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Abo-Ismail MK, Lansink N, Akanno E, Karisa BK, Crowley JJ, Moore SS, Bork E, Stothard P, Basarab JA, Plastow GS. Development and validation of a small SNP panel for feed efficiency in beef cattle. J Anim Sci 2018; 96:375-397. [PMID: 29390120 DOI: 10.1093/jas/sky020] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2017] [Accepted: 01/17/2018] [Indexed: 12/11/2022] Open
Abstract
The objective of this study was to develop and validate a customized cost-effective single nucleotide polymorphism (SNP) panel for genetic improvement of feed efficiency in beef cattle. The SNPs identified in previous association studies and through extensive analysis of candidate genomic regions and genes, were screened for their functional impact and allele frequency in Angus and Hereford breeds used as validation candidates for the panel. Association analyses were performed on genotypes of 159 SNPs from new samples of Angus (n = 160), Hereford (n = 329), and Angus-Hereford crossbred (n = 382) cattle using allele substitution and genotypic models in ASReml. Genomic heritabilities were estimated for feed efficiency traits using the full set of SNPs, SNPs associated with at least one of the traits (at P ≤ 0.05 and P < 0.10), as well as the Illumina bovine 50K representing a widely used commercial genotyping panel. A total of 63 SNPs within 43 genes showed association (P ≤ 0.05) with at least one trait. The minor alleles of SNPs located in the GHR and CAST genes were associated with decreasing effects on residual feed intake (RFI) and/or RFI adjusted for backfat (RFIf), whereas minor alleles of SNPs within MKI67 gene were associated with increasing effects on RFI and RFIf. Additionally, the minor allele of rs137400016 SNP within CNTFR was associated with increasing average daily gain (ADG). The SNPs genotypes within UMPS, SMARCAL, CCSER1, and LMCD1 genes showed significant over-dominance effects whereas other SNPs located in SMARCAL1, ANXA2, CACNA1G, and PHYHIPL genes showed additive effects on RFI and RFIf. Gene enrichment analysis indicated that gland development, as well as ion and cation transport are important physiological mechanisms contributing to variation in feed efficiency traits. The study revealed the effect of the Jak-STAT signaling pathway on feed efficiency through the CNTFR, OSMR, and GHR genes. Genomic heritability using the 63 significant (P ≤ 0.05) SNPs was 0.09, 0.09, 0.13, 0.05, 0.05, and 0.07 for ADG, dry matter intake, midpoint metabolic weight, RFI, RFIf, and backfat, respectively. These SNPs contributed to genetic variation in the studied traits and thus can potentially be used or tested to generate cost-effective molecular breeding values for feed efficiency in beef cattle.
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Affiliation(s)
- M K Abo-Ismail
- Livestock Gentec at University of Alberta, Edmonton, AB, Canada
- Animal and Poultry Production Department, Damanhour University, Damanhour, Egypt
| | - N Lansink
- Livestock Gentec at University of Alberta, Edmonton, AB, Canada
| | - E Akanno
- Livestock Gentec at University of Alberta, Edmonton, AB, Canada
| | - B K Karisa
- Livestock Gentec at University of Alberta, Edmonton, AB, Canada
| | - J J Crowley
- Livestock Gentec at University of Alberta, Edmonton, AB, Canada
- Canadian Beef Breeds Council, Calgary, AB, Canada
| | - S S Moore
- Centre for Animal Science, University of Queensland, St Lucia, Australia
| | - E Bork
- Rangeland Research Institute, Agriculture/Forestry Center, University of Alberta, Edmonton, AB, Canada
| | - P Stothard
- Livestock Gentec at University of Alberta, Edmonton, AB, Canada
| | - J A Basarab
- Alberta Agriculture and Forestry, Lacombe Research Centre, Lacombe, AB, Canada
| | - G S Plastow
- Livestock Gentec at University of Alberta, Edmonton, AB, Canada
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Abo-Ismail MK, Akanno EC, Khorshidi R, Crowley J, Chen L, Karisa BK, Li X, Wang Z, Basarab J, Li C, Stothard P, Plastow G. 0310 Assessing genetic diversity in Canadian beef cattle populations using Illumina BovineSNP50 chip. J Anim Sci 2016. [DOI: 10.2527/jam2016-0310] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Akanno EC, Abo-Ismail MK, Chen L, Li C, Basarab J, Plastow G. 0311 Joint association analysis of additive and non-additive genomic effects for growth and carcass traits of beef cattle. J Anim Sci 2016. [DOI: 10.2527/jam2016-0311] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Abo-Ismail MK, Khorshidi R, Akanno EC, Crowley J, Miller SP, Fleming A, Basarab J, Li C, Stothard P, Plastow G. 0359 Understanding the genetic archticture of Hays Converter Cattle. J Anim Sci 2016. [DOI: 10.2527/jam2016-0359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Akanno EC, Chen L, Li C, Abo-Ismail MK, Basarab J, Plastow G. P5064 Accuracy of genome-wide predictions of heterosis in beef cattle using 50K genotypes. J Anim Sci 2016. [DOI: 10.2527/jas2016.94supplement4146x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Sharma BS, Abo-Ismail MK, Schenkel FS, You Q, Verschoor CP, Pant SD, Karrow NA. Association ofTLR4polymorphisms withMycobacterium aviumsubspeciesparatuberculosisinfection status in Canadian Holsteins. Anim Genet 2015; 46:560-5. [DOI: 10.1111/age.12333] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/22/2015] [Indexed: 11/29/2022]
Affiliation(s)
- B. S. Sharma
- Animal and Poultry Science; University of Guelph; 50 Stone Road East Guelph Ontario N1G 2W1 Canada
| | - M. K. Abo-Ismail
- Animal and Poultry Science; University of Guelph; 50 Stone Road East Guelph Ontario N1G 2W1 Canada
- Department of Animal and Poultry Science; Damanhour University; Damanhour Egypt
| | - F. S. Schenkel
- Animal and Poultry Science; University of Guelph; 50 Stone Road East Guelph Ontario N1G 2W1 Canada
| | - Q. You
- Animal and Poultry Science; University of Guelph; 50 Stone Road East Guelph Ontario N1G 2W1 Canada
| | - C. P. Verschoor
- Pathology and Molecular Medicine; McMaster University; Hamilton Canada
| | - S. D. Pant
- Animal and Veterinary Sciences; Charles Sturt University; Wagga Wagga Australia
| | - N. A. Karrow
- Animal and Poultry Science; University of Guelph; 50 Stone Road East Guelph Ontario N1G 2W1 Canada
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Abo-Ismail MK, Kelly MJ, Squires EJ, Swanson KC, Bauck S, Miller SP. Identification of single nucleotide polymorphisms in genes involved in digestive and metabolic processes associated with feed efficiency and performance traits in beef cattle1,2. J Anim Sci 2013; 91:2512-29. [DOI: 10.2527/jas.2012-5756] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- M. K. Abo-Ismail
- Centre for Genetic Improvement of Livestock, Department of Animal and Poultry Science, University of Guelph, Guelph, Ontario, Canada, N1G 2W0
- Department of Animal and Poultry Science, Damanhour University, Damanhour, Egypt
| | - M. J. Kelly
- Centre for Genetic Improvement of Livestock, Department of Animal and Poultry Science, University of Guelph, Guelph, Ontario, Canada, N1G 2W0
- Queensland Alliance for Agriculture and Food Innovation University of Queensland, St Lucia, QLD 4072, Australia
| | - E. J. Squires
- Centre for Genetic Improvement of Livestock, Department of Animal and Poultry Science, University of Guelph, Guelph, Ontario, Canada, N1G 2W0
| | - K. C. Swanson
- Centre for Genetic Improvement of Livestock, Department of Animal and Poultry Science, University of Guelph, Guelph, Ontario, Canada, N1G 2W0
- Animal Sciences Department, North Dakota State University, Fargo 58108-6050
| | - S. Bauck
- GeneSeek, 4665 Innovation Drive, Suite 120, Lincoln, NE 68521
| | - S. P. Miller
- Centre for Genetic Improvement of Livestock, Department of Animal and Poultry Science, University of Guelph, Guelph, Ontario, Canada, N1G 2W0
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Salim H, Wood KM, Abo-Ismail MK, McEwen PL, Mandell IB, Miller SP, Cant JP, Swanson KC. Influence of feeding increasing levels of dry corn distillers grains plus solubles in whole corn grain-based finishing diets on total tract digestion, nutrient balance, and excretion in beef steers1,2. J Anim Sci 2012; 90:4441-8. [DOI: 10.2527/jas.2011-4332] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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