1
|
Lei H, Yang T, Mahmood S, Abo-Ismail M, Roy BC, Li C, Plastow GS, Bruce HL. A genome-wide case-control association study of dark cutting in beef cattle. CANADIAN JOURNAL OF ANIMAL SCIENCE 2021. [DOI: 10.1139/cjas-2019-0039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The genetic architecture of dark cutting was investigated with a case-control genome-wide association study on two groups of beef cattle analyzed separately and together (combined group). Groups I (n = 64) and II (n = 150) were genotyped using the 70K GeneSeek Genomic Profiler for Beef Cattle-HD and the 50K Illumina BovineSNP50v2 BeadChip, respectively. Dark cutting was analyzed as a binary trait (case versus control) using logistic regression in an additive model implemented in PLINK version 1.9. Significant loci were not identified when correcting for multiple testing (false discovery rate), suggesting that the trait is not controlled by genes with big effects, or the sample size was not large enough to detect these major genes. Regions harbouring single-nucleotide polymorphisms (SNPs) with a raw p < 0.01 using 1 MB window were analyzed for gene function using the ingenuity pathway analysis. For groups I, II, and the combined group, 449, 301, and 191 SNPs were identified, respectively. Genes identified were involved in pyruvic acid modification and release, 2-deoxyglucose clearance and disposal, sucrose recognition, energy production, and metabolism of carbohydrate. Although detected SNP associations require validation in a large population, results suggested the possibility for marker-assisted or genomic selection of beef cattle to reduce dark cutting.
Collapse
Affiliation(s)
- Huaigang Lei
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Tianfu Yang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Shahid Mahmood
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Mohammed Abo-Ismail
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
- Department of Animal Science, California Polytechnic State University, San Luis Obispo, CA 93407, USA
| | - Bimol C. Roy
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Changxi Li
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
- Agriculture and Agri-Food Canada, Lacombe Research and Development Centre, 6000 C&E Trail, Lacombe, AB T4L 1W1, Canada
| | - Graham S. Plastow
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Heather L. Bruce
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| |
Collapse
|
2
|
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.
Collapse
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
| |
Collapse
|
3
|
Akanno EC, Abo-Ismail MK, Chen L, Crowley JJ, Wang Z, Li C, Basarab JA, MacNeil MD, Plastow GS. Modeling heterotic effects in beef cattle using genome-wide SNP-marker genotypes. J Anim Sci 2018; 96:830-845. [PMID: 29373745 DOI: 10.1093/jas/skx002] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2017] [Accepted: 11/30/2017] [Indexed: 12/18/2022] Open
Abstract
An objective of commercial beef cattle crossbreeding programs is to simultaneously optimize use of additive (breed differences) and non-additive (heterosis) effects. A total of 6,794 multibreed and crossbred beef cattle with phenotype and Illumina BovineSNP50 genotype data were used to predict genomic heterosis for growth and carcass traits by applying two methods assumed to be linearly proportional to heterosis. The methods were as follows: 1) retained heterozygosity predicted from genomic breed fractions (HET1) and 2) deviation of adjusted crossbred phenotype from midparent value (HET2). Comparison of methods was based on prediction accuracy from cross-validation. Here, a mutually exclusive random sampling of all crossbred animals (n = 5,327) was performed to form five groups replicated five times with approximately 1,065 animals per group. In each run within a replicate, one group was assigned as a validation set, while the remaining four groups were combined to form the reference set. The phenotype of the animals in the validation set was assumed to be unknown; thus, it resulted in every animal having heterosis values that were predicted without using its own phenotype, allowing their adjusted phenotype to be used for validation. The same approach was used to test the impact of predicted heterosis on accuracy of genomic breeding values (GBV). The results showed positive heterotic effects for growth traits but not for carcass traits that reflect the importance of heterosis for growth traits in beef cattle. Heterosis predicted by HET1 method resulted in less variable estimates that were mostly within the range of estimates generated by HET2. Prediction accuracy was greater for HET2 (0.37-0.98) than HET1 (0.34-0.43). Proper consideration of heterosis in genomic evaluation models has debatable effects on accuracy of EBV predictions. However, opportunity exists for predicting heterosis, improving accuracy of genomic selection, and consequently optimizing crossbreeding programs in beef cattle.
Collapse
Affiliation(s)
- Everestus C Akanno
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, 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
| | - Liuhong Chen
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - John J Crowley
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.,Canadian Beef Breeds Council, Calgary, AB, Canada
| | - Zhiquan Wang
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Changxi Li
- Livestock Gentec, 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
| | - John A Basarab
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.,Lacombe Research Centre, Alberta Agriculture and Forestry, Lacombe, AB, Canada
| | - Michael D MacNeil
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada.,Delta G, Miles City, MT, USA.,Department of Animal, Wildlife and Grassland Sciences, University Free State, Bloemfontein, South Africa
| | - Graham S Plastow
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| |
Collapse
|