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Arzik Y, Kizilaslan M, Behrem S, White SN, Piel LMW, Cinar MU. Genome-Wide Scan of Wool Production Traits in Akkaraman Sheep. Genes (Basel) 2023; 14:genes14030713. [PMID: 36980985 PMCID: PMC10048666 DOI: 10.3390/genes14030713] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2022] [Revised: 12/26/2022] [Accepted: 03/10/2023] [Indexed: 03/17/2023] Open
Abstract
The objective of this study was to uncover the genetic background of wool quality, a production trait, by estimating genomic heritability and implementing GWAS in Akkaraman sheep. The wool characteristics measured included fibre diameter (FD) and staple length (SL) at the age of 8 months and yearling fibre diameter (YFD), yearling staple length (YSL) and yearling greasy fleece weight (YGFW) at 18 months of age. Animals were genotyped using the Axiom 50 K Ovine Genotyping Array. Maximum likelihood estimations of a linear mixed model (LMM) were used to estimate genomic heritability, where GWAS was conducted following a score test of each trait. Genomic heritability estimates for the traits ranged between 0.22 and 0.63, indicating that phenotypes have a moderate range of heritability. One genome- and six chromosome-wide significant SNPs were associated with the wool traits in Akkaraman lambs. Accordingly, TRIM2, MND1, TLR2, RNF175, CEP290, TMTC3, RERE, SLC45A1, SOX2, MORN1, SKI, FAAP20, PRKCZ, GABRD, CFAP74, CALML6 and TMEM52 genes as well as nine uncharacterized regions (LOC101118971, LOC105609137, LOC105603067, LOC101122892, LOC106991694, LOC106991467, LOC106991455, LOC105616534 and LOC105609719) were defined as plausible candidates. The findings of this study shed light on the genetics of wool quality and yield for the Akkaraman breed and suggests targets for breeders during systematic breeding programmes.
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Affiliation(s)
- Yunus Arzik
- Department of Animal Science, Faculty of Agriculture, Erciyes University, 38039 Kayseri, Türkiye
- International Center for Livestock Research and Training Center, Ministry of Agriculture and Forestry, 06852 Ankara, Türkiye
| | - Mehmet Kizilaslan
- Department of Animal Science, Faculty of Agriculture, Erciyes University, 38039 Kayseri, Türkiye
- International Center for Livestock Research and Training Center, Ministry of Agriculture and Forestry, 06852 Ankara, Türkiye
- Correspondence: ; Tel.: +90-553-6725986
| | - Sedat Behrem
- Department of Animal Science, Faculty of Veterinary Medicine, Aksaray University, 68100 Aksaray, Türkiye
| | - Stephen N. White
- Department of Veterinary Microbiology & Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
| | - Lindsay M. W. Piel
- USDA-ARS Animal Disease Research 3003 ADBF, Washington State University, Pullman, WA 99164, USA
| | - Mehmet Ulas Cinar
- Department of Animal Science, Faculty of Agriculture, Erciyes University, 38039 Kayseri, Türkiye
- Department of Veterinary Microbiology & Pathology, College of Veterinary Medicine, Washington State University, Pullman, WA 99164, USA
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Haq ZU, Saleem A, Khan AA, Dar MA, Ganaie AM, Beigh YA, Hamadani H, Ahmad SM. Nutrigenomics in livestock sector and its human-animal interface-a review. Vet Anim Sci 2022; 17:100262. [PMID: 35856004 PMCID: PMC9287789 DOI: 10.1016/j.vas.2022.100262] [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] [Indexed: 11/10/2022] Open
Abstract
Nutrigenomics unfolds the link between nutrition and gene expression for productivity.expression profile of intramuscular. Nutrigenomics helps scientists discover genes and DNA in each animal's cell or tissue by assisting them in selecting nutrients. It brings out the importance of micronutrition for increasing animal production. Nutrigenomics integrates nutrition, molecular biology, genomics, bioinformatics, molecular medicine, and epidemiology.
Noncommunicable diseases such as cardiovascular disease, obesity, diabetes, and cancer now outnumber all other health ailments in humans globally due to abrupt changes in lifestyle following the industrial revolution. The industrial revolution has also intensified livestock farming, resulting in an increased demand for productivity and stressed animals. The livestock industry faces significant challenges from a projected sharp increase in global food and high animal protein demand. Nutrition genomics holds great promise for the future as its advances have opened up a whole new world of disease understanding and prevention. Nutrigenomics is the study of the interactions between genes and diet. It investigates molecular relationships between nutrients and genes to identify how even minor modifications could potentially alter animal and human health/performance by using techniques like proteomics, transcriptomics, metabolomics, and lipidomics. Dietary modifications mostly studied in livestock focus mainly on health and production traits through protein, fat, mineral, and vitamin supplementation changes. Nutrigenomics meticulously selects nutrients for fine-tuning the expression of genes that match animal/human genotypes for better health, productivity, and the environment. As a step forward, nutrigenomics integrates nutrition, molecular biology, genomics, bioinformatics, molecular medicine, and epidemiology to better understand the role of food as an epigenetic factor in the occurrence of these diseases. This review aims to provide a comprehensive overview of the fundamental concepts, latest advances, and studies in the field of nutrigenomics, emphasizing the interaction of diet with gene expression, and how it relates to human and animal health along with its human-animal interphase.
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Pacht E, Murdoch B, McKay S. Examining the extent of environmental contributions toward DNA methylation and phenotypic variation. Anim Front 2021; 11:83-89. [PMID: 34934533 PMCID: PMC8683128 DOI: 10.1093/af/vfab056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- Emory Pacht
- Department of Animal and Veterinary Sciences, University of Vermont, Burlington, VT, USA
| | - Brenda Murdoch
- Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, ID, USA
| | - Stephanie McKay
- Department of Animal and Veterinary Sciences, University of Vermont, Burlington, VT, USA
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Genome-wise engineering of ruminant nutrition- nutrigenomics: applications, challenges, and future perspectives – a review. ANNALS OF ANIMAL SCIENCE 2021. [DOI: 10.2478/aoas-2021-0057] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Abstract
Use of genomic information in ruminant production systems can help relieve concerns related to food security and sustainability of production. Nutritional genomics (i.e., Nutrigenomics) is a field of research that is interested in all types of reciprocal interactions between nutrients and genomes of organisms, i.e., variable patterns of gene expression and effect of genetic variations on the nutritional environment. Devising a revolutionizing analytical approach to traditional ruminant nutrition research, the relatively novel area of ruminant nutrigenomics has several studies concerning different aspects of animal production systems. This paper aims to review the current nutrigenomics research in the frame of how nutrition of ruminants can be modified accounting for individual genetic backgrounds and gene/diet relationships behind productivity, quality, efficiency, disease resistance, fertility, and GHG emissions. Furthermore, current challenges facing ruminant nutrigenomics are evaluated and future directions for the novel area are strongly argued by this review.
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Higgins MG, Fitzsimons C, McClure MC, McKenna C, Conroy S, Kenny DA, McGee M, Waters SM, Morris DW. GWAS and eQTL analysis identifies a SNP associated with both residual feed intake and GFRA2 expression in beef cattle. Sci Rep 2018; 8:14301. [PMID: 30250203 PMCID: PMC6155370 DOI: 10.1038/s41598-018-32374-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2018] [Accepted: 09/03/2018] [Indexed: 11/09/2022] Open
Abstract
Residual feed intake (RFI), a measure of feed efficiency, is an important economic and environmental trait in beef production. Selection of low RFI (feed efficient) cattle could maintain levels of production, while decreasing feed costs and methane emissions. However, RFI is a difficult and expensive trait to measure. Identification of single nucleotide polymorphisms (SNPs) associated with RFI may enable rapid, cost effective genomic selection of feed efficient cattle. Genome-wide association studies (GWAS) were conducted in multiple breeds followed by meta-analysis to identify genetic variants associated with RFI and component traits (average daily gain (ADG) and feed intake (FI)) in Irish beef cattle (n = 1492). Expression quantitative trait loci (eQTL) analysis was conducted to identify functional effects of GWAS-identified variants. Twenty-four SNPs were associated (P < 5 × 10-5) with RFI, ADG or FI. The variant rs43555985 exhibited strongest association for RFI (P = 8.28E-06). An eQTL was identified between this variant and GFRA2 (P = 0.0038) where the allele negatively correlated with RFI was associated with increased GFRA2 expression in liver. GFRA2 influences basal metabolic rates, suggesting a mechanism by which genetic variation may contribute to RFI. This study identified SNPs that may be useful both for genomic selection of RFI and for understanding the biology of feed efficiency.
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Affiliation(s)
- Marc G Higgins
- Discipline of Biochemistry, National University of Ireland, Galway, Ireland.,Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co. Meath, Ireland
| | - Claire Fitzsimons
- Livestock Systems Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co. Meath, Ireland.,Department of Agriculture, Fisheries and the Marine, Celbridge, Co. Kildare, Ireland
| | - Matthew C McClure
- Irish Cattle Breeding Federation, Highfield House, Bandon, Co. Cork, Ireland.,ABS-Global, DeForest, WI, USA
| | - Clare McKenna
- Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co. Meath, Ireland
| | - Stephen Conroy
- Irish Cattle Breeding Federation, Highfield House, Bandon, Co. Cork, Ireland
| | - David A Kenny
- Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co. Meath, Ireland
| | - Mark McGee
- Livestock Systems Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co. Meath, Ireland
| | - Sinéad M Waters
- Animal and Bioscience Research Department, Animal & Grassland Research and Innovation Centre, Teagasc, Grange, Dunsany, Co. Meath, Ireland.
| | - Derek W Morris
- Discipline of Biochemistry, National University of Ireland, Galway, Ireland
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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] [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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Hoff JL, Decker JE, Schnabel RD, Taylor JF. Candidate lethal haplotypes and causal mutations in Angus cattle. BMC Genomics 2017; 18:799. [PMID: 29047335 PMCID: PMC5648474 DOI: 10.1186/s12864-017-4196-2] [Citation(s) in RCA: 31] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2017] [Accepted: 10/08/2017] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND If unmanaged, high rates of inbreeding in livestock populations adversely impact their reproductive fitness. In beef cattle, historical selection strategies have increased the frequency of several segregating fatal autosomal recessive polymorphisms. Selective breeding has also decreased the extent of haplotypic diversity genome-wide. By identifying haplotypes for which homozygotes are not observed but would be expected based on their frequency, candidates for developmentally lethal recessive loci can be localized. This analysis comes without the need for observation of the loss-associated phenotype (e.g., failure to implant, first trimester abortion, deformity at birth). In this study, haplotypes were estimated for 3961 registered Angus individuals using 52,545 SNP loci using findhap v2, which exploited the complex pedigree among the individuals in this population. RESULTS Seven loci were detected to possess haplotypes that were not observed in homozygous form despite a sufficiently high frequency and pedigree-based expectation of homozygote occurrence. These haplotypes were identified as candidates for harboring autosomal recessive lethal alleles. Of the genotyped individuals, 109 were resequenced to an average 27X depth of coverage to identify putative loss-of-function alleles genome-wide and had variants called using a custom in-house developed pipeline. For the candidate lethal-harboring haplotypes present in these bulls, sequence-called genotypes were used to identify concordant variants. In addition, whole-genome sequence imputation of variants was performed into the set of 3961 genotyped animals using the 109 resequenced animals to identify candidate lethal recessive variants at the seven loci. Following the imputation, no variants were identified that were fully concordant with the marker-based diplotypes. CONCLUSIONS Selective breeding programs could utilize the predicted lethal haplotypes associated with SNP genotypes. Sequencing and other methods for identifying the causal variants underlying these haplotypes can allow for more efficient methods of management such as gene editing. These two methods in total will reduce the negative impacts of inbreeding on fertility and maximize overall genetic gains.
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Affiliation(s)
- Jesse L Hoff
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Jared E Decker
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.,Informatics Institute, University of Missouri, Columbia, MO, 65211, USA
| | - Robert D Schnabel
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.,Informatics Institute, University of Missouri, Columbia, MO, 65211, USA
| | - Jeremy F Taylor
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.
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Murdoch BM, Murdoch GK, Greenwood S, McKay S. Nutritional Influence on Epigenetic Marks and Effect on Livestock Production. Front Genet 2016; 7:182. [PMID: 27822224 PMCID: PMC5075561 DOI: 10.3389/fgene.2016.00182] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2016] [Accepted: 09/27/2016] [Indexed: 12/11/2022] Open
Abstract
Nutrition represents one of the greatest environmental determinants of an individual’s health. While nutrient quantity and quality impart direct effects, the interaction of nutrition with genetic and epigenetic modifications is often overlooked despite being shown to influence biological variation in mammals. Dissecting complex traits, such as those that are diet or nutrition related, to determine the genetic and epigenetic contributions toward a phenotype can be a formidable process. Epigenetic modifications add another layer of complexity as they do not change the DNA sequence itself but can affect transcription and are important mediators of gene expression and ensuing phenotypic variation. Altered carbohydrate metabolism and rates of fat and protein deposition resulting from diet-induced hypo- or hyper-methylation highlight the capability of nutritional epigenetics to influence livestock commodity quality and quantity. This interaction can yield either products tailored to consumer preference, such as marbling in meat cuts, or potentially increasing productivity and yield both in terms of carcass yield and/or offspring performance. Understanding how these and other desirable phenotypes result from epigenetic mechanisms will facilitate their inducible potential in livestock systems. Here, we discuss the establishment of the epigenome, examples of nutritional mediated alterations of epigenetics and epigenetic effects on livestock production.
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Affiliation(s)
- Brenda M Murdoch
- Department of Animal and Veterinary Science, University of Idaho, Moscow ID, USA
| | - Gordon K Murdoch
- Department of Animal and Veterinary Science, University of Idaho, Moscow ID, USA
| | - Sabrina Greenwood
- Department of Animal and Veterinary Sciences, University of Vermont, Burlington VT, USA
| | - Stephanie McKay
- Department of Animal and Veterinary Sciences, University of Vermont, Burlington VT, USA
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Yaro M, Munyard KA, Stear MJ, Groth DM. Molecular identification of livestock breeds: a tool for modern conservation biology. Biol Rev Camb Philos Soc 2016; 92:993-1010. [DOI: 10.1111/brv.12265] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 02/14/2016] [Accepted: 02/18/2016] [Indexed: 12/22/2022]
Affiliation(s)
- Mohammed Yaro
- School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Faculty of Health Sciences; Curtin University; GPO Box U1987 Perth WA 6845 Australia
| | - Kylie A. Munyard
- School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Faculty of Health Sciences; Curtin University; GPO Box U1987 Perth WA 6845 Australia
| | - Michael J. Stear
- Institute of Biodiversity, Animal Health and Comparative Medicine; University of Glasgow; Bearsden Road Glasgow G61 1QH U.K
| | - David M. Groth
- School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Faculty of Health Sciences; Curtin University; GPO Box U1987 Perth WA 6845 Australia
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