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Doyle JL, Purfield DC, Moore T, Carthy TR, Walsh SW, Veerkamp RF, Evans RD, Berry DP. Identification of genomic regions that exhibit sexual dimorphism for size and muscularity in cattle. J Anim Sci 2021; 99:6157006. [PMID: 33677555 DOI: 10.1093/jas/skab070] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Accepted: 02/26/2021] [Indexed: 12/11/2022] Open
Abstract
Sexual dimorphism, the phenomenon whereby males and females of the same species are distinctive in some aspect of appearance or size, has previously been documented in cattle for traits such as growth rate and carcass merit using a quantitative genetics approach. No previous study in cattle has attempted to document sexual dimorphism at a genome level; therefore, the objective of the present study was to determine whether genomic regions associated with size and muscularity in cattle exhibited signs of sexual dimorphism. Analyses were undertaken on 10 linear-type traits that describe the muscular and skeletal characteristics of both males and females of five beef cattle breeds: 1,444 Angus (AA), 6,433 Charolais (CH), 1,129 Hereford, 8,745 Limousin (LM), and 1,698 Simmental. Genome-wide association analyses were undertaken using imputed whole-genome sequence data for each sex separately by breed. For each single-nucleotide polymorphism (SNP) that was segregating in both sexes, the difference between the allele substitution effect sizes for each sex, in each breed separately, was calculated. Suggestively (P ≤ 1 × 10-5) sexually dimorphic SNPs that were segregating in both males and females were detected for all traits in all breeds, although the location of these SNPs differed by both trait and breed. Significantly (P ≤ 1 × 10-8) dimorphic SNPs were detected in just three traits in the AA, seven traits in the CH, and three traits in the LM. The vast majority of all segregating autosomal SNPs (86% in AA to 94% in LM) had the same minor allele in both males and females. Differences (P ≤ 0.05) in allele frequencies between the sexes were observed for between 36% (LM) and 66% (AA) of the total autosomal SNPs that were segregating in both sexes. Dimorphic SNPs were located within a number of genes related to muscularity and/or size including the NAB1, COL5A2, and IWS1 genes on BTA2 that are located close to, and thought to be co-inherited with, the MSTN gene. Overall, sexual dimorphism exists in cattle at the genome level, but it is not consistent by either trait or breed.
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Affiliation(s)
- Jennifer L Doyle
- Teagasc, Animal and Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland.,Department of Science, Waterford Institute of Technology, Cork Road, Co. Waterford, Ireland
| | - Deirdre C Purfield
- Department of Biological Sciences, Cork Institute of Technology, Bishopstown, Co. Cork, Ireland
| | - Tom Moore
- School of Biochemistry and Cell Biology, University College Cork, Western Gateway Building, Western Road, Cork, Ireland
| | - Tara R Carthy
- Teagasc, Animal and Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Siobhan W Walsh
- Department of Science, Waterford Institute of Technology, Cork Road, Co. Waterford, Ireland
| | - Roel F Veerkamp
- Animal Breeding and Genomics Centre, Wageningen University and Research Centre, Livestock Research, Wageningen, the Netherlands
| | - Ross D Evans
- Irish Cattle Breeding Federation, Bandon, Co. Cork, Ireland
| | - Donagh P Berry
- Teagasc, Animal and Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland
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Berry DP. Invited review: Beef-on-dairy-The generation of crossbred beef × dairy cattle. J Dairy Sci 2021; 104:3789-3819. [PMID: 33663845 DOI: 10.3168/jds.2020-19519] [Citation(s) in RCA: 44] [Impact Index Per Article: 14.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2020] [Accepted: 11/26/2020] [Indexed: 02/06/2023]
Abstract
Because a growing proportion of the beef output in many countries originates from dairy herds, the most critical decisions about the genetic merit of most carcasses harvested are being made by dairy producers. Interest in the generation of more valuable calves from dairy females is intensifying, and the most likely vehicle is the use of appropriately selected beef bulls for mating to the dairy females. This is especially true given the growing potential to undertake more beef × dairy matings as herd metrics improve (e.g., reproductive performance) and technological advances are more widely adopted (e.g., sexed semen). Clear breed differences (among beef breeds but also compared with dairy breeds) exist for a whole plethora of performance traits, but considerable within-breed variability has also been demonstrated. Although such variability has implications for the choice of bull to mate to dairy females, the fact that dairy females themselves exhibit such genetic variability implies that "one size fits all" may not be appropriate for bull selection. Although differences in a whole series of key performance indicators have been documented between beef and beef-on-dairy animals, of particular note is the reported lower environmental hoofprint associated with beef-on-dairy production systems if the environmental overhead of the mature cow is attributed to the milk she eventually produces. Despite the known contribution of beef (i.e., both surplus calves and cull cows) to the overall gross output of most dairy herds globally, and the fact that each dairy female contributes half her genetic merit to her progeny, proxies for meat yield (i.e., veal or beef) are not directly considered in the vast majority of dairy cow breeding objectives. Breeding objectives to identify beef bulls suitable for dairy production systems are now being developed and validated, demonstrating the financial benefit of using such breeding objectives over and above a focus on dairy bulls or easy-calving, short-gestation beef bulls. When this approach is complemented by management-based decision-support tools, considerable potential exists to improve the profitability and sustainability of modern dairy production systems by exploiting beef-on-dairy breeding strategies using the most appropriate beef bulls.
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Affiliation(s)
- D P Berry
- Teagasc, Animal and Grassland Research and Innovation Centre, Moorepark, Fermoy P61 P302, Co. Cork, Ireland.
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Naserkheil M, Lee DH, Mehrban H. Improving the accuracy of genomic evaluation for linear body measurement traits using single-step genomic best linear unbiased prediction in Hanwoo beef cattle. BMC Genet 2020; 21:144. [PMID: 33267771 PMCID: PMC7709290 DOI: 10.1186/s12863-020-00928-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Accepted: 10/27/2020] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Recently, there has been a growing interest in the genetic improvement of body measurement traits in farm animals. They are widely used as predictors of performance, longevity, and production traits, and it is worthwhile to investigate the prediction accuracies of genomic selection for these traits. In genomic prediction, the single-step genomic best linear unbiased prediction (ssGBLUP) method allows the inclusion of information from genotyped and non-genotyped relatives in the analysis. Hence, we aimed to compare the prediction accuracy obtained from a pedigree-based BLUP only on genotyped animals (PBLUP-G), a traditional pedigree-based BLUP (PBLUP), a genomic BLUP (GBLUP), and a single-step genomic BLUP (ssGBLUP) method for the following 10 body measurement traits at yearling age of Hanwoo cattle: body height (BH), body length (BL), chest depth (CD), chest girth (CG), chest width (CW), hip height (HH), hip width (HW), rump length (RL), rump width (RW), and thurl width (TW). The data set comprised 13,067 phenotypic records for body measurement traits and 1523 genotyped animals with 34,460 single-nucleotide polymorphisms. The accuracy for each trait and model was estimated only for genotyped animals using five-fold cross-validations. RESULTS The accuracies ranged from 0.02 to 0.19, 0.22 to 0.42, 0.21 to 0.44, and from 0.36 to 0.55 as assessed using the PBLUP-G, PBLUP, GBLUP, and ssGBLUP methods, respectively. The average predictive accuracies across traits were 0.13 for PBLUP-G, 0.34 for PBLUP, 0.33 for GBLUP, and 0.45 for ssGBLUP methods. Our results demonstrated that averaged across all traits, ssGBLUP outperformed PBLUP and GBLUP by 33 and 43%, respectively, in terms of prediction accuracy. Moreover, the least root of mean square error was obtained by ssGBLUP method. CONCLUSIONS Our findings suggest that considering the ssGBLUP model may be a promising way to ensure acceptable accuracy of predictions for body measurement traits, especially for improving the prediction accuracy of selection candidates in ongoing Hanwoo breeding programs.
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Affiliation(s)
- Masoumeh Naserkheil
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, P.O. Box: 4111, Karaj, 77871-31587 Iran
| | - Deuk Hwan Lee
- Department of Animal Life and Environment Sciences, Hankyong National University, Jungang-ro 327, Anseong-si, Gyeonggi-do South Korea
| | - Hossein Mehrban
- Department of Animal Science, Shahrekord University, P.O. Box: 115, Shahrekord, 88186-34141 Iran
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Costilla R, Kemper KE, Byrne EM, Porto-Neto LR, Carvalheiro R, Purfield DC, Doyle JL, Berry DP, Moore SS, Wray NR, Hayes BJ. Genetic control of temperament traits across species: association of autism spectrum disorder risk genes with cattle temperament. Genet Sel Evol 2020; 52:51. [PMID: 32842956 PMCID: PMC7448488 DOI: 10.1186/s12711-020-00569-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2020] [Accepted: 08/07/2020] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Temperament traits are of high importance across species. In humans, temperament or personality traits correlate with psychological traits and psychiatric disorders. In cattle, they impact animal welfare, product quality and human safety, and are therefore of direct commercial importance. We hypothesized that genetic factors that contribute to variation in temperament among individuals within a species will be shared between humans and cattle. Using imputed whole-genome sequence data from 9223 beef cattle from three cohorts, a series of genome-wide association studies was undertaken on cattle flight time, a temperament phenotype measured as the time taken for an animal to cover a short-fixed distance after release from an enclosure. We also investigated the association of cattle temperament with polymorphisms in bovine orthologs of risk genes for neuroticism, schizophrenia, autism spectrum disorders (ASD), and developmental delay disorders in humans. RESULTS Variants with the strongest associations were located in the bovine orthologous region that is involved in several behavioural and cognitive disorders in humans. These variants were also partially validated in independent cattle cohorts. Genes in these regions (BARHL2, NDN, SNRPN, MAGEL2, ABCA12, KIFAP3, TOPAZ1, FZD3, UBE3A, and GABRA5) were enriched for the GO term neuron migration and were differentially expressed in brain and pituitary tissues in humans. Moreover, variants within 100 kb of ASD susceptibility genes were associated with cattle temperament and explained 6.5% of the total additive genetic variance in the largest cattle cohort. The ASD genes with the most significant associations were GABRB3 and CUL3. Using the same 100 kb window, a weak association was found with polymorphisms in schizophrenia risk genes and no association with polymorphisms in neuroticism and developmental delay disorders risk genes. CONCLUSIONS Our analysis showed that genes identified in a meta-analysis of cattle temperament contribute to neuron development functions and are differentially expressed in human brain tissues. Furthermore, some ASD susceptibility genes are associated with cattle temperament. These findings provide evidence that genetic control of temperament might be shared between humans and cattle and highlight the potential for future analyses to leverage results between species.
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Affiliation(s)
- Roy Costilla
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia
| | - Kathryn E. Kemper
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
| | - Enda M. Byrne
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Laercio R. Porto-Neto
- Commonwealth Scientific and Industrial Research Organization (CSIRO), Agriculture and Food, Brisbane, Australia
| | - Roberto Carvalheiro
- School of Agricultural and Veterinarian Sciences, Sao Paulo State University, Sao Paolo, Brazil
| | | | - Jennifer L. Doyle
- Teagasc, Animal and Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork Ireland
| | - Donagh P. Berry
- Teagasc, Animal and Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork Ireland
| | - Stephen S. Moore
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia
| | - Naomi R. Wray
- Institute for Molecular Bioscience, The University of Queensland, Brisbane, Australia
- Queensland Brain Institute, The University of Queensland, Brisbane, Australia
| | - Ben J. Hayes
- Queensland Alliance for Agriculture and Food Innovation, The University of Queensland, Brisbane, Australia
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Berry D, Coyne J, Doyle J, Evans R. The use of subjectively assessed muscular and skeletal traits on live cattle to aid in differentiation between animal genetically divergent in carcass kill out metrics. Livest Sci 2020. [DOI: 10.1016/j.livsci.2020.103984] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Doyle JL, Berry DP, Veerkamp RF, Carthy TR, Walsh SW, Evans RD, Purfield DC. Genomic Regions Associated With Skeletal Type Traits in Beef and Dairy Cattle Are Common to Regions Associated With Carcass Traits, Feed Intake and Calving Difficulty. Front Genet 2020; 11:20. [PMID: 32117439 PMCID: PMC7010604 DOI: 10.3389/fgene.2020.00020] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 01/07/2020] [Indexed: 12/22/2022] Open
Abstract
Linear type traits describing the skeletal characteristics of an animal are moderately to strongly genetically correlated with a range of other performance traits in cattle including feed intake, reproduction traits and carcass merit; thus, type traits could also provide useful insights into the morphological differences among animals underpinning phenotypic differences in these complex traits. The objective of the present study was to identify genomic regions associated with five subjectively scored skeletal linear traits, to determine if these associated regions are common in multiple beef and dairy breeds, and also to determine if these regions overlap with those proposed elsewhere to be associated with correlated performance traits. Analyses were carried out using linear mixed models on imputed whole genome sequence data separately in 1,444 Angus, 1,129 Hereford, 6,433 Charolais, 8,745 Limousin, 1,698 Simmental, and 4,494 Holstein-Friesian cattle, all scored for the linear type traits. There was, on average, 18 months difference in age at assessment of the beef versus the dairy animals. While the majority of the identified quantitative trait loci (QTL), and thus genes, were both trait-specific and breed-specific, a large-effect pleiotropic QTL on BTA6 containing the NCAPG and LCORL genes was associated with all skeletal traits in the Limousin population and with wither height in the Angus. Other than that, little overlap existed in detected QTLs for the skeletal type traits in the other breeds. Only two QTLs overlapped the beef and dairy breeds; both QTLs were located on BTA5 and were associated with height in both the Angus and the Holstein-Friesian, despite the difference in age at assessment. Several detected QTLs in the present study overlapped with QTLs documented elsewhere that are associated with carcass traits, feed intake, and calving difficulty. While most breeding programs select for the macro-traits like carcass weight, carcass conformation, and feed intake, the higher degree of granularity with selection on the individual linear type traits in a multi-trait index underpinning the macro-level goal traits, presents an opportunity to help resolve genetic antagonisms among morphological traits in the pursuit of the animal with optimum performance metrics.
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Affiliation(s)
- Jennifer L Doyle
- Animal and Grassland Research and Innovation Centre, Moorepark, Teagasc, Fermoy, Ireland.,Department of Science, Waterford Institute of Technology, Waterford, Ireland
| | - Donagh P Berry
- Animal and Grassland Research and Innovation Centre, Moorepark, Teagasc, Fermoy, Ireland
| | - Roel F Veerkamp
- Animal Breeding and Genomics Centre, Wageningen Livestock Research, Wageningen University & Research, Wageningen, Netherlands
| | - Tara R Carthy
- Animal and Grassland Research and Innovation Centre, Moorepark, Teagasc, Fermoy, Ireland
| | - Siobhan W Walsh
- Department of Science, Waterford Institute of Technology, Waterford, Ireland
| | - Ross D Evans
- Animal Breeding and Genomics Centre, Wageningen Livestock Research, Wageningen University & Research, Wageningen, Netherlands.,Irish Cattle Breeding Federation, Bandon, Ireland
| | - Deirdre C Purfield
- Animal and Grassland Research and Innovation Centre, Moorepark, Teagasc, Fermoy, Ireland
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Doyle JL, Berry DP, Veerkamp RF, Carthy TR, Evans RD, Walsh SW, Purfield DC. Genomic regions associated with muscularity in beef cattle differ in five contrasting cattle breeds. Genet Sel Evol 2020; 52:2. [PMID: 32000665 PMCID: PMC6993462 DOI: 10.1186/s12711-020-0523-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2019] [Accepted: 01/17/2020] [Indexed: 01/19/2023] Open
Abstract
BACKGROUND Linear type traits, which reflect the muscular characteristics of an animal, could provide insight into how, in some cases, morphologically very different animals can yield the same carcass weight. Such variability may contribute to differences in the overall value of the carcass since primal cuts vary greatly in price; such variability may also hinder successful genome-based association studies. Therefore, the objective of our study was to identify genomic regions that are associated with five muscularity linear type traits and to determine if these significant regions are common across five different breeds. Analyses were carried out using linear mixed models on imputed whole-genome sequence data in each of the five breeds, separately. Then, the results of the within-breed analyses were used to conduct an across-breed meta-analysis per trait. RESULTS We identified many quantitative trait loci (QTL) that are located across the whole genome and associated with each trait in each breed. The only commonality among the breeds and traits was a large-effect pleiotropic QTL on BTA2 that contained the MSTN gene, which was associated with all traits in the Charolais and Limousin breeds. Other plausible candidate genes were identified for muscularity traits including PDE1A, PPP1R1C and multiple collagen and HOXD genes. In addition, associated (gene ontology) GO terms and KEGG pathways tended to differ between breeds and between traits especially in the numerically smaller populations of Angus, Hereford, and Simmental breeds. Most of the SNPs that were associated with any of the traits were intergenic or intronic SNPs located within regulatory regions of the genome. CONCLUSIONS The commonality between the Charolais and Limousin breeds indicates that the genetic architecture of the muscularity traits may be similar in these breeds due to their similar origins. Conversely, there were vast differences in the QTL associated with muscularity in Angus, Hereford, and Simmental. Knowledge of these differences in genetic architecture between breeds is useful to develop accurate genomic prediction equations that can operate effectively across breeds. Overall, the associated QTL differed according to trait, which suggests that breeding for a morphologically different (e.g. longer and wider versus shorter and smaller) more efficient animal may become possible in the future.
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Affiliation(s)
- Jennifer L. Doyle
- Teagasc, Animal and Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork Ireland
- Department of Science, Waterford Institute of Technology, Cork Road, Waterford, Co. Waterford Ireland
| | - Donagh P. Berry
- Teagasc, Animal and Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork Ireland
| | - Roel F. Veerkamp
- Animal Breeding and Genomics Centre, Wageningen University and Research Centre, Livestock Research, Wageningen, The Netherlands
| | - Tara R. Carthy
- Teagasc, Animal and Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork Ireland
| | - Ross D. Evans
- Irish Cattle Breeding Federation, Bandon, Co. Cork Ireland
| | - Siobhán W. Walsh
- Department of Science, Waterford Institute of Technology, Cork Road, Waterford, Co. Waterford Ireland
| | - Deirdre C. Purfield
- Teagasc, Animal and Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork Ireland
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Berry DP, Pabiou T, Fanning R, Evans RD, Judge MM. Linear classification scores in beef cattle as predictors of genetic merit for individual carcass primal cut yields1. J Anim Sci 2019; 97:2329-2341. [PMID: 31100112 DOI: 10.1093/jas/skz138] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2019] [Accepted: 04/17/2019] [Indexed: 11/14/2022] Open
Abstract
Having access to early predictions of both the genetic merit and expected phenotypic performance of an individual or its progeny can contribute to more informed decision-making. The objective here was to evaluate the usefulness of routinely available subjectively scored linear conformation information on live animals to predict genetic merit for primal carcass cut yields of their relatives. Data on 6 muscular and 6 skeletal traits on 43,078 live animals were used; the weights of up to 14 primal cuts plus 3 groups of primal cuts of 31,827 cattle were also used. Genetic correlations between the linear scores and the primal cut weights were estimated using sire linear mixed models; correlations were estimated with or without phenotypic adjustment of the primal cut weights to a constant carcass weight. The genetic correlations between each of the muscular and skeletal linear type traits with each of the primal cut weights (not adjusted for carcass weight) were all positive with the exception of the correlations between both chest width and pelvic length with cuberoll. On average, the muscular type traits were more strongly correlated (on average 0.42) with the primal cut weights than the skeletal traits (on average 0.35). Moreover, the average of the genetic correlations between each of the 6 muscular traits with all 8 hindquarter traits was, on average, 10% to 18% stronger than the average of the genetic correlations between the same muscular traits with all 5 forequarter primal cuts. When adjusted for differences in carcass weight, the correlations between all linear scores and the carcass traits regressed to zero or became negative. The skeletal traits were, in general, weakly genetically correlated with the primal cuts adjusted to a common carcass weight. The average of the genetic correlation between the muscular type traits and the primal cuts adjusted for differences in carcass weight was only 0.09 with only 13 of the 84 pairwise correlations being stronger than 0.30; the genetic correlation between silverside with the muscular traits was all stronger than 0.30, whereas the majority of the muscular traits had a correlation stronger than 0.30 with the topside primal cut. In fact, the average of the genetic correlations between the topside and silverside cuts with all the muscular traits was 0.50 and 0.42, respectively, with none of the correlations being negative.
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Affiliation(s)
- Donagh P Berry
- Teagasc, Animal and Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland
| | - Thierry Pabiou
- ICBF, Highfield House, Shinagh, Bandon, Co.Cork, Ireland
| | - Rory Fanning
- Slaney Food International, Ryland Lower, Bunclody, Co. Wexford, Ireland
| | - Ross D Evans
- ICBF, Highfield House, Shinagh, Bandon, Co.Cork, Ireland
| | - Michelle M Judge
- Teagasc, Animal and Grassland Research and Innovation Centre, Moorepark, Fermoy, Co. Cork, Ireland
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