer to 1 than PBLUP across the studied traits. Thus, the ssGBLUP seems to be more suitable for improving the accuracy of predictions for primal cut yields, which can be considered a starting point in future genomic evaluation for these traits in Hanwoo breeding practice.

show abstract

Section: Discussionsupporting

confidence: 91%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 1 more Smart Citation

Evaluation of Genome-Enabled Prediction for Carcass Primal Cut Yields Using Single-Step Genomic Best Linear Unbiased Prediction in Hanwoo Cattle

Naserkheil

Mehrban

Lee

et al. 2021

Genes

Self Cite

View full text Add to dashboard Cite

show abstract

“…To the best of our knowledge, no study has been published on the genomic evaluation of Hanwoo based on a large number of genotyped cows, steers, and young animals. Recently, Mehrban et al (2021) demonstrated the enhanced accuracy of single-step genomic prediction using a multi-trait model compared to that using a single-trait model.…”

Section: Introductionmentioning

confidence: 99%

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

Koo¹,

Alkhoder²,

Choi

et al. 2023

Journal of Animal Science

View full text Add to dashboard Cite

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.

show abstract

“…Furthermore, the incorporation of genome-wide SNP panels into genetic evaluation models enables us to estimate the genomic breeding value (GEBV) that results in an improved accuracy of genomic prediction and an increased selection response for the traits of interest in cattle [ 14 ]. In recent years, the importance of genomic selection as a promising tool for gains in the accuracy of predictions compared with conventional genetic methods for carcass traits in Hanwoo breeding programs have been investigated in several studies [ 15 , 16 , 17 , 18 , 19 , 20 , 21 ]. The objective of the present review is to summarize studies concerning the identification of genomic regions and respective candidate genes and their corresponding pathways connected to carcass and growth traits in Hanwoo cattle.…”

Section: Introductionmentioning

confidence: 99%

Exploring and Identifying Candidate Genes and Genomic Regions Related to Economically Important Traits in Hanwoo Cattle

Naserkheil

Manzari

Dang

et al. 2022

CIMB

Self Cite

View full text Add to dashboard Cite

The purpose of the current review was to explore and summarize different studies concerning the detection and characterization of candidate genes and genomic regions associated with economically important traits in Hanwoo beef cattle. Hanwoo cattle, the indigenous premium beef cattle of Korea, were introduced for their marbled fat, tenderness, characteristic flavor, and juiciness. To date, there has been a strong emphasis on the genetic improvement of meat quality and yields, such as backfat thickness (BFT), marbling score (MS), carcass weight (CW), eye muscle area (EMA), and yearling weight (YW), as major selection criteria in Hanwoo breeding programs. Hence, an understanding of the genetics controlling these traits along with precise knowledge of the biological mechanisms underlying the traits would increase the ability of the industry to improve cattle to better meet consumer demands. With the development of high-throughput genotyping, genomewide association studies (GWAS) have allowed the detection of chromosomal regions and candidate genes linked to phenotypes of interest. This is an effective and useful tool for accelerating the efficiency of animal breeding and selection. The GWAS results obtained from the literature review showed that most positional genes associated with carcass and growth traits in Hanwoo are located on chromosomes 6 and 14, among which LCORL, NCAPG, PPARGC1A, ABCG2, FAM110B, FABP4, DGAT1, PLAG1, and TOX are well known. In conclusion, this review study attempted to provide comprehensive information on the identified candidate genes associated with the studied traits and genes enriched in the functional terms and pathways that could serve as a valuable resource for future research in Hanwoo breeding programs.

show abstract

Multi-Trait Single-Step GBLUP Improves Accuracy of Genomic Prediction for Carcass Traits Using Yearling Weight and Ultrasound Traits in Hanwoo

Cited by 13 publications

References 55 publications

Evaluation of Genome-Enabled Prediction for Carcass Primal Cut Yields Using Single-Step Genomic Best Linear Unbiased Prediction in Hanwoo Cattle

Evaluation of Genome-Enabled Prediction for Carcass Primal Cut Yields Using Single-Step Genomic Best Linear Unbiased Prediction in Hanwoo Cattle

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

Exploring and Identifying Candidate Genes and Genomic Regions Related to Economically Important Traits in Hanwoo Cattle

Contact Info

Product

Resources

About