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Virtuoso MCS, Hosseini A, Aalhus JL, Juárez M, Bruce HL, Li C, Basarab JA, Valente TS, Plastow G. Genetic parameter estimates for sensory and meat quality traits measured at 3 and 29 days of aging of beef from Canadian crossbred cattle. Meat Sci 2024; 207:109351. [PMID: 37804588 DOI: 10.1016/j.meatsci.2023.109351] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2023] [Revised: 09/13/2023] [Accepted: 10/02/2023] [Indexed: 10/09/2023]
Abstract
Genetic parameters were estimated for objective and subjective traits assessed after 3 and 29 days aging in meat samples of 1154 commercial beef cattle. Meat attributes [Warner-Bratzler shear force (WBSF), intramuscular fat (IMF), and pH] and sensory traits [flavor intensity (FI), off-flavor (OF), connective tissue (CT), overall tenderness (OT), sustained juiciness (SJ), and overall palatability (OP)] were available. The animal mixed model used included additive genetic and residual effects as random effects, contemporary group as fixed effect and genomic breed composition and slaughter age as covariates. Genetic parameters were estimated using airemlf90 software and single-step genomic BLUP. Heritability estimates for OT (3 and 29 d), OP (3 d) and OF (29 d) were of moderate magnitude ranging from 0.18 ± 0.07 to 0.31 ± 0.07. Heritabilities were negligible or of low magnitude for all other sensory traits with values ranging from 0.03 ± 0.05 to 0.14 ± 0.07. Among objectively measured traits, the estimate of heritability for meat pH was moderate at day 3 (0.20 ± 0.08) and negligible at 29 (0.00 ± 0.05). For IMF and WBSF the heritability estimates were 0.43 ± 0.09 and 0.54 ± 0.09, and 0.22 ± 0.07 and 0.19 ± 0.07 for day 3 and 29, respectively. Genetic correlations between days for each sensory trait tended to be of high and positive magnitude ranging from 0.54 ± 0.60 to 0.99 ± 0.28. Genetic and phenotypic correlations of subjectively assessed traits were consistent in direction and magnitude with WBSF (negative) and IMF (positive) suggesting that genetic selection based on objectively measured traits can be used for meat quality improvement and to increase consumer satisfaction. In addition, selection can be implemented using sensory traits collected after 3 days of aging.
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Affiliation(s)
- Marcos Claudio S Virtuoso
- UNESP, Universidade Estadual Paulista, Faculdade de Ciências Agrárias e Veterinárias, Programa de Pós-graduação em Agronomia (Genética e Melhoramento de Plantas), Jaboticabal, SP, Brazil; Department of Agricultural, Food and Nutritional Sciences, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Anahid Hosseini
- Department of Agricultural, Food and Nutritional Sciences, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Jennifer L Aalhus
- Lacombe Research Centre, Agriculture and Agri-Food Canada, 6000 C & E Trail, Lacombe, Alberta T4L 1W1, Canada
| | - Manuel Juárez
- Lacombe Research Centre, Agriculture and Agri-Food Canada, 6000 C & E Trail, Lacombe, Alberta T4L 1W1, Canada
| | - Heather L Bruce
- Department of Agricultural, Food and Nutritional Sciences, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Changxi Li
- Department of Agricultural, Food and Nutritional Sciences, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada; Lacombe Research Centre, Agriculture and Agri-Food Canada, 6000 C & E Trail, Lacombe, Alberta T4L 1W1, Canada
| | - John A Basarab
- Department of Agricultural, Food and Nutritional Sciences, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Tiago S Valente
- Department of Agricultural, Food and Nutritional Sciences, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada.
| | - Graham Plastow
- Department of Agricultural, Food and Nutritional Sciences, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada.
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Li J, Wang Y, Mukiibi R, Karisa B, Plastow GS, Li C. Integrative analyses of genomic and metabolomic data reveal genetic mechanisms associated with carcass merit traits in beef cattle. Sci Rep 2022; 12:3389. [PMID: 35232965 PMCID: PMC8888742 DOI: 10.1038/s41598-022-06567-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Accepted: 02/01/2022] [Indexed: 11/09/2022] Open
Abstract
Improvement of carcass merit traits is a priority for the beef industry. Discovering DNA variants and genes associated with variation in these traits and understanding biological functions/processes underlying their associations are of paramount importance for more effective genetic improvement of carcass merit traits in beef cattle. This study integrates 10,488,742 imputed whole genome DNA variants, 31 plasma metabolites, and animal phenotypes to identify genes and biological functions/processes that are associated with carcass merit traits including hot carcass weight (HCW), rib eye area (REA), average backfat thickness (AFAT), lean meat yield (LMY), and carcass marbling score (CMAR) in a population of 493 crossbred beef cattle. Regression analyses were performed to identify plasma metabolites associated with the carcass merit traits, and the results showed that 4 (3-hydroxybutyric acid, acetic acid, citric acid, and choline), 6 (creatinine, L-glutamine, succinic acid, pyruvic acid, L-lactic acid, and 3-hydroxybutyric acid), 4 (fumaric acid, methanol, D-glucose, and glycerol), 2 (L-lactic acid and creatinine), and 5 (succinic acid, fumaric acid, lysine, glycine, and choline) plasma metabolites were significantly associated with HCW, REA, AFAT, LMY, and CMAR (P-value < 0.1), respectively. Combining the results of metabolome-genome wide association studies using the 10,488,742 imputed SNPs, 103, 160, 83, 43, and 109 candidate genes were identified as significantly associated with HCW, REA, AFAT, LMY, and CMAR (P-value < 1 × 10-5), respectively. By applying functional enrichment analyses for candidate genes of each trait, 26, 24, 26, 24, and 28 significant cellular and molecular functions were predicted for HCW, REA, AFAT, LMY, and CMAR, respectively. Among the five topmost significantly enriched biological functions for carcass merit traits, molecular transport and small molecule biochemistry were two top biological functions associated with all carcass merit traits. Lipid metabolism was the most significant biological function for LMY and CMAR and it was also the second and fourth highest biological function for REA and HCW, respectively. Candidate genes and enriched biological functions identified by the integrative analyses of metabolites with phenotypic traits and DNA variants could help interpret the results of previous genome-wide association studies for carcass merit traits. Our integrative study also revealed additional potential novel genes associated with these economically important traits. Therefore, our study improves understanding of the molecular and biological functions/processes that influence carcass merit traits, which could help develop strategies to enhance genomic prediction of carcass merit traits with incorporation of metabolomic data. Similarly, this information could guide management practices, such as nutritional interventions, with the purpose of boosting specific carcass merit traits.
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Affiliation(s)
- Jiyuan Li
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Yining Wang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.,Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada
| | - Robert Mukiibi
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Scotland, UK
| | - Brian Karisa
- Results Driven Agriculture Research, Edmonton, AB, Canada
| | - Graham S Plastow
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.
| | - Changxi Li
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada. .,Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada.
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Li J, Mukiibi R, Wang Y, Plastow GS, Li C. Identification of candidate genes and enriched biological functions for feed efficiency traits by integrating plasma metabolites and imputed whole genome sequence variants in beef cattle. BMC Genomics 2021; 22:823. [PMID: 34781903 PMCID: PMC8591823 DOI: 10.1186/s12864-021-08064-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Accepted: 10/07/2021] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND Feed efficiency is one of the key determinants of beef industry profitability and sustainability. However, the cellular and molecular background behind feed efficiency is largely unknown. This study combines imputed whole genome DNA variants and 31 plasma metabolites to dissect genes and biological functions/processes that are associated with residual feed intake (RFI) and its component traits including daily dry matter intake (DMI), average daily gain (ADG), and metabolic body weight (MWT) in beef cattle. RESULTS Regression analyses between feed efficiency traits and plasma metabolites in a population of 493 crossbred beef cattle identified 5 (L-valine, lysine, L-tyrosine, L-isoleucine, and L-leucine), 4 (lysine, L-lactic acid, L-tyrosine, and choline), 1 (citric acid), and 4 (L-glutamine, glycine, citric acid, and dimethyl sulfone) plasma metabolites associated with RFI, DMI, ADG, and MWT (P-value < 0.1), respectively. Combining the results of metabolome-genome wide association studies using 10,488,742 imputed SNPs, 40, 66, 15, and 40 unique candidate genes were identified as associated with RFI, DMI, ADG, and MWT (P-value < 1 × 10-5), respectively. These candidate genes were found to be involved in some key metabolic processes including metabolism of lipids, molecular transportation, cellular function and maintenance, cell morphology and biochemistry of small molecules. CONCLUSIONS This study identified metabolites, candidate genes and enriched biological functions/processes associated with RFI and its component traits through the integrative analyses of metabolites with phenotypic traits and DNA variants. Our findings could enhance the understanding of biochemical mechanisms of feed efficiency traits and could lead to improvement of genomic prediction accuracy via incorporating metabolite data.
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Affiliation(s)
- Jiyuan Li
- Department of Agriculture, Food & Nutritional Science, University of Alberta, T6G 2P5, Edmonton, Alberta, Canada
| | - Robert Mukiibi
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, Scotland, UK
| | - Yining Wang
- Department of Agriculture, Food & Nutritional Science, University of Alberta, T6G 2P5, Edmonton, Alberta, Canada
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, 6000 C&E Trail, Alberta, T4L 1W1, Lacombe, Canada
| | - Graham S Plastow
- Department of Agriculture, Food & Nutritional Science, University of Alberta, T6G 2P5, Edmonton, Alberta, Canada.
| | - Changxi Li
- Department of Agriculture, Food & Nutritional Science, University of Alberta, T6G 2P5, Edmonton, Alberta, Canada.
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, 6000 C&E Trail, Alberta, T4L 1W1, Lacombe, Canada.
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Zamorano-Algandar R, Sánchez-Castro MA, Hernández-Cordero AI, Enns RM, Speidel SE, Thomas MG, Medrano JF, Rincón G, Leyva-Corona JC, Luna-Nevárez G, Reyna-Granados JR, Luna-Nevárez P. Molecular marker prediction for days open and pregnancy rate in Holstein cows managed in a warm climate. Livest Sci 2021. [DOI: 10.1016/j.livsci.2021.104536] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
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5
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Li J, Akanno EC, Valente TS, Abo-Ismail M, Karisa BK, Wang Z, Plastow GS. Genomic Heritability and Genome-Wide Association Studies of Plasma Metabolites in Crossbred Beef Cattle. Front Genet 2020; 11:538600. [PMID: 33193612 PMCID: PMC7542097 DOI: 10.3389/fgene.2020.538600] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2020] [Accepted: 09/01/2020] [Indexed: 11/16/2022] Open
Abstract
Metabolites, substrates or products of metabolic processes, are involved in many biological functions, such as energy metabolism, signaling, stimulatory and inhibitory effects on enzymes and immunological defense. Metabolomic phenotypes are influenced by combination of genetic and environmental effects allowing for metabolome-genome-wide association studies (mGWAS) as a powerful tool to investigate the relationship between these phenotypes and genetic variants. The objectives of this study were to estimate genomic heritability and perform mGWAS and in silico functional enrichment analyses for a set of plasma metabolites in Canadian crossbred beef cattle. Thirty-three plasma metabolites and 45,266 single nucleotide polymorphisms (SNPs) were available for 475 animals. Genomic heritability for all metabolites was estimated using genomic best linear unbiased prediction (GBLUP) including genomic breed composition as covariates in the model. A single-step GBLUP implemented in BLUPF90 programs was used to determine SNP P values and the proportion of genetic variance explained by SNP windows containing 10 consecutive SNPs. The top 10 SNP windows that explained the largest genetic variation for each metabolite were identified and mapped to detect corresponding candidate genes. Functional enrichment analyses were performed on metabolites and their candidate genes using the Ingenuity Pathway Analysis software. Eleven metabolites showed low to moderate heritability that ranged from 0.09 ± 0.15 to 0.36 ± 0.15, while heritability estimates for 22 metabolites were zero or negligible. This result indicates that while variations in 11 metabolites were due to genetic variants, the majority are largely influenced by environment. Three significant SNP associations were detected for betaine (rs109862186), L-alanine (rs81117935), and L-lactic acid (rs42009425) based on Bonferroni correction for multiple testing (family wise error rate <0.05). The SNP rs81117935 was found to be located within the Catenin Alpha 2 gene (CTNNA2) showing a possible association with the regulation of L-alanine concentration. Other candidate genes were identified based on additive genetic variance explained by SNP windows of 10 consecutive SNPs. The observed heritability estimates and the candidate genes and networks identified in this study will serve as baseline information for research into the utilization of plasma metabolites for genetic improvement of crossbred beef cattle.
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Affiliation(s)
- Jiyuan Li
- Livestock Gentec, Department of Agriculture, Food and Nutritional Science, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Everestus C Akanno
- Livestock Gentec, Department of Agriculture, Food and Nutritional Science, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Tiago S Valente
- Livestock Gentec, Department of Agriculture, Food and Nutritional Science, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada.,Department of Animal Science, Ethology and Animal Ecology Research Group, São Paulo State University, Jaboticabal, Brazil
| | - Mohammed Abo-Ismail
- Livestock Gentec, Department of Agriculture, Food and Nutritional Science, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada.,Department of Animal Science, College of Agriculture, Food and Environmental Sciences, California Polytechnic State University, San Luis Obispo, CA, United States
| | - Brian K Karisa
- Ministry of Agriculture and Forestry, Edmonton, AB, Canada
| | - Zhiquan Wang
- Livestock Gentec, Department of Agriculture, Food and Nutritional Science, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
| | - Graham S Plastow
- Livestock Gentec, Department of Agriculture, Food and Nutritional Science, Faculty of Agricultural, Life and Environmental Sciences, University of Alberta, Edmonton, AB, Canada
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6
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Wang Y, Zhang F, Mukiibi R, Chen L, Vinsky M, Plastow G, Basarab J, Stothard P, Li C. Genetic architecture of quantitative traits in beef cattle revealed by genome wide association studies of imputed whole genome sequence variants: II: carcass merit traits. BMC Genomics 2020; 21:38. [PMID: 31931697 PMCID: PMC6958779 DOI: 10.1186/s12864-019-6273-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 11/12/2019] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Genome wide association studies (GWAS) were conducted on 7,853,211 imputed whole genome sequence variants in a population of 3354 to 3984 animals from multiple beef cattle breeds for five carcass merit traits including hot carcass weight (HCW), average backfat thickness (AFAT), rib eye area (REA), lean meat yield (LMY) and carcass marbling score (CMAR). Based on the GWAS results, genetic architectures of the carcass merit traits in beef cattle were elucidated. RESULTS The distributions of DNA variant allele substitution effects approximated a bell-shaped distribution for all the traits while the distribution of additive genetic variances explained by single DNA variants conformed to a scaled inverse chi-squared distribution to a greater extent. At a threshold of P-value < 10-5, 51, 33, 46, 40, and 38 lead DNA variants on multiple chromosomes were significantly associated with HCW, AFAT, REA, LMY, and CMAR, respectively. In addition, lead DNA variants with potentially large pleiotropic effects on HCW, AFAT, REA, and LMY were found on chromosome 6. On average, missense variants, 3'UTR variants, 5'UTR variants, and other regulatory region variants exhibited larger allele substitution effects on the traits in comparison to other functional classes. The amounts of additive genetic variance explained per DNA variant were smaller for intergenic and intron variants on all the traits whereas synonymous variants, missense variants, 3'UTR variants, 5'UTR variants, downstream and upstream gene variants, and other regulatory region variants captured a greater amount of additive genetic variance per sequence variant for one or more carcass merit traits investigated. In total, 26 enriched cellular and molecular functions were identified with lipid metabolisms, small molecular biochemistry, and carbohydrate metabolism being the most significant for the carcass merit traits. CONCLUSIONS The GWAS results have shown that the carcass merit traits are controlled by a few DNA variants with large effects and many DNA variants with small effects. Nucleotide polymorphisms in regulatory, synonymous, and missense functional classes have relatively larger impacts per sequence variant on the variation of carcass merit traits. The genetic architecture as revealed by the GWAS will improve our understanding on genetic controls of carcass merit traits in beef cattle.
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Affiliation(s)
- Yining Wang
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB Canada
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB Canada
| | - Feng Zhang
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB Canada
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB Canada
- State Key Laboratory for Swine Genetics, Breeding and Production Technology, Jiangxi Agricultural University, Nanchang, Jiangxi China
- Present Address: Institute of Translational Medicine, Nanchang University, Nanchang, Jiangxi China
| | - Robert Mukiibi
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB Canada
| | - Liuhong Chen
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB Canada
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB Canada
| | - Michael Vinsky
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB Canada
| | - Graham Plastow
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB Canada
| | - John Basarab
- Alberta Agriculture and Forestry, Lacombe Research and Development Centre, 6000 C&E Trail, Lacombe, AB Canada
| | - Paul Stothard
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB Canada
| | - Changxi Li
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, Lacombe, AB Canada
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB Canada
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Zhu B, Guo P, Wang Z, Zhang W, Chen Y, Zhang L, Gao H, Wang Z, Gao X, Xu L, Li J. Accuracies of genomic prediction for twenty economically important traits in Chinese Simmental beef cattle. Anim Genet 2019; 50:634-643. [PMID: 31502261 PMCID: PMC6900049 DOI: 10.1111/age.12853] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/31/2019] [Indexed: 12/12/2022]
Abstract
Genomic prediction has been widely utilized to estimate genomic breeding values (GEBVs) in farm animals. In this study, we conducted genomic prediction for 20 economically important traits including growth, carcass and meat quality traits in Chinese Simmental beef cattle. Five approaches (GBLUP, BayesA, BayesB, BayesCπ and BayesR) were used to estimate the genomic breeding values. The predictive accuracies ranged from 0.159 (lean meat percentage estimated by BayesCπ) to 0.518 (striploin weight estimated by BayesR). Moreover, we found that the average predictive accuracies across 20 traits were 0.361, 0.361, 0.367, 0.367 and 0.378, and the averaged regression coefficients were 0.89, 0.86, 0.89, 0.94 and 0.95 for GBLUP, BayesA, BayesB, BayesCπ and BayesR respectively. The genomic prediction accuracies were mostly moderate and high for growth and carcass traits, whereas meat quality traits showed relatively low accuracies. We concluded that Bayesian regression approaches, especially for BayesR and BayesCπ, were slightly superior to GBLUP for most traits. Increasing with the sizes of reference population, these two approaches are feasible for future application of genomic selection in Chinese beef cattle.
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Affiliation(s)
- B Zhu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,National Centre of Beef Cattle Genetic Evaluation, Beijing, 100193, China
| | - P Guo
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,College of Computer and Information Engineering, Tianjin Agricultural University, Tianjin, 300384, China
| | - Z Wang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - W Zhang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Y Chen
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - L Zhang
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - H Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,National Centre of Beef Cattle Genetic Evaluation, Beijing, 100193, China
| | - Z Wang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2R3, Canada
| | - X Gao
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - L Xu
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - J Li
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.,National Centre of Beef Cattle Genetic Evaluation, Beijing, 100193, China
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Akanno EC, Ekine-Dzivenu C, Chen L, Vinsky M, Abo-Ismail MK, MacNeil MD, Plastow G, Basarab J, Li C, Fitzsimmons C. Evaluation of a genomic-enhanced sorting system for feeder cattle1. J Anim Sci 2019; 97:1066-1075. [PMID: 30821333 DOI: 10.1093/jas/skz026] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2018] [Accepted: 01/23/2019] [Indexed: 11/13/2022] Open
Abstract
This study evaluated the use of molecular breeding values (MBVs) for carcass traits to sort steers into quality grid and lean meat yield (LMY) groups. A discovery set of 2,609 animals with genotypes and carcass phenotypes was used to predict MBVs for LMY and marbling score (MBS) for 299 Angus, 181 Charolais, and 638 Kinsella Composite steers using genomic best linear unbiased prediction. Steers were sorted in silico into four MBV groups namely Quality (with MBVs greater than the mean for LMY and MBS), Lean (with MBVs greater than the mean for LMY but less than or equal to the mean for MBS), Marbling (with MBVs greater than the mean for MBS but less than or equal to the mean for LMY), and Other (with MBVs lower than the mean for LMY and MBS). Carcass phenotypes on the steers were then collected at slaughter and evaluated for consistency with the assigned MBV groups using descriptive statistics and least square analysis. Accuracy of MBV predictions was assessed by Pearson's correlation between predicted MBV and adjusted phenotype divided by the square root of trait heritability. Genomic breed compositions were predicted for all steers to correct for possible population stratification and breed effects in the test model. The number of steers that met the expected carcass outcome was counted to produce actual percentages for each MBV group. Results showed that on average, Quality and Marbling groups had greater back-fat and more marbling across the three populations while Lean group had leaner carcasses. Carcass weights were similar across MBV groups. Within MBV groups, decreases in variability were observed for most traits suggesting improvement in carcass uniformity. Greater than 70% of the steers in Quality, Lean, and Marbling groups met the Quality Grid and Y1-LMY target for Angus and Charolais but not for Kinsella composite. The accuracy of MBV prediction ranged from 0.43 to 0.59 indicating that up to 35% of the observed carcass trait variability can be predicted, which suggests utility of MBV as a marker-assisted management tool to sort feeder cattle into uniform carcass endpoint groups under similar environmental and management conditions. Further investigation is warranted to evaluate the performance of feeder cattle sorted based on MBV and managed for different carcass endpoints as well as the cost-benefit implications for feedlot operations.
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Affiliation(s)
- Everestus C Akanno
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Chinyere Ekine-Dzivenu
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Liuhong Chen
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Michael Vinsky
- Agriculture and Agri-Food Canada, Lacombe Research and Development Centre, Lacombe, AB, Canada
| | - Mohammed K Abo-Ismail
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.,Department of Animal and Poultry Production, Damanhour University, Damanhour, Egypt
| | - Michael D MacNeil
- University of the Free State, South Africa and Delta G 145 Ice Cave Road, Miles City, Montana
| | - Graham Plastow
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - John Basarab
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.,Alberta Agriculture and Forestry, Lacombe Research and Development Centre, Lacombe, AB, Canada
| | - Changxi Li
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.,Agriculture and Agri-Food Canada, Lacombe Research and Development Centre, Lacombe, AB, Canada
| | - Carolyn Fitzsimmons
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.,Agriculture and Agri-Food Canada, Lacombe Research and Development Centre, Lacombe, AB, Canada
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9
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Genomic selection for meat quality traits in Nelore cattle. Meat Sci 2019; 148:32-37. [DOI: 10.1016/j.meatsci.2018.09.010] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2017] [Revised: 09/11/2018] [Accepted: 09/17/2018] [Indexed: 11/24/2022]
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10
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Basarab J, Crowley J, Abo-Ismail M, Manafiazar G, Akanno E, Baron V, Plastow G. Genomic retained heterosis effects on fertility and lifetime productivity in beef heifers. CANADIAN JOURNAL OF ANIMAL SCIENCE 2018. [DOI: 10.1139/cjas-2017-0192] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
This study evaluated the effects of three genomic indicators of heterosis on female fertility and lifetime productivity, and quantified changes over 11 production cycles in a crossbred cow herd. Pedigree-based breed composition (pBC) was determined and used to calculate retained heterozygosity for 412 replacement heifers born from 2004 to 2014 at the Lacombe Research and Development Centre (AB, Canada). Heifers were followed as cows over 1050 mating opportunities, 11 production cycles, and five parities. Heifers and their sires (51) were genotyped and these genotypes were used to predict each animal’s genomic breed composition (gBC) and three genomic indicators of heterosis: (1) retained heterozygosity (RHETg), (2) heterozygous proportion (H), and (3) retained heterosis (RHg). Correlations between pedigree and genomic breed fractions for Angus, Hereford, and Charolais were high (rp = 0.74–0.94; P < 0.001). Genomic indicators of heterosis were highly related (rp = 0.61 for RHETg vs. H; 0.71 for RHg vs. H; 0.96 for RHETg vs. RHg; P < 0.001). Each 10% change in RHETg resulted in 51 ± 20 d longer survival (P = 0.011) in the herd and 35.7 ± 15.2 kg more (P = 0.019) calf wean weight per cow exposed to breeding when summed over five parities. These differences resulted in an extra $161 per heifer in a year. Optimizing heterosis using genomic tools can be very beneficial for the cow herd if applied correctly.
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Affiliation(s)
- J.A. Basarab
- Alberta Agriculture and Forestry, Lacombe Research and Development Centre, 6000 C & E Trail, Lacombe, AB T4L 1W1, Canada
- Livestock Gentec, University of Alberta, 1400 College Plaza, 8215-112st NW, Edmonton, AB T6G 2C8, Canada
| | - J.J. Crowley
- Livestock Gentec, University of Alberta, 1400 College Plaza, 8215-112st NW, Edmonton, AB T6G 2C8, Canada
- Canadian Beef Breeds Council, 292140 Wagon Wheel Blvd, Rocky View county, AB T4A 0E2, Canada
| | - M.K. Abo-Ismail
- Livestock Gentec, University of Alberta, 1400 College Plaza, 8215-112st NW, Edmonton, AB T6G 2C8, Canada
- Department of Animal and Poultry Production, Damanhour University, Damanhour, Egypt
| | - G.M. Manafiazar
- Livestock Gentec, University of Alberta, 1400 College Plaza, 8215-112st NW, Edmonton, AB T6G 2C8, Canada
| | - E.C. Akanno
- Livestock Gentec, University of Alberta, 1400 College Plaza, 8215-112st NW, Edmonton, AB T6G 2C8, Canada
| | - V.S. Baron
- Agriculture and Agri-Food Canada, Lacombe Research and Development Centre, 6000 C & E Trail, Lacombe, AB T4L 1W1, Canada
| | - G. Plastow
- Livestock Gentec, University of Alberta, 1400 College Plaza, 8215-112st NW, Edmonton, AB T6G 2C8, Canada
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Ekine-Dzivenu C, Vinsky M, Basarab JA, Aalhus JL, Dugan MER, Li C. Phenotypic and genetic correlations of fatty acid composition in subcutaneous adipose tissue with carcass merit and meat tenderness traits in Canadian beef cattle. J Anim Sci 2017; 95:5184-5196. [PMID: 29293784 PMCID: PMC6292258 DOI: 10.2527/jas2017.1966] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2017] [Accepted: 09/20/2017] [Indexed: 01/11/2023] Open
Abstract
Bivariate animal models were used to estimate phenotypic and genetic correlations between 9 carcass merit and meat tenderness traits with 25 individual and grouped fatty acids in the subcutaneous adipose tissue of a population of 1,366 Canadian beef cattle finishing heifers and steers. In general, phenotypic correlations were low (<0.25 in magnitude) except for moderate phenotypic correlations of 9-17:1 (-0.29 ± 0.16), 18:0 (0.26 ± 0.14), 11-18:1 (-0.33 ± 0.15), 11-18:1 (0.35 ± 0.14) with Warner-Bratzler shear force measured 3 d postmortem and between 14:0 (-0.36 ± 0.1), 9-14:1 (-0.34 ± 0.08), 9-16:1 (-0.36 ± 0.08), 9-18:1 (0.26 ± 0.07), and sum of branched-chain fatty acids (BCFA; -0.27 ± 0.06) and back fat thickness (BFAT). Genetic correlations were also low for most of the traits. However, moderate to moderately high genetic correlations (0.25 to 0.50 in magnitude) were detected for some traits, including 17:0 (0.4 ± 0.11), 18:0 (0.44 ± 0.12), 9-14:1 (-0.47 ± 0.11), 9-16:1 (-0.43 ± 0.11), and the -6:-3 PUFA ratio (-0.5 ± 0.15) with HCW; 9-14:1 (-0.41 ± 0.13) and 9-16:1 (-0.42 ± 0.13) with BFAT; 17:0 (0.43 ± 0.19) and BCFA (0.45 ± 0.19) with lean meat yield; 13-18:1 (0.40 ± 0.15) with carcass marbling score; sum of CLA (0.45 ± 0.22), 18:2-6 (0.47 ± 0.17), and sum of PUFA (0.48 ± 0.17) with overall tenderness measured 3 d postmortem; the -6:-3 PUFA ratio (0.41 ± 0.22) and sum of CLA (0.42 ± 0.25) with overall tenderness measured 29 d postmortem; and BCFA (0.41 ± 0.27) with Warner-Bratzler shear force measured 29 d postmortem. The genetic correlations observed in this study suggest that contents of some fatty acids in beef tissue and carcass merit and meat tenderness traits are likely influenced by a subset of the same genes in beef cattle. Due to some antagonistic genetic correlations, multiple-trait economic indexes are recommended when fatty acid composition, carcass merit, and meat tenderness traits are included in the breeding objective.
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Casiró S, Velez-Irizarry D, Ernst CW, Raney NE, Bates RO, Charles MG, Steibel JP. Genome-wide association study in an F2 Duroc x Pietrain resource population for economically important meat quality and carcass traits. J Anim Sci 2017; 95:545-558. [PMID: 28380601 DOI: 10.2527/jas.2016.1003] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Meat quality is essential for consumer acceptance, it ultimately impacts pork production profitability and it is subject to genetic control. The objective of this study was to map genomic regions associated with economically important meat quality and carcass traits. We performed a genome-wide association (GWA) analysis to map regions associated with 38 meat quality and carcass traits recorded for 948 F2 pigs from the Michigan State University Duroc × Pietrain resource population. The F0, F1, and 336 F2 pigs were genotyped with the Illumina Porcine SNP60 BeadChip, while the remaining F2 pigs were genotyped with the GeneSeek Genomic Profiler for Porcine Low Desnisty (LD) chip, and imputed with high accuracy ( = 0.97). Altogether the genomic dataset comprised 1,019 animals and 44,911 SNP. A Gaussian linear mixed model was fitted to estimate the breeding values and the variance components. A linear transformation was performed to estimate the marker effects and variances. Type I error rate was controlled at a False Discovery Rate of 5%. Seven putative QTL found in this study were previously reported in other studies. Two novel QTL associated with tenderness (TEN) were located on SSC3 [135.6:137.5Mb; False Discovery rate (FDR) < 0.03] and SSC5 (67.3:69.1Mb; FDR < 0.02). The QTL region identified on SSC15 includes Protein Kinase AMP-activated ɣ 3-subunit gene (), which has been associated with 24-h pH (pH24), drip loss (DL) and cook yield (CY). Also, novel candidate genes were identified for TEN in the region on SSC5 [A Kinase (PRKA) Anchor Protein 3 (], and for tenth rib backfat thickness (BF10) [Carnitine O-Acetyltransferase ()] on SSC1. The association of gene polymorphisms with pork quality traits has been reported for several pig populations. However, there are no SNP for this gene on the chip used, thus we genotyped the animals for 2 non-synonymous variants ( and ). We then performed a GWA conditioning on the genotype of both SNP and was associated with pH24, DL, protein content (PRO) and CY ( < 0.004) and T30N with Juiciness, TEN, shear force, pH24, PRO, and CY < 0.04). Finally, we performed a GWA conditioning on the genotype of the SNP peak detected in this study, and T30N remained associated only with PRO ( < 0.02). Therefore, in this study we identified 2 novel QTL regions, suggest 2 novel candidate genes, and conclude that other SNP in PRKAG3 or nearby gene(s) explain the observed associations on SSC15 in this population.
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Affiliation(s)
- P.E. Strydom
- Agriculture Research Council–Animal Production Institute, Private Bag X2, Irene, 0062, South Africa
- Department of Animal Sciences, Stellenbosch University, Private Bag X1 Matieland, 7602, South Africa
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Bernal Rubio YL, Gualdrón Duarte JL, Bates RO, Ernst CW, Nonneman D, Rohrer GA, King DA, Shackelford SD, Wheeler TL, Cantet RJC, Steibel JP. Implementing meta-analysis from genome-wide association studies for pork quality traits. J Anim Sci 2016; 93:5607-17. [PMID: 26641170 DOI: 10.2527/jas.2015-9502] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Pork quality plays an important role in the meat processing industry. Thus, different methodologies have been implemented to elucidate the genetic architecture of traits affecting meat quality. One of the most common and widely used approaches is to perform genome-wide association (GWA) studies. However, a limitation of many GWA in animal breeding is the limited power due to small sample sizes in animal populations. One alternative is to implement a meta-analysis of GWA (MA-GWA) combining results from independent association studies. The objective of this study was to identify significant genomic regions associated with meat quality traits by performing MA-GWA for 8 different traits in 3 independent pig populations. Results from MA-GWA were used to search for genes possibly associated with the set of evaluated traits. Data from 3 pig data sets (U.S. Meat Animal Research Center, commercial, and Michigan State University Pig Resource Population) were used. A MA was implemented by combining -scores derived for each SNP in every population and then weighting them using the inverse of estimated variance of SNP effects. A search for annotated genes retrieved genes previously reported as candidates for shear force (calpain-1 catalytic subunit [] and calpastatin []), as well as for ultimate pH, purge loss, and cook loss (protein kinase, AMP-activated, γ 3 noncatalytic subunit []). In addition, novel candidate genes were identified for intramuscular fat and cook loss (acyl-CoA synthetase family member 3 mitochondrial []) and for the objective measure of muscle redness, CIE a* (glycogen synthase 1, muscle [] and ferritin, light polypeptide []). Thus, implementation of MA-GWA allowed integration of results for economically relevant traits and identified novel genes to be tested as candidates for meat quality traits in pig populations.
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Meuwissen T, Hayes B, Goddard M. Genomic selection: A paradigm shift in animal breeding. Anim Front 2016. [DOI: 10.2527/af.2016-0002] [Citation(s) in RCA: 223] [Impact Index Per Article: 27.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Affiliation(s)
| | - Ben Hayes
- Department of Economic Development, Jobs, Transport and Resources and Dairy Futures Cooperative Research Centre, Agribio, 5 Ring Road, Bundoora, VIC 3083, Australia; School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083, Australia
| | - Mike Goddard
- Department of Economic Development, Jobs, Transport and Resources and Dairy Futures Cooperative Research Centre, Agribio, 5 Ring Road, Bundoora, VIC 3083, Australia; Faculty of veterinary and agricultural sciences, University of Melbourne, Parkville, Australia
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16
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Thompson NM, DeVuyst EA, Brorsen BW, Lusk JL. Yield and quality grade outcomes as affected by molecular breeding values for commercial beef cattle1. J Anim Sci 2015; 93:2045-55. [DOI: 10.2527/jas.2014-8511] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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