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

There has been a growing interest in the genetic improvement of carcass traits as an important and primary breeding goal in the beef cattle industry over the last few decades. The use of correlated traits and molecular information can aid in obtaining more accurate estimates of breeding values. This study aimed to assess the improvement in the accuracy of genetic predictions for carcass traits by using ultrasound measurements and yearling weight along with genomic information in Hanwoo beef cattle by comparing four evaluation models using the estimators of the recently developed linear regression method. We compared the performance of single-trait pedigree best linear unbiased prediction [ST-BLUP and single-step genomic (ST-ssGBLUP)], as well as multi-trait (MT-BLUP and MT-ssGBLUP) models for the studied traits at birth and yearling date of steers. The data comprised of 15,796 phenotypic records for yearling weight and ultrasound traits as well as 5,622 records for carcass traits (backfat thickness, carcass weight, eye muscle area, and marbling score), resulting in 43,949 single-nucleotide polymorphisms from 4,284 steers and 2,332 bulls. Our results indicated that averaged across all traits, the accuracy of ssGBLUP models (0.52) was higher than that of pedigree-based BLUP (0.34), regardless of the use of single- or multi-trait models. On average, the accuracy of prediction can be further improved by implementing yearling weight and ultrasound data in the MT-ssGBLUP model (0.56) for the corresponding carcass traits compared to the ST-ssGBLUP model (0.49). Moreover, this study has shown the impact of genomic information and correlated traits on predictions at the yearling date (0.61) using MT-ssGBLUP models, which was advantageous compared to predictions at birth date (0.51) in terms of accuracy. Thus, using genomic information and high genetically correlated traits in the multi-trait model is a promising approach for practical genomic selection in Hanwoo cattle, especially for traits that are difficult to measure.

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Integrating Single-Step GWAS and Bipartite Networks Reconstruction Provides Novel Insights into Yearling Weight and Carcass Traits in Hanwoo Beef Cattle

Animals ◽

10.3390/ani10101836 ◽

2020 ◽

Vol 10 (10) ◽

pp. 1836

Author(s):

Masoumeh Naserkheil ◽

Abolfazl Bahrami ◽

Deukhwan Lee ◽

Hossein Mehrban

Keyword(s):

Beef Cattle ◽

Complex Traits ◽

Genome Wide Association Study ◽

Additive Genetic Variance ◽

Carcass Traits ◽

Single Step ◽

Bipartite Networks ◽

Muscle Area ◽

Eye Muscle ◽

Network Analyses

In recent years, studies on the biological mechanisms underlying complex traits have been facilitated by innovations in high-throughput genotyping technology. We conducted a weighted single-step genome-wide association study (WssGWAS) to evaluate backfat thickness, carcass weight, eye muscle area, marbling score, and yearling weight in a cohort of 1540 Hanwoo beef cattle using BovineSNP50 BeadChip. The WssGWAS uncovered thirty-three genomic regions that explained more than 1% of the additive genetic variance, mostly located on chromosomes 6 and 14. Among the identified window regions, seven quantitative trait loci (QTL) had pleiotropic effects and twenty-six QTL were trait-specific. Significant pathways implicated in the measured traits through Gene Ontology (GO) term enrichment analysis included the following: lipid biosynthetic process, regulation of lipid metabolic process, transport or localization of lipid, regulation of growth, developmental growth, and multicellular organism growth. Integration of GWAS results of the studied traits with pathway and network analyses facilitated the exploration of the respective candidate genes involved in several biological functions, particularly lipid and growth metabolism. This study provides novel insight into the genetic bases underlying complex traits and could be useful in developing breeding schemes aimed at improving growth and carcass traits in Hanwoo beef cattle.

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Applying the Metafounders Approach for Genomic Evaluation in a Multibreed Beef Cattle Population

Frontiers in Genetics ◽

10.3389/fgene.2020.556399 ◽

2020 ◽

Vol 11 ◽

Author(s):

Vinícius Silva Junqueira ◽

Paulo Sávio Lopes ◽

Daniela Lourenco ◽

Fabyano Fonseca e Silva ◽

Fernando Flores Cardoso

Keyword(s):

Beef Cattle ◽

Variance Components ◽

Genetic Relationships ◽

A Priori ◽

Predictive Ability ◽

Single Step ◽

Pedigree Information ◽

Phenotypic Variance ◽

Genomic Information ◽

The Impact

Pedigree information is incomplete by nature and commonly not well-established because many of the genetic ties are not known a priori or can be wrong. The genomic era brought new opportunities to assess relationships between individuals. However, when pedigree and genomic information are used simultaneously, which is the case of single-step genomic BLUP (ssGBLUP), defining the genetic base is still a challenge. One alternative to overcome this challenge is to use metafounders, which are pseudo-individuals that describe the genetic relationship between the base population individuals. The purpose of this study was to evaluate the impact of metafounders on the estimation of breeding values for tick resistance under ssGBLUP for a multibreed population composed by Hereford, Braford, and Zebu animals. Three different scenarios were studied: pedigree-based model (BLUP), ssGBLUP, and ssGBLUP with metafounders (ssGBLUPm). In ssGBLUPm, a total of four different metafounders based on breed of origin (i.e., Hereford, Braford, Zebu, and unknown) were included for the animals with missing parents. The relationship coefficient between metafounders was in average 0.54 (ranging from 0.34 to 0.96) suggesting an overlap between ancestor populations. The estimates of metafounder relationships indicate that Hereford and Zebu breeds have a possible common ancestral relationship. Inbreeding coefficients calculated following the metafounder approach had less negative values, suggesting that ancestral populations were large enough and that gametes inherited from the historical population were not identical. Variance components were estimated based on ssGBLUPm, ssGBLUP, and BLUP, but the values from ssGBLUPm were scaled to provide a fair comparison with estimates from the other two models. In general, additive, residual, and phenotypic variance components in the Hereford population were smaller than in Braford across different models. The addition of genomic information increased heritability for Hereford, possibly because of improved genetic relationships. As expected, genomic models had greater predictive ability, with an additional gain for ssGBLUPm over ssGBLUP. The increase in predictive ability was greater for Herefords. Our results show the potential of using metafounders to increase accuracy of GEBV, and therefore, the rate of genetic gain in beef cattle populations with partial levels of missing pedigree information.

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Growth Performance and Carcass Traits Responses to Dried Distillers’ Grain with Solubles Feeding of Growing Awassi Ram Lambs

Animals ◽

10.3390/ani9110954 ◽

2019 ◽

Vol 9 (11) ◽

pp. 954 ◽

Cited By ~ 1

Author(s):

Safa’ M. Hatamleh ◽

Belal S. Obeidat

Keyword(s):

Meat Quality ◽

Control Diet ◽

Average Daily Gain ◽

Carcass Traits ◽

Quality Parameters ◽

Muscle Area ◽

Eye Muscle ◽

Distillers Grain ◽

Dried Distillers Grain ◽

The Impact

This study considers the impact of dried distillers’ grain with solubles (DDGS) in diets of lambs. Randomly; 27 lambs were distributed to one of three diets. Diets were: a control diet (CON; n = 9), a 125 (DDGS125; n = 9) or a 250 g/kg DDGS (DDGS250; n = 9) of dietary dry matter (DM). The lambs were fed using these diets for 91 days. To assess carcass traits; five lambs were randomly selected at the end of the study. No significant differences were detected in intake and digestibility of DM; crude protein and fiber. Average daily gain did not differ among diets. Carcass characteristics did not differ among diets. With the exception of shear force and redness, which were greater in DDGS250 than in DDGS125 and CON diets, meat quality parameters were unaffected. Eye muscle area decreased in DDGS125 than in DDGS250 and CON diet. These results demonstrate that the feeding of lambs on DDGS at 125 or 250 g/kg DM did not have any impact on growth. These diets only had a simple effect on the characteristics of carcass and meat quality. These results suggest that it would be suitable to introduce these feeds into sheep nutrition in the future.

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Estimation of Genetic Parameters by Single-Trait and Multi-Trait Models for Carcass Traits in Hanwoo Cattle

Animals ◽

10.3390/ani9121061 ◽

2019 ◽

Vol 9 (12) ◽

pp. 1061

Author(s):

Swati Srivastava ◽

Bryan Irvine Lopez ◽

Sara de las Heras-Saldana ◽

Jong-Eun Park ◽

Dong-Hyun Shin ◽

...

Keyword(s):

Genetic Parameters ◽

Carcass Traits ◽

Meat Production ◽

Nucleotide Polymorphisms ◽

Genomic Information ◽

Marbling Score ◽

Muscle Area ◽

Eye Muscle ◽

Hanwoo Cattle ◽

Genomic Model

Hanwoo breed is preferred in South Korea because of the high standards in marbling and the palatability of its meat. Numerous studies have been conducted and are ongoing to increase the meat production and quality in this beef population. The aim of this study was to estimate and compare genetic parameters for carcass traits using BLUPF90 software. Four models were constructed, single trait pedigree model (STPM), single-trait genomic model (STGM), multi-trait pedigree model (MTPM), and multi-trait genomic model (MTGM), using the pedigree, phenotype, and genomic information of 7991 Hanwoo cattle. Four carcass traits were evaluated: Back fat thickness (BFT), carcass weight (CWT), eye muscle area (EMA), and marbling score (MS). Heritability estimates of 0.40 and 0.41 for BFT, 0.33 and 0.34 for CWT, 0.36 and 0.37 for EMA, and 0.35 and 0.38 for MS were obtained for the single-trait pedigree model and the multi-trait pedigree model, respectively, in Hanwoo. Further, the genomic model showed more improved results compared to the pedigree model, with heritability of 0.39 (CWT), 0.39 (EMA), and 0.46 (MS), except for 0.39 (BFT), which may be due to random events. Utilization of genomic information in the form of single nucleotide polymorphisms (SNPs) has allowed more capturing of the variance from the traits improving the variance components.

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Weighted Genomic Best Linear Unbiased Prediction for Carcass Traits in Hanwoo Cattle

Genes ◽

10.3390/genes10121019 ◽

2019 ◽

Vol 10 (12) ◽

pp. 1019 ◽

Cited By ~ 3

Author(s):

Bryan Irvine Lopez ◽

Seung-Hwan Lee ◽

Jong-Eun Park ◽

Dong-Hyun Shin ◽

Jae-Don Oh ◽

...

Keyword(s):

Genomic Prediction ◽

Carcass Traits ◽

Best Linear Unbiased Prediction ◽

Birth Date ◽

Muscle Area ◽

Eye Muscle ◽

Linear Unbiased Prediction ◽

Best Linear Unbiased ◽

Hanwoo Cattle ◽

Unbiased Prediction

The genomic best linear unbiased prediction (GBLUP) method has been widely used in routine genomic evaluation as it assumes a common variance for all single nucleotide polymorphism (SNP). However, this is unlikely in the case of traits influenced by major SNP. Hence, the present study aimed to improve the accuracy of GBLUP by using the weighted GBLUP (WGBLUP), which gives more weight to important markers for various carcass traits of Hanwoo cattle, such as backfat thickness (BFT), carcass weight (CWT), eye muscle area (EMA), and marbling score (MS). Linear and different nonlinearA SNP weighting procedures under WGBLUP were evaluated and compared with unweighted GBLUP and traditional pedigree-based methods (PBLUP). WGBLUP methods were assessed over ten iterations. Phenotypic data from 10,215 animals from different commercial herds that were slaughtered at approximately 30-month-old of age were used. All these animals were genotyped using Illumina Bovine 50k SNP chip and were divided into a training and a validation population by birth date on 1 November 2015. Genomic prediction accuracies obtained in the nonlinearA weighting methods were higher than those of the linear weighting for all traits. Moreover, unlike with linear methods, no sudden drops in the accuracy were noted after the peak was reached in nonlinearA methods. The average accuracies using PBLUP were 0.37, 0.49, 0.40, and 0.37, and 0.62, 0.74, 0.67, and 0.65 using GBLUP for BFT, CWT, EMA, and MS, respectively. Moreover, these accuracies of genomic prediction were further increased to 4.84% and 2.70% for BFT and CWT, respectively by using the nonlinearA method under the WGBLUP model. For EMA and MS, WGBLUP was as accurate as GBLUP. Our results indicate that the WGBLUP using a nonlinearA weighting method provides improved predictions for CWT and BFT, suggesting that the ability of WGBLUP over the other models by weighting selected SNPs appears to be trait-dependent.

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THI Modulation of Genetic and Non-genetic Variance Components for Carcass Traits in Hanwoo Cattle

Frontiers in Genetics ◽

10.3389/fgene.2020.576377 ◽

2020 ◽

Vol 11 ◽

Author(s):

Yoonji Chung ◽

Seung Hwan Lee ◽

Hak-Kyo Lee ◽

Dajeong Lim ◽

Julius van der Werf ◽

...

Keyword(s):

Beef Cattle ◽

Carcass Traits ◽

Reaction Norm ◽

Genetic Effects ◽

Additive Models ◽

Residual Effects ◽

Environment Interaction ◽

Marbling Score ◽

Muscle Area ◽

Eye Muscle

The phenotype of carcass traits in beef cattle are affected by random genetic and non-genetic effects, which both can be modulated by an environmental variable such as Temperature-Humidity Index (THI), a key environmental factor in cattle production. In this study, a multivariate reaction norm model (MRNM) was used to assess if the random genetic and non-genetic (i.e., residual) effects of carcass weight (CW), back fat thickness (BFT), eye muscle area (EMA), and marbling score (MS) were modulated by THI, using 9,318 Hanwoo steers (N = 8,964) and cows (N = 354) that were genotyped on the Illumina Bovine SNP50 BeadChip (50K). THI was measured based on the period of 15–45 days before slaughter. Both the correlation and the interaction between THI and random genetic and non-genetic effects were accounted for in the model. In the analyses, it was shown that the genetic effects of EMA and the non-genetic effects of CW and MS were significantly modulated by THI. No significant THI modulation of such effects was found for BFT. These results highlight the relevance of THI changes for the genetic and non-genetic variation of CW, EMA, and MS in Hanwoo beef cattle. Importantly, heritability estimates for CW, EMA, and MS from additive models without considering THI interactions were underestimated. Moreover, the significance of interaction can be biased if not properly accounting for the correlation between THI and genetic and non-genetic effects. Thus, we argue that the estimation of genetic parameters should be based on appropriate models to avoid any potential bias of estimates. Our finding should serve as a basis for future studies aiming at revealing genotype by environment interaction in estimation and genomic prediction of breeding values.

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Effects of early weaning on growth, feed efficiency and carcass traits in Shorthorn cattle

Animal Production Science ◽

10.1071/an09153 ◽

2010 ◽

Vol 50 (4) ◽

pp. 315 ◽

Cited By ~ 7

Author(s):

M. L. Wolcott ◽

H.-U. Graser ◽

D. J. Johnston

Keyword(s):

Feed Intake ◽

Feed Efficiency ◽

Carcass Traits ◽

Residual Feed Intake ◽

Carcass Composition ◽

Early Weaning ◽

Feed Conversion ◽

Muscle Area ◽

Eye Muscle ◽

The Impact

This study aimed to examine the impact of early weaning on residual feed intake, and other production and carcass traits, in a group of cattle subjected to early or conventional weaning treatments, but otherwise managed as contemporaries. Shorthorn (n = 140) calves were randomly allocated by sex and sire to early and conventional weaning treatments. Early weaned animals (n = 69) were weaned at an average of 123 days of age and 145 kg liveweight, while conventionally weaned steers and heifers (n = 71) were 259 days old at weaning and 273 kg. Following conventional weaning, animals were managed as contemporaries through backgrounding, and entered feedlot finishing at a mean age of 353 and 408 days for heifers and steers, respectively, for finishing and feed intake testing. At the conclusion of feed intake testing hip height was measured, and animals were ultrasound scanned to assess fat depth, eye muscle area and percent intramuscular fat. Early weaned animals were significantly lighter (P < 0.001) than their conventionally weaned contemporaries, when weighed at conventional weaning. The weight difference observed at conventional weaning of 19.4 kg between treatment groups persisted throughout the experiment, with significant (P < 0.05) differences of 17.1, 15.6 and 15.8 kg at feedlot entry, and the start and end of the feed intake test period, respectively. Weaning treatment also approached significance for daily feed intake (P = 0.06), with early weaned animals tending to eat less than their conventionally weaned contemporaries (daily feed intake = 11.6 and 12.0 kg, respectively). Weaning treat\ment did not significantly affect feed efficiency whether measured as residual feed intake (P = 0.64) or feed conversion ratio (P = 0.27). None of the other traits measured were significantly affected by weaning treatment. These data showed that early weaning, as implemented for this experiment, resulted in animals that were lighter than their conventionally weaned contemporaries through backgrounding and finishing. Weaning treatment did not, however, influence feed efficiency or the post-weaning growth and carcass composition traits measured for this experiment.

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Genomic Prediction Using Alternative Strategies of Weighted Single-Step Genomic BLUP for Yearling Weight and Carcass Traits in Hanwoo Beef Cattle

Genes ◽

10.3390/genes12020266 ◽

2021 ◽

Vol 12 (2) ◽

pp. 266

Author(s):

Hossein Mehrban ◽

Masoumeh Naserkheil ◽

Deuk Hwan Lee ◽

Chungil Cho ◽

Taejeong Choi ◽

...

Keyword(s):

Quantitative Trait Loci ◽

Beef Cattle ◽

Genomic Prediction ◽

Quantitative Trait ◽

Carcass Traits ◽

Best Linear Unbiased Prediction ◽

Single Step ◽

Linear Unbiased Prediction ◽

Single Nucleotide ◽

Best Linear Unbiased

The weighted single-step genomic best linear unbiased prediction (GBLUP) method has been proposed to exploit information from genotyped and non-genotyped relatives, allowing the use of weights for single-nucleotide polymorphism in the construction of the genomic relationship matrix. The purpose of this study was to investigate the accuracy of genetic prediction using the following single-trait best linear unbiased prediction methods in Hanwoo beef cattle: pedigree-based (PBLUP), un-weighted (ssGBLUP), and weighted (WssGBLUP) single-step genomic methods. We also assessed the impact of alternative single and window weighting methods according to their effects on the traits of interest. The data was comprised of 15,796 phenotypic records for yearling weight (YW) and 5622 records for carcass traits (backfat thickness: BFT, carcass weight: CW, eye muscle area: EMA, and marbling score: MS). Also, the genotypic data included 6616 animals for YW and 5134 for carcass traits on the 43,950 single-nucleotide polymorphisms. The ssGBLUP showed significant improvement in genomic prediction accuracy for carcass traits (71%) and yearling weight (99%) compared to the pedigree-based method. The window weighting procedures performed better than single SNP weighting for CW (11%), EMA (11%), MS (3%), and YW (6%), whereas no gain in accuracy was observed for BFT. Besides, the improvement in accuracy between window WssGBLUP and the un-weighted method was low for BFT and MS, while for CW, EMA, and YW resulted in a gain of 22%, 15%, and 20%, respectively, which indicates the presence of relevant quantitative trait loci for these traits. These findings indicate that WssGBLUP is an appropriate method for traits with a large quantitative trait loci effect.

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The area of eye muscle of beef cattle carcasses

Australian Journal of Experimental Agriculture ◽

10.1071/ea9630249 ◽

1963 ◽

Vol 3 (10) ◽

pp. 249

Author(s):

RM Seebeck

Keyword(s):

Beef Cattle ◽

Cross Sectional Area ◽

Carcass Weight ◽

Sectional Area ◽

Muscle Area ◽

Cross Sectional ◽

Eye Muscle ◽

Angus Cattle ◽

The Cross

Variations in the cross-sectional area of eye muscle of carcasses cut between the tenth and eleventh ribs were investigated, using 105 Hereford and 51 Angus steers aged 20 months. These cattle consisted of three groups, born in successive years. At constant carcass weight, statistically significant differences in eye muscle area were found between breeds and between years. Breed and year differences were also found in eye muscle area with width and depth of eye muscle constant, so that there are limitations to the estimation of eye muscle area from width and depth measurements. A nomograph is given for estimating eye muscle area from width and depth for Hereford and Angus cattle, when all animals are reared in the same year and environment. The use of eye muscle area as an indicator of weight of carcass muscle is discussed.

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36 Effect of Blending and Tuning Relationship Matrices in Single-step Genomic BLUP

Journal of Animal Science ◽

10.1093/jas/skab235.032 ◽

2021 ◽

Vol 99 (Supplement_3) ◽

pp. 19-20

Author(s):

Taylor M McWhorter ◽

Andre Garcia ◽

Matias Bermann ◽

Andres Legarra ◽

Ignacio Aguilar ◽

...

Keyword(s):

Single Step ◽

Fixation Index ◽

Genomic Information ◽

Software Suite ◽

Genetic Base ◽

Actual Difference ◽

The Impact ◽

Genomic Predictions

Abstract Single-step GBLUP (ssGBLUP) relies on the combination of genomic (G) and pedigree relationships for all (A) and genotyped animals (A22). The procedure implemented in the BLUPF90 software suite first involves combining a small percentage of A22 into G (blending) to avoid singularity problems, then an adjustment to account for the fact the genetic base in G and A22 is different (tuning). However, blending before tuning may not reflect the actual difference between pedigree and genomic base because the blended matrix already contains a portion of A22. The objective of this study was to evaluate the impact of tuning before blending on predictivity, bias, and inflation of GEBV, indirect predictions (IP), and SNP effects from ssGBLUP using American Angus and US Holstein data. We used four different scenarios to obtain genomic predictions: BlendFirst_TunedG2, TuneFirst_TunedG2, BlendFirst_TunedG4, and TuneFirst_TunedG4. TunedG2 adjusts mean diagonals and off-diagonals of G to be similar to the ones in A22, whereas TunedG4 adjusts based on the fixation index. Over 6 million growth records were available for Angus and 5.9 million udder depth records for Holsteins. Genomic information was available on 51,478 Angus and 105,116 Holstein animals. Predictivity and reliability were obtained for 19,056 and 1,711 validation Angus and Holsteins, respectively. We observed the same predictivity and reliability for GEBV or IP in all four scenarios, ranging from 0.47 to 0.60 for Angus and was 0.67 for Holsteins. Slightly less bias was observed when tuning was done before blending. Correlation of SNP effects between scenarios was > 0.99. Refined tuning before blending had no impact on GEBV and marginally reduced the bias. This option will be implemented in the BLUPF90 software suite.

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