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Hossain MN, Gao Y, Hatfield MJ, de Avila JM, McClure MC, Du M. Cold exposure impacts DNA methylation patterns in cattle sperm. Front Genet 2024; 15:1346150. [PMID: 38444759 PMCID: PMC10912962 DOI: 10.3389/fgene.2024.1346150] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Accepted: 01/23/2024] [Indexed: 03/07/2024] Open
Abstract
DNA methylation is influenced by various exogenous factors such as nutrition, temperature, toxicants, and stress. Bulls from the Pacific Northwest region of the United States and other northern areas are exposed to extreme cold temperatures during winter. However, the effects of cold exposure on the methylation patterns of bovine sperm remain unclear. To address, DNA methylation profiles of sperm collected during late spring and winter from the same bulls were analyzed using whole genome bisulfite sequencing (WGBS). Bismark (0.22.3) were used for mapping the WGBS reads and R Bioconductor package DSS was used for differential methylation analysis. Cold exposure induced 3,163 differentially methylated cytosines (DMCs) with methylation difference ≥10% and a q-value < 0.05. We identified 438 differentially methylated regions (DMRs) with q-value < 0.05, which overlapped with 186 unique genes. We also identified eight unique differentially methylated genes (DMGs) (Pax6, Macf1, Mest, Ubqln1, Smg9, Ctnnb1, Lsm4, and Peg10) involved in embryonic development, and nine unique DMGs (Prmt6, Nipal1, C21h15orf40, Slc37a3, Fam210a, Raly, Rgs3, Lmbr1, and Gan) involved in osteogenesis. Peg10 and Mest, two paternally expressed imprinted genes, exhibited >50% higher methylation. The differential methylation patterns of six distinct DMRs: Peg10, Smg9 and Mest related to embryonic development and Lmbr1, C21h15orf40 and Prtm6 related to osteogenesis, were assessed by methylation-specific PCR (MS-PCR), which confirmed the existence of variable methylation patterns in those locations across the two seasons. In summary, cold exposure induces differential DNA methylation patterns in genes that appear to affect embryonic development and osteogenesis in the offspring. Our findings suggest the importance of replicating the results of the current study with a larger sample size and exploring the potential of these changes in affecting offspring development.
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Affiliation(s)
- Md Nazmul Hossain
- Nutrigenomics and Growth Biology Laboratory, Department of Animal Sciences, Washington State University, Pullman, WA, United States
- Department of Livestock Production and Management, Faculty of Veterinary, Animal, and Biomedical Sciences, Sylhet Agricultural University, Sylhet, Bangladesh
| | - Yao Gao
- Nutrigenomics and Growth Biology Laboratory, Department of Animal Sciences, Washington State University, Pullman, WA, United States
| | - Michael J. Hatfield
- Nutrigenomics and Growth Biology Laboratory, Department of Animal Sciences, Washington State University, Pullman, WA, United States
| | - Jeanene M. de Avila
- Nutrigenomics and Growth Biology Laboratory, Department of Animal Sciences, Washington State University, Pullman, WA, United States
| | | | - Min Du
- Nutrigenomics and Growth Biology Laboratory, Department of Animal Sciences, Washington State University, Pullman, WA, United States
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Al-Khudhair A, VanRaden PM, Null DJ, Neupane M, McClure MC, Dechow CD. New mutation within a common haplotype is associated with calf muscle weakness in Holsteins. J Dairy Sci 2024:S0022-0302(24)00025-0. [PMID: 38246543 DOI: 10.3168/jds.2023-24121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/23/2023] [Accepted: 12/19/2023] [Indexed: 01/23/2024]
Abstract
A recessive haplotype resulting in elevated calf mortality but with apparent incomplete penetrance was previously linked to the end of chromosome 16 (78.7 to 80.7Mbp). Genotype analysis of 5.6 million Holsteins indicated that the haplotype was common and traced back to 1952 with a key ancestor born in 1984 (HOUSA1964484, Southwind) identified from chip genotypes as homozygous for the suspect haplotype. Sequence data from Southwind, an affected calf, and the sire of the affected calf was scanned for candidate mutations. A missense mutation with a deleterious projected impact at 79,613,592 bp was homozygous in the affected calf and heterozygous in the calf's sire and Southwind. Sequence data available from the Cooperative Dairy DNA Repository for 299 other Holsteins indicated a 97% concordance with the haplotype and an 89% call rate. Exon amino acid sequence appears to be broadly conserved in the CACNA1S gene, and mutations in humans and mice can cause phenotypes of temporary or permanent paralysis analogous to those in calves suffering from muscle weakness (HMW). Improved methods for using pedigree to track new mutations within existing haplotypes were developed and applied to the haplotypes for both muscle weakness and Holstein cholesterol deficiency (HCD). For HCD, concordance of the gene test with its haplotype status was greatly improved. For both defects, haplotype status was matched to heifer livability records for 558K calves. For HMW, only 46 heifers with livability records were homozygous and traced only to Southwind on both sides. Of those, 52% of those died before 18 mo at an average age of 1.7 ± 1.6 mo, but that death rate may be underestimated if only healthier calves were genotyped. The death rate was 2.4% for noncarriers. Different reporting methods or dominance effects may be needed to include HMW and other partially lethal effects in selection and mating. Direct tests are needed for new mutations within existing common haplotypes because tracking can be difficult even with accurate pedigrees when the original haplotype has high frequency.
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Affiliation(s)
- A Al-Khudhair
- USDA, Agricultural Research Service, Animal Genomics and Improvement Laboratory, Beltsville, MD 20705-2350
| | - P M VanRaden
- USDA, Agricultural Research Service, Animal Genomics and Improvement Laboratory, Beltsville, MD 20705-2350.
| | - D J Null
- USDA, Agricultural Research Service, Animal Genomics and Improvement Laboratory, Beltsville, MD 20705-2350
| | - M Neupane
- USDA, Agricultural Research Service, Animal Genomics and Improvement Laboratory, Beltsville, MD 20705-2350
| | | | - C D Dechow
- Pennsylvania State University, University Park, PA
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Keogh K, Carthy TR, McClure MC, Waters SM, Kenny DA. Genome-wide association study of economically important traits in Charolais and Limousin beef cows. Animal 2020; 15:100011. [PMID: 33515994 DOI: 10.1016/j.animal.2020.100011] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 07/27/2020] [Accepted: 07/30/2020] [Indexed: 01/14/2023] Open
Abstract
Genomic selection has proven effective for advancing genetic gain for key profit traits in dairy cattle production systems. However, its impact to-date on genetic improvement programs for beef cattle has been less effective. Despite this, the technology is thought to be particularly useful for low heritability traits such as those associated with reproductive efficiency. The objective of this study was to identify genetic variants associated with key determinants of reproductive and overall productive efficiency in beef cows. The analysis employed a large dataset derived from the national genetic evaluation program in Ireland for two of the most predominant beef breeds, viz. Charolais (n = 5 244 cows) and Limousin (n = 7 304 cows). Single nucleotide polymorphisms (SNPs) were identified as being statistically significantly associated (adj. P < 0.05) with both reproductive and productive traits for both breed types. However, there was little across breed commonality, with only two SNPs (rs110240246 and rs110344317; adj. P < 0.05) located within the genomic regions of the LCORL and MSTN genes respectively, identified in both Charolais and Limousin populations, associated with traits including carcass weight, cull-cow weight and live-weight. Significant SNPs within the MSTN gene were also associated with both reproduction and production related traits within each breed. Finally, traits including calving difficulty, calf mortality and calving interval were associated with SNPs within genomic regions comprising genes involved in cellular growth and lipid metabolism. Genetic variants identified as associated with both important reproductive efficiency and production related traits from this study warrant further analyses for their potential incorporation into breeding programmes to support the sustainability of beef cattle production.
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Affiliation(s)
- K Keogh
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc Grange, Dunsany, Co. Meath C15 PW93, Ireland
| | - T R Carthy
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc Grange, Dunsany, Co. Meath C15 PW93, Ireland
| | - M C McClure
- Irish Cattle Breeding Federation, Highfield House, Shinagh, Bandon, Co. Cork, Ireland
| | - S M Waters
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc Grange, Dunsany, Co. Meath C15 PW93, Ireland
| | - D A Kenny
- Animal and Bioscience Research Department, Animal and Grassland Research and Innovation Centre, Teagasc Grange, Dunsany, Co. Meath C15 PW93, Ireland.
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Jenko J, McClure MC, Matthews D, McClure J, Johnsson M, Gorjanc G, Hickey JM. Analysis of a large dataset reveals haplotypes carrying putatively recessive lethal and semi-lethal alleles with pleiotropic effects on economically important traits in beef cattle. Genet Sel Evol 2019; 51:9. [PMID: 30836944 PMCID: PMC6402105 DOI: 10.1186/s12711-019-0452-z] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2018] [Accepted: 02/21/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND In livestock, deleterious recessive alleles can result in reduced economic performance of homozygous individuals in multiple ways, e.g. early embryonic death, death soon after birth, or semi-lethality with incomplete penetrance causing reduced viability. While death is an easy phenotype to score, reduced viability is not as easy to identify. However, it can sometimes be observed as reduced conception rates, longer calving intervals, or lower survival for live born animals. METHODS In this paper, we searched for haplotypes that carry putatively recessive lethal or semi-lethal alleles in 132,725 genotyped Irish beef cattle from five breeds: Aberdeen Angus, Charolais, Hereford, Limousin, and Simmental. We phased the genotypes in sliding windows along the genome and used five tests to identify haplotypes with absence of or reduced homozygosity. Then, we associated the identified haplotypes with 44,351 insemination records that indicated early embryonic death, and postnatal survival records. Finally, we assessed haplotype pleiotropy by estimating substitution effects on estimates of breeding value for 15 economically important traits in beef production. RESULTS We found support for one haplotype that carries a putatively recessive lethal (chromosome 16 in Simmental) and two haplotypes that carry semi-lethal alleles (chromosome 14 in Aberdeen Angus and chromosome 19 in Charolais), with population frequencies of 8.8, 15.2, and 14.4%, respectively. These three haplotypes showed pleiotropic effects on economically important traits for beef production. Their allele substitution effects are €2.30, €3.42, and €1.47 for the terminal index and €1.03, - €3.11, and - €0.88 for the replacement index, where the standard deviations for the terminal index are €22.52, €18.65, and €22.70 and for the replacement index they are €31.35, €29.82, and €35.79. We identified ZFAT as the candidate gene for semi-lethality in Aberdeen Angus, several candidate genes for the lethal Simmental haplotype, and no candidate genes for the semi-lethal Charolais haplotype. CONCLUSIONS We analysed genotype, reproduction, survival, and production data to detect haplotypes that carry putatively recessive lethal or semi-lethal alleles in Irish beef cattle and identified one lethal and two semi-lethal haplotypes, which have pleiotropic effects on economically important traits in beef production.
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Affiliation(s)
- Janez Jenko
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, Scotland, UK
| | | | | | | | - Martin Johnsson
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, Scotland, UK.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, 750 07, Uppsala, Sweden
| | - Gregor Gorjanc
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, Scotland, UK
| | - John M Hickey
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, Midlothian, Scotland, UK.
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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] [What about the content of this article? (0)] [Affiliation(s)] [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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McClure MC, McCarthy J, Flynn P, McClure JC, Dair E, O'Connell DK, Kearney JF. SNP Data Quality Control in a National Beef and Dairy Cattle System and Highly Accurate SNP Based Parentage Verification and Identification. Front Genet 2018; 9:84. [PMID: 29599798 PMCID: PMC5862794 DOI: 10.3389/fgene.2018.00084] [Citation(s) in RCA: 31] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2017] [Accepted: 02/27/2018] [Indexed: 11/13/2022] Open
Abstract
A major use of genetic data is parentage verification and identification as inaccurate pedigrees negatively affect genetic gain. Since 2012 the international standard for single nucleotide polymorphism (SNP) verification in Bos taurus cattle has been the ISAG SNP panels. While these ISAG panels provide an increased level of parentage accuracy over microsatellite markers (MS), they can validate the wrong parent at ≤1% misconcordance rate levels, indicating that more SNP are needed if a more accurate pedigree is required. With rapidly increasing numbers of cattle being genotyped in Ireland that represent 61 B. taurus breeds from a wide range of farm types: beef/dairy, AI/pedigree/commercial, purebred/crossbred, and large to small herd size the Irish Cattle Breeding Federation (ICBF) analyzed different SNP densities to determine that at a minimum ≥500 SNP are needed to consistently predict only one set of parents at a ≤1% misconcordance rate. For parentage validation and prediction ICBF uses 800 SNP (ICBF800) selected based on SNP clustering quality, ISAG200 inclusion, call rate (CR), and minor allele frequency (MAF) in the Irish cattle population. Large datasets require sample and SNP quality control (QC). Most publications only deal with SNP QC via CR, MAF, parent-progeny conflicts, and Hardy-Weinberg deviation, but not sample QC. We report here parentage, SNP QC, and a genomic sample QC pipelines to deal with the unique challenges of >1 million genotypes from a national herd such as SNP genotype errors from mis-tagging of animals, lab errors, farm errors, and multiple other issues that can arise. We divide the pipeline into two parts: a Genotype QC and an Animal QC pipeline. The Genotype QC identifies samples with low call rate, missing or mixed genotype classes (no BB genotype or ABTG alleles present), and low genotype frequencies. The Animal QC handles situations where the genotype might not belong to the listed individual by identifying: >1 non-matching genotypes per animal, SNP duplicates, sex and breed prediction mismatches, parentage and progeny validation results, and other situations. The Animal QC pipeline make use of ICBF800 SNP set where appropriate to identify errors in a computationally efficient yet still highly accurate method.
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Affiliation(s)
| | | | | | | | - Emma Dair
- Irish Cattle Breeding Federation, Cork, Ireland
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McClure MC, McClure JC, McCarthy J. Rate of bovine heteropaternal superfecundation in the Irish National Herd: twins with different sires. Anim Genet 2017; 48:721-723. [PMID: 29076162 DOI: 10.1111/age.12619] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/12/2017] [Indexed: 11/28/2022]
Affiliation(s)
| | | | - John McCarthy
- Irish Cattle Breeding Federation, Bandon, Co. Cork, Ireland
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Judge MM, Kearney JF, McClure MC, Sleator RD, Berry DP. Evaluation of developed low-density genotype panels for imputation to higher density in independent dairy and beef cattle populations. J Anim Sci 2016; 94:949-62. [PMID: 27065257 DOI: 10.2527/jas.2015-0044] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
The objective of this study was to develop, using alternative algorithms, low-density SNP genotyping panels (384 to 12,000 SNP), which can be accurately imputed to higher-density panels across independent cattle populations. Single nucleotide polymorphisms were selected based on genomic characteristics (i.e., linkage disequilibrium [LD], minor allele frequency [MAF], and genomic distance) in a population of 1,267 Holstein-Friesian animals genotyped on the Illumina Bovine50 Beadchip (54,001 SNP). Single nucleotide polymorphism selection methods included 1) random; 2) equidistant location; 3) combination of SNP MAF and LD structure while maintaining relatively equal genomic distance between adjacent SNP; 4) a combination of high MAF, genomic distance between selected and candidate SNP, and correlation between genotypes of selected and candidate SNP; and 5) a machine learning algorithm. The panels were validated separately in 1) a population of 750 Holstein-Friesian animals with masked genotypes to reflect the lower-density SNP densities under investigation (1,249 animals with complete genotypes included in reference population) and 2) a population of 359 Limousin and Charolais cattle with high (777,962 SNP)-density genotypes (1,918 animals with complete genotypes included in the reference population). Irrespective of SNP selection method, imputation accuracy in both populations improved at a diminishing rate as the number of SNP included in the lower-density genotype panel increased. Additionally, the variability in mean imputation accuracy per individual decreased as the panel density increased. The SNP selection method had a major impact on the mean allele concordance rate, although its impact diminished as the panel density increased. Imputation accuracy for SNP selected using a combination of high SNP MAF, LD structure, and relatively equal genomic distance between SNP outperformed all other selection methods in densities < 12,000 SNP. Using this method of SNP selection, the correlation between the imputed and actual genotypes for the 3,000 SNP panel was 0.90 and 0.96 when applied to the beef and dairy populations, respectively; the respective correlations for the 6,000 SNP panel were 0.95 and 0.98. It is necessary to include between 3,000 and 6,000 SNP in a low-density panel to achieve adequate imputation accuracy to either medium density (approximately 50,000 SNP in the dairy population) or high density (approximately 700,000 SNP in the beef population) across diverse and independent populations.
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Huson HJ, Kim ES, Godfrey RW, Olson TA, McClure MC, Chase CC, Rizzi R, O'Brien AMP, Van Tassell CP, Garcia JF, Sonstegard TS. Genome-wide association study and ancestral origins of the slick-hair coat in tropically adapted cattle. Front Genet 2014; 5:101. [PMID: 24808908 PMCID: PMC4010767 DOI: 10.3389/fgene.2014.00101] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2014] [Accepted: 04/08/2014] [Indexed: 11/13/2022] Open
Abstract
The slick hair coat (SLICK) is a dominantly inherited trait typically associated with tropically adapted cattle that are from Criollo descent through Spanish colonization of cattle into the New World. The trait is of interest relative to climate change, due to its association with improved thermo-tolerance and subsequent increased productivity. Previous studies localized the SLICK locus to a 4 cM region on chromosome (BTA) 20 and identified signatures of selection in this region derived from Senepol cattle. The current study compares three slick-haired Criollo-derived breeds including Senepol, Carora, and Romosinuano and three additional slick-haired cross-bred lineages to non-slick ancestral breeds. Genome-wide association (GWA), haplotype analysis, signatures of selection, runs of homozygosity (ROH), and identity by state (IBS) calculations were used to identify a 0.8 Mb (37.7-38.5 Mb) consensus region for the SLICK locus on BTA20 in which contains SKP2 and SPEF2 as possible candidate genes. Three specific haplotype patterns are identified in slick individuals, all with zero frequency in non-slick individuals. Admixture analysis identified common genetic patterns between the three slick breeds at the SLICK locus. Principal component analysis (PCA) and admixture results show Senepol and Romosinuano sharing a higher degree of genetic similarity to one another with a much lesser degree of similarity to Carora. Variation in GWA, haplotype analysis, and IBS calculations with accompanying population structure information supports potentially two mutations, one common to Senepol and Romosinuano and another in Carora, effecting genes contained within our refined location for the SLICK locus.
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Affiliation(s)
- Heather J Huson
- Department of Animal Science, Cornell University Ithaca, NY, USA ; Bovine Functional Genomics Laboratory, United States Department of Agriculture, Agricultural Research Services Beltsville, MD, USA
| | - Eui-Soo Kim
- Bovine Functional Genomics Laboratory, United States Department of Agriculture, Agricultural Research Services Beltsville, MD, USA ; Department of Animal Science, Iowa State University Ames, IA, USA
| | - Robert W Godfrey
- Agricultural Experiment Station, University of the Virgin Islands St. Croix, Virgin Islands
| | - Timothy A Olson
- Department of Animal Science, University of Florida Gainsville, FL, USA
| | - Matthew C McClure
- Bovine Functional Genomics Laboratory, United States Department of Agriculture, Agricultural Research Services Beltsville, MD, USA ; Irish Cattle Breeding Federation Cork, Ireland
| | - Chad C Chase
- Meat Animal Research Center, United States Department of Agriculture, Agricultural Research Services Clay Center, NE, USA
| | - Rita Rizzi
- Department of Veterinary Medicine, Milan University Milan, Italy
| | - Ana M P O'Brien
- Division of Livestock Sciences, BOKU University of Natural Resources and Life Sciences Vienna, Austria
| | - Curt P Van Tassell
- Bovine Functional Genomics Laboratory, United States Department of Agriculture, Agricultural Research Services Beltsville, MD, USA
| | - José F Garcia
- Faculdade de Medicina Veterinária de Araçatuba, UNESP - Univ Estadual Paulista Brazil
| | - Tad S Sonstegard
- Bovine Functional Genomics Laboratory, United States Department of Agriculture, Agricultural Research Services Beltsville, MD, USA
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Berry DP, McClure MC, Mullen MP. Within- and across-breed imputation of high-density genotypes in dairy and beef cattle from medium- and low-density genotypes. J Anim Breed Genet 2013; 131:165-72. [PMID: 24906026 DOI: 10.1111/jbg.12067] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2013] [Accepted: 11/05/2013] [Indexed: 11/28/2022]
Abstract
The objective of this study was to evaluate, using three different genotype density panels, the accuracy of imputation from lower- to higher-density genotypes in dairy and beef cattle. High-density genotypes consisting of 777,962 single-nucleotide polymorphisms (SNP) were available on 3122 animals comprised of 269, 196, 710, 234, 719, 730 and 264 Angus, Belgian Blue, Charolais, Hereford, Holstein-Friesian, Limousin and Simmental bulls, respectively. Three different genotype densities were generated: low density (LD; 6501 autosomal SNPs), medium density (50K; 47,770 autosomal SNPs) and high density (HD; 735,151 autosomal SNPs). Imputation from lower- to higher-density genotype platforms was undertaken within and across breeds exploiting population-wide linkage disequilibrium. The mean allele concordance rate per breed from LD to HD when undertaken using a single breed or multiple breed reference population varied from 0.956 to 0.974 and from 0.947 to 0.967, respectively. The mean allele concordance rate per breed from 50K to HD when undertaken using a single breed or multiple breed reference population varied from 0.987 to 0.994 and from 0.987 to 0.993, respectively. The accuracy of imputation was generally greater when the reference population was solely comprised of the breed to be imputed compared to when the reference population comprised of multiple breeds, although the impact was less when imputing from 50K to HD compared to imputing from LD.
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Affiliation(s)
- D P Berry
- Animal & Grassland Research and Innovation Centre, Cork, Ireland
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11
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McClure MC, Sonstegard TS, Wiggans GR, Van Eenennaam AL, Weber KL, Penedo CT, Berry DP, Flynn J, Garcia JF, Carmo AS, Regitano LCA, Albuquerque M, Silva MVGB, Machado MA, Coffey M, Moore K, Boscher MY, Genestout L, Mazza R, Taylor JF, Schnabel RD, Simpson B, Marques E, McEwan JC, Cromie A, Coutinho LL, Kuehn LA, Keele JW, Piper EK, Cook J, Williams R, Van Tassell CP. Imputation of microsatellite alleles from dense SNP genotypes for parentage verification across multiple Bos taurus and Bos indicus breeds. Front Genet 2013; 4:176. [PMID: 24065982 PMCID: PMC3776237 DOI: 10.3389/fgene.2013.00176] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2013] [Accepted: 08/22/2013] [Indexed: 11/26/2022] Open
Abstract
To assist cattle producers transition from microsatellite (MS) to single nucleotide polymorphism (SNP) genotyping for parental verification we previously devised an effective and inexpensive method to impute MS alleles from SNP haplotypes. While the reported method was verified with only a limited data set (N = 479) from Brown Swiss, Guernsey, Holstein, and Jersey cattle, some of the MS-SNP haplotype associations were concordant across these phylogenetically diverse breeds. This implied that some haplotypes predate modern breed formation and remain in strong linkage disequilibrium. To expand the utility of MS allele imputation across breeds, MS and SNP data from more than 8000 animals representing 39 breeds (Bos taurus and B. indicus) were used to predict 9410 SNP haplotypes, incorporating an average of 73 SNPs per haplotype, for which alleles from 12 MS markers could be accurately be imputed. Approximately 25% of the MS-SNP haplotypes were present in multiple breeds (N = 2 to 36 breeds). These shared haplotypes allowed for MS imputation in breeds that were not represented in the reference population with only a small increase in Mendelian inheritance inconsistancies. Our reported reference haplotypes can be used for any cattle breed and the reported methods can be applied to any species to aid the transition from MS to SNP genetic markers. While ~91% of the animals with imputed alleles for 12 MS markers had ≤1 Mendelian inheritance conflicts with their parents' reported MS genotypes, this figure was 96% for our reference animals, indicating potential errors in the reported MS genotypes. The workflow we suggest autocorrects for genotyping errors and rare haplotypes, by MS genotyping animals whose imputed MS alleles fail parentage verification, and then incorporating those animals into the reference dataset.
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Affiliation(s)
- Matthew C McClure
- Bovine Functional Genomics Laboratory, BARC, Agriculture Research Service, United States Department of Agriculture Beltsville, MD, USA
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12
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Sonstegard TS, Cole JB, VanRaden PM, Van Tassell CP, Null DJ, Schroeder SG, Bickhart D, McClure MC. Identification of a nonsense mutation in CWC15 associated with decreased reproductive efficiency in Jersey cattle. PLoS One 2013; 8:e54872. [PMID: 23349982 PMCID: PMC3551820 DOI: 10.1371/journal.pone.0054872] [Citation(s) in RCA: 74] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2012] [Accepted: 12/17/2012] [Indexed: 12/22/2022] Open
Abstract
With the recent advent of genomic tools for cattle, several recessive conditions affecting fertility have been identified and selected against, such as deficiency of uridine monophosphate synthase, complex vertebral malformation, and brachyspina. The current report refines the location of a recessive haplotype affecting fertility in Jersey cattle using crossover haplotypes, discovers the causative mutation using whole genome sequencing, and examines the gene's role in embryo loss. In an attempt to identify unknown recessive lethal alleles in the current dairy population, a search using deep Mendelian sampling of 5,288 Jersey cattle was conducted for high-frequency haplotypes that have a deficit of homozygotes at the population level. This search led to the discovery of a putative recessive lethal in Jersey cattle on Bos taurus autosome 15. The haplotype, denoted JH1, was associated with reduced fertility, and further investigation identified one highly-influential Jersey bull as the putative source ancestor. By combining SNP analysis of whole-genome sequences aligned to the JH1 interval and subsequent SNP validation a nonsense mutation in CWC15 was identified as the likely causative mutation underlying the fertility phenotype. No homozygous recessive individuals were found in 749 genotyped animals, whereas all known carriers and carrier haplotypes possessed one copy of the mutant allele. This newly identified lethal has been responsible for a substantial number of spontaneous abortions in Jersey dairy cattle throughout the past half-century. With the mutation identified, selection against the deleterious allele in breeding schemes will aid in reducing the incidence of this defect in the population. These results also show that carrier status can be imputed with high accuracy. Whole-genome resequencing proved to be a powerful strategy to rapidly identify a previously mapped deleterious mutation in a known carrier of a recessive lethal allele.
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Affiliation(s)
- Tad S. Sonstegard
- Bovine Functional Genomics, United States Department of Agriculture, Agricultural Research Service, Beltsville, Maryland, United States of America
| | - John B. Cole
- Animal Improvement Programs Laboratories, United States Department of Agriculture, Agricultural Research Service, Beltsville, Maryland, United States of America
- * E-mail:
| | - Paul M. VanRaden
- Animal Improvement Programs Laboratories, United States Department of Agriculture, Agricultural Research Service, Beltsville, Maryland, United States of America
| | - Curtis P. Van Tassell
- Bovine Functional Genomics, United States Department of Agriculture, Agricultural Research Service, Beltsville, Maryland, United States of America
| | - Daniel J. Null
- Animal Improvement Programs Laboratories, United States Department of Agriculture, Agricultural Research Service, Beltsville, Maryland, United States of America
| | - Steven G. Schroeder
- Bovine Functional Genomics, United States Department of Agriculture, Agricultural Research Service, Beltsville, Maryland, United States of America
| | - Derek Bickhart
- Bovine Functional Genomics, United States Department of Agriculture, Agricultural Research Service, Beltsville, Maryland, United States of America
| | - Matthew C. McClure
- Bovine Functional Genomics, United States Department of Agriculture, Agricultural Research Service, Beltsville, Maryland, United States of America
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Decker JE, Vasco DA, McKay SD, McClure MC, Rolf MM, Kim J, Northcutt SL, Bauck S, Woodward BW, Schnabel RD, Taylor JF. A novel analytical method, Birth Date Selection Mapping, detects response of the Angus (Bos taurus) genome to selection on complex traits. BMC Genomics 2012; 13:606. [PMID: 23140540 PMCID: PMC3532096 DOI: 10.1186/1471-2164-13-606] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2012] [Accepted: 10/31/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Several methods have recently been developed to identify regions of the genome that have been exposed to strong selection. However, recent theoretical and empirical work suggests that polygenic models are required to identify the genomic regions that are more moderately responding to ongoing selection on complex traits. We examine the effects of multi-trait selection on the genome of a population of US registered Angus beef cattle born over a 50-year period representing approximately 10 generations of selection. We present results from the application of a quantitative genetic model, called Birth Date Selection Mapping, to identify signatures of recent ongoing selection. RESULTS We show that US Angus cattle have been systematically selected to alter their mean additive genetic merit for most of the 16 production traits routinely recorded by breeders. Using Birth Date Selection Mapping, we estimate the time-dependency of allele frequency for 44,817 SNP loci using genomic best linear unbiased prediction, generalized least squares, and BayesCπ analyses. Finally, we reconstruct the primary phenotypes that have historically been exposed to selection from a genome-wide analysis of the 16 production traits and gene ontology enrichment analysis. CONCLUSIONS We demonstrate that Birth Date Selection Mapping utilizing mixed models corrects for time-dependent pedigree sampling effects that lead to spurious SNP associations and reveals genomic signatures of ongoing selection on complex traits. Because multiple traits have historically been selected in concert and most quantitative trait loci have small effects, selection has incrementally altered allele frequencies throughout the genome. Two quantitative trait loci of large effect were not the most strongly selected of the loci due to their antagonistic pleiotropic effects on strongly selected phenotypes. Birth Date Selection Mapping may readily be extended to temporally-stratified human or model organism populations.
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Affiliation(s)
- Jared E Decker
- Division of Animal Sciences, University of Missouri, Columbia, 65211, USA
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14
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McClure MC, Ramey HR, Rolf MM, McKay SD, Decker JE, Chapple RH, Kim JW, Taxis TM, Weaber RL, Schnabel RD, Taylor JF. Genome-wide association analysis for quantitative trait loci influencing Warner-Bratzler shear force in five taurine cattle breeds. Anim Genet 2012; 43:662-73. [PMID: 22497286 PMCID: PMC3506923 DOI: 10.1111/j.1365-2052.2012.02323.x] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/06/2011] [Indexed: 01/09/2023]
Abstract
We performed a genome-wide association study for Warner–Bratzler shear
force (WBSF), a measure of meat tenderness, by genotyping 3360 animals from five
breeds with 54 790 BovineSNP50 and 96 putative single-nucleotide polymorphisms
(SNPs) within μ-calpain [HUGO nomenclature
calpain 1, (mu/I) large subunit; CAPN1]
and calpastatin (CAST). Within- and
across-breed analyses estimated SNP allele substitution effects (ASEs) by
genomic best linear unbiased prediction (GBLUP) and variance components by
restricted maximum likelihood under an animal model incorporating a genomic
relationship matrix. GBLUP estimates of ASEs from the across-breed analysis were
moderately correlated (0.31–0.66) with those from the individual
within-breed analyses, indicating that prediction equations for molecular
estimates of breeding value developed from across-breed analyses should be
effective for genomic selection within breeds. We identified 79 genomic regions
associated with WBSF in at least three breeds, but only eight were detected in
all five breeds, suggesting that the within-breed analyses were underpowered,
that different quantitative trait loci (QTL) underlie variation between breeds
or that the BovineSNP50 SNP density is insufficient to detect common QTL among
breeds. In the across-breed analysis, CAPN1 was followed by
CAST as the most strongly associated WBSF QTL genome-wide,
and associations with both were detected in all five breeds. We show that none
of the four commercialized CAST and CAPN1SNP
diagnostics are causal for associations with WBSF, and we putatively fine-map
the CAPN1 causal mutation to a 4581-bp region. We estimate that
variation in CAST and CAPN1 explains 1.02 and
1.85% of the phenotypic variation in WBSF respectively.
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Affiliation(s)
- M C McClure
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
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15
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Abstract
Estimated breeding values for average daily feed intake (AFI; kg/day), residual feed intake (RFI; kg/day) and average daily gain (ADG; kg/day) were generated using a mixed linear model incorporating genomic relationships for 698 Angus steers genotyped with the Illumina BovineSNP50 assay. Association analyses of estimated breeding values (EBVs) were performed for 41 028 single nucleotide polymorphisms (SNPs), and permutation analysis was used to empirically establish the genome-wide significance threshold (P < 0.05) for each trait. SNPs significantly associated with each trait were used in a forward selection algorithm to identify genomic regions putatively harbouring genes with effects on each trait. A total of 53, 66 and 68 SNPs explained 54.12% (24.10%), 62.69% (29.85%) and 55.13% (26.54%) of the additive genetic variation (when accounting for the genomic relationships) in steer breeding values for AFI, RFI and ADG, respectively, within this population. Evaluation by pathway analysis revealed that many of these SNPs are in genomic regions that harbour genes with metabolic functions. The presence of genetic correlations between traits resulted in 13.2% of SNPs selected for AFI and 4.5% of SNPs selected for RFI also being selected for ADG in the analysis of breeding values. While our study identifies panels of SNPs significant for efficiency traits in our population, validation of all SNPs in independent populations will be necessary before commercialization.
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Affiliation(s)
- M M Rolf
- Division of Animal Sciences, University of Missouri, Columbia, 65211, USA.
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McClure MC, Morsci NS, Schnabel RD, Kim JW, Yao P, Rolf MM, McKay SD, Gregg SJ, Chapple RH, Northcutt SL, Taylor JF. A genome scan for quantitative trait loci influencing carcass, post-natal growth and reproductive traits in commercial Angus cattle. Anim Genet 2011; 41:597-607. [PMID: 20477797 DOI: 10.1111/j.1365-2052.2010.02063.x] [Citation(s) in RCA: 160] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
Abstract
To gain insight into the number of loci of large effect that underlie variation in cattle, a quantitative trait locus (QTL) scan for 14 economically important traits was performed in two commercial Angus populations using 390 microsatellites, 11 single nucleotide polymorphisms (SNPs) and one duplication loci. The first population comprised 1769 registered Angus bulls born between 1955 and 2003, with Expected Progeny Differences computed by the American Angus Association. The second comprised 38 half-sib families containing 1622 steers with six post-natal growth and carcass phenotypes. Linkage analysis was performed by half-sib least squares regression with gridqtl or Bayesian Markov chain Monte Carlo analysis of complex pedigrees with loki. Of the 673 detected QTL, only 118 have previously been reported, reflecting both the conservative approach to QTL reporting in the literature, and the more liberal approach taken in this study. From 33 to 71% of the genetic variance and 35 to 56% of the phenotypic variance in each trait was explained by the detected QTL. To analyse the effects of 11 SNPs and one duplication locus within candidate genes on each trait, a single marker analysis was performed by fitting an additive allele substitution model in both mapping populations. There were 53 associations detected between the SNP/duplication loci and traits with -log(10) P(nominal) ≥ 4.0, where each association explained 0.92% to 4.4% of the genetic variance and 0.01% to 1.86% of the phenotypic variance. Of these associations, only six SNP/duplication loci were located within 8 cM of a QTL peak for the trait, with two being located at the QTL peak: SST_DG156121:c.362A>G for ribeye muscle area and TG_X05380:c.422C>T for calving ease. Strong associations between several SNP/duplication loci and trait variation were obtained in the absence of any detected linked QTL. However, we reject the causality of several commercialized DNA tests, including an association between TG_X05380:c.422C>T and marbling in Angus cattle.
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Affiliation(s)
- M C McClure
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211, USA
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17
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Rolf MM, Taylor JF, Schnabel RD, McKay SD, McClure MC, Northcutt SL, Kerley MS, Weaber RL. Impact of reduced marker set estimation of genomic relationship matrices on genomic selection for feed efficiency in Angus cattle. BMC Genet 2010; 11:24. [PMID: 20403185 PMCID: PMC2868785 DOI: 10.1186/1471-2156-11-24] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2009] [Accepted: 04/19/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Molecular estimates of breeding value are expected to increase selection response due to improvements in the accuracy of selection and a reduction in generation interval, particularly for traits that are difficult or expensive to record or are measured late in life. Several statistical methods for incorporating molecular data into breeding value estimation have been proposed, however, most studies have utilized simulated data in which the generated linkage disequilibrium may not represent the targeted livestock population. A genomic relationship matrix was developed for 698 Angus steers and 1,707 Angus sires using 41,028 single nucleotide polymorphisms and breeding values were estimated using feed efficiency phenotypes (average daily feed intake, residual feed intake, and average daily gain) recorded on the steers. The number of SNPs needed to accurately estimate a genomic relationship matrix was evaluated in this population. RESULTS Results were compared to estimates produced from pedigree-based mixed model analysis of 862 Angus steers with 34,864 identified paternal relatives but no female ancestors. Estimates of additive genetic variance and breeding value accuracies were similar for AFI and RFI using the numerator and genomic relationship matrices despite fewer animals in the genomic analysis. Bootstrap analyses indicated that 2,500-10,000 markers are required for robust estimation of genomic relationship matrices in cattle. CONCLUSIONS This research shows that breeding values and their accuracies may be estimated for commercially important sires for traits recorded in experimental populations without the need for pedigree data to establish identity by descent between members of the commercial and experimental populations when at least 2,500 SNPs are available for the generation of a genomic relationship matrix.
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Affiliation(s)
- Megan M Rolf
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211-5300, USA
| | - Jeremy F Taylor
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211-5300, USA
| | - Robert D Schnabel
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211-5300, USA
| | - Stephanie D McKay
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211-5300, USA
| | - Matthew C McClure
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211-5300, USA
| | | | - Monty S Kerley
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211-5300, USA
| | - Robert L Weaber
- Division of Animal Sciences, University of Missouri, Columbia, MO 65211-5300, USA
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McClure MC, McKay SD, Schnabel RD, Taylor JF. Assessment of DNA extracted from FTA cards for use on the Illumina iSelect BeadChip. BMC Res Notes 2009; 2:107. [PMID: 19531223 PMCID: PMC2704227 DOI: 10.1186/1756-0500-2-107] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2009] [Accepted: 06/16/2009] [Indexed: 11/23/2022] Open
Abstract
Background As FTA® cards provide an ideal medium for the field collection of DNA we sought to assess the quality of genomic DNA extracted from this source for use on the Illumina BovineSNP50 iSelect BeadChip which requires unbound, relatively intact (fragment sizes ≥ 2 kb), and high-quality DNA. Bovine blood and nasal swab samples collected on FTA cards were extracted using the commercially available GenSolve kit with a minor modification. The call rate and concordance of genotypes from each sample were compared to those obtained from whole blood samples extracted by standard PCI extraction. Findings An ANOVA analysis indicated no significant difference (P > 0.72) in BovineSNP50 genotype call rate between DNA extracted from FTA cards by the GenSolve kit or extracted from whole blood by PCI. Two sample t-tests demonstrated that the DNA extracted from the FTA cards produced genotype call and concordance rates that were not different to those produced by assaying DNA samples extracted by PCI from whole blood. Conclusion We conclude that DNA extracted from FTA cards by the GenSolve kit is of sufficiently high quality to produce results comparable to those obtained from DNA extracted from whole blood when assayed by the Illumina iSelect technology. Additionally, we validate the use of nasal swabs as an alternative to venous blood or buccal samples from animal subjects for reliably producing high quality genotypes on this platform.
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Affiliation(s)
- Matthew C McClure
- Division of Animal Sciences, University of Missouri-Columbia, Columbia, MO, USA.
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19
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Abstract
The availability of whole genome sequences for individual species will change the landscape for livestock genomic research. Animal scientists will have access to whole-genome sequence-based technologies such as high-throughput SNP genotyping assays, gene expression profiling, methylation profiling, RNA interference, and genome resequencing that will revolutionize the scale upon which research will be conducted. These technologies will also alter the ways we think about addressing industry and scientific problems. In this review, we discuss the scientific bases for these emerging technologies and present recent highlights of their application in human, model species, and livestock as well as their potential for future applications in livestock. Additionally, we discuss strategies for their use in the genetic improvement and management of livestock. In particular, we present a strategy for the simultaneous identification of causal mutations underlying phenotypic traits in livestock and discuss issues that will arise in the application of whole genome selection for the prediction of genetic merit in livestock. We also point out that the statistical analysis that underlies the whole genome selection methodology is a sophisticated enhancement of single marker association mapping analysis to allow the entire genome to be simultaneously analyzed.
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Affiliation(s)
- E M Sellner
- Division of Animal Sciences, University of Missouri, Columbia 65211, USA
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20
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Abstract
Adult male rats were exposed to a diet containing 500 ppm added lead as lead acetate (group lead-diet) or a control diet containing no added chemicals (group control-diet) for 61 days prior to commencing fixed-ratio 32 (FR 32) lever press training for water reinforcement. After steady state responding was achieved, all animals received serial administrations of acute doses of ethanol prior to the daily training session. Specifically, lead-diet and control-diet rats received i.p. injections of .25, .5, .75, 1.0, and 1.25 g/kg ethanol, in ascending order, alternating daily with injections of saline. The results revealed a dose-dependent rate-depressant effect, with higher doses of ethanol producing more behavioral suppression than lower doses for both groups. In addition, at the dose of 1.0 g/kg it was observed that the suppressive effects of ethanol on schedule-controlled responding were reduced among lead-treated animals relative to controls. These data are discussed in terms of lead-induced attenuation of the pharmacologic effects of ethanol.
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Affiliation(s)
- C A Grover
- Department of Medical Pharmacology and Toxicology, Texas A&M University, College Station 77843
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