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Oliver KF, Geary TW, Kiser JN, Galliou JM, Van Emon ML, Seabury CM, Spencer TE, Neibergs HL. Loci associated with conception rate in crossbred beef heifers. PLoS One 2020; 15:e0230422. [PMID: 32271764 PMCID: PMC7145093 DOI: 10.1371/journal.pone.0230422] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2019] [Accepted: 03/01/2020] [Indexed: 11/18/2022] Open
Abstract
The inability of beef cattle to maintain full term pregnancies has become an economic concern for the beef industry. Herd management and nutritional improvements have alleviated environmental impacts on embryonic and fetal loss, yet additional gains can be made through genomic selection. The objectives of this study were to identify loci and gene-sets in crossbred beef heifers associated with the number of services required to become pregnant (TBRD) and heifer conception rate at first service (HCR1). Heifers (n = 709) from a commercial beef operation underwent one round of artificial insemination, before exposure to bulls for natural service for 50 days. Pregnancy and time of conception was determined by ultrasound 35 days after the breeding season. Heifers were genotyped using the GeneSeek (Lincoln, NE) Bovine GGP50K BeadChip prior to genome-wide association analyses (GWAA) conducted using an EIGENSTRAT-like model to identify loci associated (P < 1 × 10−5) with TBRD and HCR1. One locus was associated (P = 8.97 × 10−6) with TBRD on BTA19 and included the positional candidate gene ASIC2, which is differentially expressed in the endometrium of fertility classified heifers, and the positional candidate gene, SPACA3. Gene-set enrichment analyses using SNP (GSEA-SNP) data, was performed and identified one gene-set, oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen as enriched (NES = 3.15) with TBRD and contained nine leading edge genes that contributed to the enrichment of the gene set. The enriched gene-set is involved in catalyzing oxidation-reduction reactions, which have been associated with oxidative stressors impacting pregnancy success. No loci were associated nor gene-sets enriched with HCR1. Identification of loci, positional candidate genes, gene-sets and leading edge genes enriched for fertility facilitate genomic selection that allows producers to select for reproductively superior cattle, reduce costs associated with infertility, and increase percent calf crop.
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Affiliation(s)
- K. F. Oliver
- Department of Animal Sciences, Washington State University, Pullman, WA, United States of America
| | - T. W. Geary
- USDA-ARS Fort Keogh LARRL, Miles City, MT, United States of America
| | - J. N. Kiser
- Department of Animal Sciences, Washington State University, Pullman, WA, United States of America
| | - J. M. Galliou
- Department of Animal Sciences, Washington State University, Pullman, WA, United States of America
| | - M. L. Van Emon
- Department of Animal and Range Sciences, Montana State University, Bozeman, MT, United States of America
| | - C. M. Seabury
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, TX, United States of America
| | - T. E. Spencer
- Division of Animal Sciences, University of Missouri, Columbia, MO, United States of America
| | - H. L. Neibergs
- Department of Animal and Range Sciences, Montana State University, Bozeman, MT, United States of America
- * E-mail:
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Kiser JN, Cornmesser MA, Blackburn R, McGuirk SM, Taylor JF, Seabury CM, Womack JE, Neibergs HL. Validating loci associated with bovine respiratory disease complex in pre-weaned Holstein calves. Anim Genet 2019; 51:91-94. [PMID: 31696966 DOI: 10.1111/age.12878] [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: 05/28/2019] [Revised: 09/20/2019] [Accepted: 10/17/2019] [Indexed: 11/28/2022]
Abstract
Bovine respiratory disease (BRD) is considered one of the most economically important diseases in the cattle industry. Ultimately, the selection of cattle that are less susceptible to disease will allow producers to reduce the prevalence of BRD and lessen its economic impact. The objective of this study was to validate previously identified loci associated with susceptibility to BRD in an independent population of 140 pre-weaned Holstein calves from Wisconsin (WI). Using the McGuirk health scoring system, calves were classified as either clinically affected with BRD (n = 35) or healthy (n = 105). Additive genotypic tests were performed for genomic regions previously associated with susceptibility to BRD in calves from California (CA) and New Mexico (NM). Using this method, 4 loci (P < 0.01) consisting of 10 SNP were validated in the WI population, including 2 loci from CA, 1 locus from NM, and 1 locus from a combined CA + NM population. Most of the positional candidate genes and transcription factor binding site motifs associated with these loci have functions related to innate and adaptive immune responses. The validation of loci associated with susceptibility to BRD in independent populations allows producers to more reliably select cattle that are less susceptible to BRD, improving animal welfare, decreasing the annual revenue losses, and lowering the prevalence of the disease.
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Affiliation(s)
- J N Kiser
- Department of Animal Sciences, Washington State University, Pullman, WA, 99164, USA
| | - M A Cornmesser
- Department of Animal Sciences, Washington State University, Pullman, WA, 99164, USA
| | - R Blackburn
- School of Veterinary Medicine, University of Wisconsin - Madison, Madison, WI, 53706, USA
| | - S M McGuirk
- Department of Medical Sciences, School of Veterinary Medicine, University of Wisconsin - Madison, Madison, WI, 53706, USA
| | - J F Taylor
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - C M Seabury
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA
| | - J E Womack
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA
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- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA
| | - H L Neibergs
- Department of Animal Sciences, Washington State University, Pullman, WA, 99164, USA
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Clancey E, Kiser JN, Moraes JGN, Dalton JC, Spencer TE, Neibergs HL. Genome-wide association analysis and gene set enrichment analysis with SNP data identify genes associated with 305-day milk yield in Holstein dairy cows. Anim Genet 2019; 50:254-258. [PMID: 30994194 DOI: 10.1111/age.12792] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/23/2018] [Indexed: 11/29/2022]
Abstract
Milk production traits, such as 305-day milk yield (305MY), have been under direct selection to improve production in dairy cows. Over the past 50 years, the average milk yield has nearly doubled, and over 56% of the increase is attributable to genetic improvement. As such, additional improvements in milk yield are still possible as new loci are identified. The objectives of this study were to detect SNPs and gene sets associated with 305MY in order to identify new candidate genes contributing to variation in milk production. A population of 781 primiparous Holstein cows from six central Washington dairies with records of 305MY and energy corrected milk were used to perform a genome-wide association analysis (GWAA) using the Illumina BovineHD BeadChip (777 962 SNPs) to identify QTL associated with 305MY (P < 1.0 × 10-5 ). A gene set enrichment analysis with SNP data (GSEA-SNP) was performed to identify gene sets (normalized enrichment score > 3.0) and leading edge genes (LEGs) influencing 305MY. The GWAA identified three QTL comprising 34 SNPs and 30 positional candidate genes. In the GSEA-SNP, five gene sets with 58 unique and 24 shared LEGs contributed to 305MY. Identification of QTL and LEGs associated with 305MY can provide additional targets for genomic selection to continue to improve 305MY in dairy cattle.
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Affiliation(s)
- E Clancey
- Department of Animal Sciences, Center for Reproductive Biology, Washington State University, PO Box 646310, Pullman, WA, 99164-6310, USA
| | - J N Kiser
- Department of Animal Sciences, Center for Reproductive Biology, Washington State University, PO Box 646310, Pullman, WA, 99164-6310, USA
| | - J G N Moraes
- Division of Animal Sciences, S158A Animal Sciences Research Center, University of Missouri, Columbia, MO, 65211, USA
| | - J C Dalton
- Department of Animal and Veterinary Sciences, Caldwell Research and Extension Center, University of Idaho, 1904 E Chicago St, Suite A, B, Caldwell, ID, 83605, USA
| | - T E Spencer
- Division of Animal Sciences, S158A Animal Sciences Research Center, University of Missouri, Columbia, MO, 65211, USA
| | - H L Neibergs
- Department of Animal Sciences, Center for Reproductive Biology, Washington State University, PO Box 646310, Pullman, WA, 99164-6310, USA
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Neupane M, Kiser JN, Neibergs HL. Gene set enrichment analysis of SNP data in dairy and beef cattle with bovine respiratory disease. Anim Genet 2018; 49:527-538. [PMID: 30229962 DOI: 10.1111/age.12718] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/21/2018] [Indexed: 02/01/2023]
Abstract
Bovine respiratory disease (BRD) is a complex disease that is associated with infection by bacterial and viral pathogens when cattle fail to adequately respond to stress. The objective of this study was to use gene set enrichment analysis of SNP data (GSEA-SNP) and a network analysis (ingenuity pathway analysis) to identify gene sets, genes within gene sets (leading-edge genes) and upstream regulators associated with BRD in pre-weaned dairy calves and beef feedlot cattle. BRD cases and controls were diagnosed using the McGuirk health scoring system. Holstein calves were sampled from commercial calf-raising facilities in California (1003 cases and 1011 controls) and New Mexico (376 cases and 372 controls). Commercial feedlot cattle were sampled from Colorado (500 cases and 499 controls) and Washington (504 cases and 497 controls). There were 102 and 237 unique leading-edge genes identified in the dairy calf and beef cattle populations respectively. Six leading-edge genes (ADIPOQ, HTR2A, MIF, PDE6G, PRDX3 and SNCA) were associated with BRD in both dairy and beef cattle. Network analysis identified glucose as the most influential upstream regulator in dairy cattle, whereas in beef cattle, TNF was the most influential upstream regulator. The genes, gene sets and upstream regulators associated with BRD have common functions associated with immunity, inflammation and pulmonary disease and provide insights into the mechanisms that are critical to BRD susceptibility in cattle.
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Affiliation(s)
- M Neupane
- Department Animal Sciences, Washington State University, P.O. Box 646310, Pullman, WA, 99164-6310, USA
| | - J N Kiser
- Department Animal Sciences, Washington State University, P.O. Box 646310, Pullman, WA, 99164-6310, USA
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- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station, TX, 77843, USA
| | - H L Neibergs
- Department Animal Sciences, Washington State University, P.O. Box 646310, Pullman, WA, 99164-6310, USA
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Neibergs HL, Kiser JN, Neupane M, Seabury CM, Taylor JF, Cornmesser MA, McGuirk S, Blackburn R, Consortium BRD, Womack JE. 204 Genome-Wide Association Analysis Identifies QTL Associated with Clinical and Sub-Clinical Bovine Respiratory Disease. J Anim Sci 2018. [DOI: 10.1093/jas/sky073.201] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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)
- H L Neibergs
- Department of Animal Science, Washington State University, Pullman, WA
| | - J N Kiser
- Department of Animal Science, Washington State University, Pullman, WA
| | - M Neupane
- Department of Animal Science, Washington State University, Pullman, WA
| | - C M Seabury
- Department of Veterinary Pathobiology, College of Veterinary Medicine & Biomedical Sciences, Texas A&M University System, College Station, TX
| | | | - M A Cornmesser
- Department of Animal Science, Washington State University, Pullman, WA
| | - S McGuirk
- University of Wisconsin, Madison, WI
| | | | | | - J E Womack
- Texas A&M University, College Station, TX
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Kiser JN, Lawrence TE, Neupane M, Seabury CM, Taylor JF, Womack JE, Neibergs HL. Rapid Communication: Subclinical bovine respiratory disease - loci and pathogens associated with lung lesions in feedlot cattle. J Anim Sci 2018; 95:2726-2731. [PMID: 28727052 PMCID: PMC7110184 DOI: 10.2527/jas.2017.1548] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Bovine respiratory disease (BRD) is an economically important disease of feedlot cattle that is caused by viral and bacterial pathogen members of the BRD complex. Many cases of subclinical BRD go untreated and are not detected until slaughter, when lung lesions are identified. The objectives of this study were to identify which BRD pathogens were associated with the presence of lung lesions at harvest and to identify genomic loci that were associated with susceptibility to lung lesions as defined by consolidation of the lung and/or the presence of fibrin tissue. Steers from a Colorado feedlot (n = 920) were tested for the presence of viral and bacterial pathogens using deep pharyngeal and mid-nasal swabs collected on entry into the study. Pathogen profiles were compared between cattle with or without lung consolidation (LC), fibrin tissue in the lung (FT), a combination of LC and FT in the same lung (lung lesions [LL]), and hyperinflated lungs (HIF) at harvest. Genotyping was conducted using the Illumina BovineHD BeadChip. Genomewide association analyses (GWAA) were conducted using EMMAX (efficient mixed-model association eXpedited), and pseudoheritabilities were estimated. The pathogen profile comparisons revealed that LC (P = 0.01, odds ratio [OR] = 3.37) and LL cattle (P = 0.04, OR = 4.58) were more likely to be infected with bovine herpes virus-1 and that HIF cattle were more likely to be infected with Mycoplasma spp. (P = 0.04, OR = 4.33). Pseudoheritability estimates were 0.25 for LC, 0.00 for FT, 0.28 for LL, and 0.13 for HIF. Because pseudoheritability for FT was estimated to be 0, GWAA results for FT were not reported. There were 4 QTL that were moderately associated (P < 1 × 10−5) with only LC, 2 that were associated with only LL, and 1 that was associated with LC and LL. Loci associated with HIF included 12 that were moderately associated and 3 that were strongly associated (uncorrected P < 5 × 10−7). A 24-kb region surrounding significant lead SNP was investigated to identify positional candidate genes. Many positional candidate genes underlying or flanking the detected QTL have been associated with signal transduction, cell adhesion, or gap junctions, which have functional relevance to the maintenance of lung health. The identification of pathogens and QTL associated with the presence of lung abnormalities in cattle exhibiting subclinical BRD allows the identification of loci that may not be detected through manifestation of clinical disease alone.
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Kiser JN, Neupane M, White SN, Neibergs HL. Identification of genes associated with susceptibility to Mycobacterium avium ssp. paratuberculosis (Map) tissue infection in Holstein cattle using gene set enrichment analysis-SNP. Mamm Genome 2017; 29:539-549. [PMID: 29185027 DOI: 10.1007/s00335-017-9725-4] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2017] [Accepted: 11/18/2017] [Indexed: 02/07/2023]
Abstract
Multiple genome-wide association analyses have investigated susceptibility to bovine paratuberculosis, but few loci have been identified across independent cattle populations. A SNP-based gene set enrichment analysis (GSEA-SNP) allows expanded identification of genes with moderate effects on a trait through the enrichment of gene sets instead of identifying only few loci with large effects. Therefore, the objective of this study was to identify genes that were moderately associated with Mycobacterium avium ssp. paratuberculosis (Map) tissue infection using GSEA-SNP in Holstein cattle from the Pacific Northwest (PNW; n = 205) and from the PNW and Northeast (PNW+NE; n = 245) which were previously genotyped with the Illumina BovineSNP50 BeadChip. The GSEA-SNP utilized 4389 gene sets from five databases. For each annotated gene in the UMD3.1 assembly (n = 19,723), the most significant SNP within each gene and its surrounding region (10 kb up- and downstream) was selected as a proxy for that gene. Any gene set with a normalized enrichment score > 2.5 was considered enriched. Thirteen gene sets (8 PNW GSEA-SNP; 5 PNW+NE) were enriched in these analyses and all have functions that relate to nuclear factor kappa beta. Nuclear factor kappa beta is critical to gut immune responses, implicated in host immune responses to other mycobacterial diseases, and has established roles in inflammation as well as cancer. Gene sets and genes moderately associated with Map infection could be used in genomic selection to allow producers to select for less susceptible cattle, lower the prevalence of the disease, and reduce economic losses.
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Affiliation(s)
- J N Kiser
- Department of Animal Sciences, Washington State University, Pullman, WA, 99164, USA.
| | - M Neupane
- Department of Animal Sciences, Washington State University, Pullman, WA, 99164, USA
| | - S N White
- USDA-ARS Animal Disease Research Unit, Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, 99164, USA
| | - H L Neibergs
- Department of Animal Sciences, Washington State University, Pullman, WA, 99164, USA
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Mutch JL, Neibergs HL, Neupane M, Michal JJ, Garrick DJ, Kerley MS, Shike DW, Beever JE, Hansen SL, Taylor JF, Efficiency Consortium USF, Johnson KA. 587 The role of diet composition fed during residual feed intake determinations and the impact of the diet on the gene sets associated with efficiency as determined by a gene set enrichment analysis. J Anim Sci 2017. [DOI: 10.2527/asasann.2017.587] [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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Kiser JN, White SN, Johnson KA, Hoff JL, Taylor JF, Neibergs HL. Identification of loci associated with susceptibility to subspecies () tissue infection in cattle. J Anim Sci 2017; 95:1080-1091. [PMID: 28380509 DOI: 10.2527/jas.2016.1152] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Johne's disease is a contagious bacterial infection of cattle caused by ssp. (). A previous genome-wide association analysis (GWAA) in Holstein cattle identified QTL on BTA3 and BTA9 that were highly associated (P < 5 × 10) and on BTA1, BTA16, and BTA21 that were moderately associated (P < 5 × 10) with Map tissue infection. The objectives of this study were to validate previous GWAA results in Jersey cattle ( = 57), Holstein cattle from the Pacific Northwest (PNW, = 205) and a combined Holstein population from the PNW and the Northeast (PNW + NE, = 423), and also identify new loci associated with tissue infection. DNA was genotyped using the Illumina BovineSNP50 BeadChip, and the PNW + NE data was also imputed to whole genome sequence level using Run4 of the 1000 Bull Genomes project with Beagle v 4.1 and FImpute. Cases were ileocecal node positive and controls were negative for by quantitative PCR (qPCR). Individuals were removed for SNP call rate < 90%, and SNP were removed for genotype call rate < 90% or minor allele frequency < 1%. For the Jersey, PNW, and PNW + NE, GWAA were conducted using an allelic dosage model. For the PNW and the PNW + NE, an additional efficient mixed-model association eXpedited (EMMAX) analysis was performed using additive, dominance and recessive models. Seven QTL on BTA22 were identified in the Jersey population with the most significant ( = 4.45 × 10) located at 21.7 megabases (Mb). Six QTL were associated in the PNW and the PNW + NE analyses, including a QTL previously identified on BTA16 in the NE population. The most significant locus for the PNW was located on BTA21 at 61 Mb ( = 8.61 × 10) while the most significant locus for the PNW + NE was on BTA12 at 90 Mb ( = 2.33 × 10). No additional QTL were identified with the imputed GWAA. Putative positional candidate genes were identified within 50 kb 5' and 3' of each QTL. Two positional candidate genes were identified in Jersey cattle, 1 identified in the PNW and 8 in the PNW + NE populations. Many identified positional candidate genes are involved in signal transduction, have immunological functions, or have putative functional relevance in entry into host cells. This study supported 2 previously identified SNP within a QTL on BTA16 and identified 16 new QTL, including 2 found in the PNW and the PNW+NE, associated with tissue infection.
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Taylor JF, Beever JE, Decker JE, Freetly HC, Garrick DJ, Hansen SL, Johnson KA, Kerley MS, Loy DD, Neibergs HL, Saatchi M, Schnabel RD, Seabury CM, Shike DW, Spangler ML, Weaber RL. 331 The genetic improvement of feed efficiency in beef cattle. J Anim Sci 2017. [DOI: 10.2527/asasmw.2017.331] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [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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Kiser JN, Lawrence TE, Neupane M, Seabury CM, Taylor JF, Womack JE, Neibergs HL. Rapid Communication: Subclinical bovine respiratory disease – loci and pathogens associated with lung lesions in feedlot cattle. J Anim Sci 2017. [DOI: 10.2527/jas2017.1548] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [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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Kiser JN, White SN, Johnson KA, Hoff JL, Taylor JF, Neibergs HL. Identification of loci associated with susceptibility to subspecies ( ) tissue infection in cattle. J Anim Sci 2017. [DOI: 10.2527/jas2016.1152] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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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Neibergs JS, Neibergs HL. 0289 The value of genetic selection in reducing economic losses from bovine respiratory disease complex in beef cattle feedlots. J Anim Sci 2016. [DOI: 10.2527/jam2016-0289] [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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Pierce CF, Kiser JN, Hoff JL, Neupane M, White SN, Taylor JF, Neibergs HL. 0203 Identification of loci on chromosome 3 associated with susceptibility to bovine paratuberculosis using genotypes imputed to whole genome sequence in Holstein cows. J Anim Sci 2016. [DOI: 10.2527/jam2016-0203] [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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Spencer TE, Neibergs HL, Hansen PJ, Cole JB, Dalton J, Moore DA, Chahine M, De Vries A. 0694 Improving fertility of dairy cattle using translational genomics. J Anim Sci 2016. [DOI: 10.2527/jam2016-0694] [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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Mutch JL, Neupane M, Seabury CM, Neibergs HL, Tizioto PC, Garrick DJ, Kerley MS, Shike DW, Beever JE, Taylor JF, Johnson KA. 1496 Identification of biological pathways involved in residual feed intake in Hereford cattle through gene set enrichment analysis. J Anim Sci 2016. [DOI: 10.2527/jam2016-1496] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [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)
- J. L. Mutch
- Department of Animal Sciences, Washington State University, Pullman
| | - M. Neupane
- Department of Animal Sciences, Washington State University, Pullman
| | - C. M. Seabury
- College of Veterinary Medicine, Texas A&M University, College Station
| | - H. L. Neibergs
- Department of Animal Sciences, Washington State University, Pullman
| | | | - D. J. Garrick
- Department of Animal Science, Iowa State University, Ames
| | | | | | | | | | - K. A. Johnson
- Department of Animal Sciences, Washington State University, Pullman
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Gershwin LJ, Vaneenennaam A, Taylor JF, Kim J, Toaff-Rosenstein RL, Neibergs HL, Womack JE. 0284 Differential gene expression in cattle challenged with single pathogens of the bovine respiratory disease complex. J Anim Sci 2016. [DOI: 10.2527/jam2016-0284] [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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Thomas MG, Enns RM, Hagevoort R, Neibergs JS, Van Eenennaam AL, Neibergs HL, Womack JE. 1750 Integrated program for reducing bovine respiratory disease complex (BRDC) in cattle, coordinated agricultural project (CAP): Translation of multi-omics research results into teaching programs. J Anim Sci 2016. [DOI: 10.2527/jam2016-1750] [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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Neupane M, Hoff JL, Taylor JF, Seabury CM, Womack JE, Bovine T, Neibergs HL. 0753 Refinement of the DST locus associated with bovine respiratory disease complex in Holstein calves. J Anim Sci 2016. [DOI: 10.2527/jam2016-0753] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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. Neupane
- Department of Animal Sciences, Washington State University, Pullman
| | | | | | | | | | | | - H. L. Neibergs
- Department of Animal Sciences, Washington State University, Pullman
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Taylor JF, Neibergs HL, Seabury CM, Vaneenennaam A, Decker JE, Hoff JL, Tizioto PC, Womack JE, Schnabel RD. 0286 Identification of causal variants underlying pathogen susceptibility and translation to genetic improvement. J Anim Sci 2016. [DOI: 10.2527/jam2016-0286] [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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Keuter E, Seabury CM, Neupane M, Kiser JN, Moraes J, Burns G, Spencer TE, Neibergs HL. 0746 Identification of loci associated with fertility in United States Holstein heifers. J Anim Sci 2016. [DOI: 10.2527/jam2016-0746] [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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Seabury CM, Neibergs HL, Taylor JF, Womack JE. 0285 Genome-wide association study of bovine respiratory disease complex in U.S. feedlot cattle. J Anim Sci 2016. [DOI: 10.2527/jam2016-0285] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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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Kiser JN, Hoff JL, White SN, Taylor JF, Neibergs HL. 0335 Identification of loci associated with susceptibility to bovine paratuberculosis using imputed genotypes based on whole genome sequencing. J Anim Sci 2016. [DOI: 10.2527/jam2016-0335] [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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VanTassell CP, Spangler G, Bickhart DM, Wiggans GR, Cole JB, Taylor JF, Neibergs HL, Seabury CM, Van Eenennaam AL, Womack JE. 0288 Calculation of genomic predicted transmitting abilities for bovine respiratory disease complex in Holsteins. J Anim Sci 2016. [DOI: 10.2527/jam2016-0288] [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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Neupane M, Taylor JF, Seabury CM, Womack JE, Neibergs HL. 0287 Gene set enrichment analysis of bovine respiratory disease complex SNP data in feedlot cattle. J Anim Sci 2016. [DOI: 10.2527/jam2016-0287] [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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Kiser JN, Seabury CM, Taylor JF, Womack JE, Hagevoort R, Lehenbauer TW, Aly SS, Van Eenennaam AL, Neibergs HL. 0375 Clinical signs associated with bovine respiratory disease diagnosis and high heritability in beef and dairy cattle. J Anim Sci 2016. [DOI: 10.2527/jam2016-0375] [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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Scraggs E, Zanella R, Wojtowicz A, Taylor JF, Gaskins CT, Reeves JJ, de Avila JM, Neibergs HL. Estimation of inbreeding and effective population size of full-blood Wagyu cattle registered with the American Wagyu Cattle Association. J Anim Breed Genet 2013; 131:3-10. [PMID: 24373025 DOI: 10.1111/jbg.12066] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [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: 06/27/2013] [Accepted: 11/07/2013] [Indexed: 11/29/2022]
Abstract
The objective of this research was to examine the population structure of full-blood (100%) Wagyu cattle registered in the United States with the American Wagyu Association, with the aim of estimating and comparing the levels of inbreeding from both pedigree and genotypic data. A total of 4132 full-blood Wagyu cattle pedigrees were assessed and used to compute the inbreeding coefficients (FIT and FST ) and the effective population size (Ne ) from pedigree data for the period 1994 to 2011. In addition to pedigree analysis, 47 full-blood Wagyu cattle representing eight prominent sire lines in the American Wagyu cattle population were genotyped using the Illumina BovineSNP50 BeadChip. Genotypic data were then used to estimate genomic inbreeding coefficients (FROH ) by calculating runs of homozygosity. The mean inbreeding coefficient based on the pedigree data was estimated at 4.80%. The effective population size averaged 17 between the years 1994 and 2011 with an increase of 42.9 in 2000 and a drop of 1.8 in 2011. Examination of the runs of homozygosity revealed that the 47 Wagyu cattle from the eight prominent sire lines had a mean genomic inbreeding coefficient (FROH ) estimated at 9.08% compared to a mean inbreeding coefficient based on pedigree data of 4.8%. These data suggest that the mean genotype inbreeding coefficient of full-blood Wagyu cattle exceeds the inbreeding coefficient identified by pedigree. Inbreeding has increased slowly at a rate of 0.03% per year over the past 17 years. Wagyu breeders should continue to utilize many sires from divergent lines and consider outcrossing to other breeds to enhance genetic diversity and minimize the adverse effects of inbreeding in Wagyu.
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Affiliation(s)
- E Scraggs
- Department of Animal Sciences, Washington State University, Pullman, WA, USA
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Affiliation(s)
- H. L. Neibergs
- Department of Animal Sciences, Washington State University, Pullman 99164
| | - K. A. Johnson
- Department of Animal Sciences, Washington State University, Pullman 99164
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Zanella R, Whitlock RH, Neibergs HL. Short communication: refinement of genetic regions associated with Mycobacterium avium subspecies paratuberculosis tissue infection and tolerance to Johne's disease. J Dairy Sci 2011; 94:4230-6. [PMID: 21787960 DOI: 10.3168/jds.2011-4192] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2011] [Accepted: 04/19/2011] [Indexed: 02/01/2023]
Abstract
Johne's disease is a highly transmissible bacterial disease caused by Mycobacterium avium ssp. paratuberculosis (MAP). The objective of this study was to refine the locus associated with MAP tissue infection and the locus associated with tolerance to Johne's disease. Using a genome-wide association analysis, single nucleotide polymorphisms associated with MAP tissue infection and tolerance to Johne's disease on Bos taurus autosome (BTA)3 and BTA15, respectively, have previously been identified. A 235-kb region on BTA3 was evaluated with 42 single nucleotide polymorphisms, and a 193-kb region on BTA15 was evaluated with 54 single nucleotide polymorphisms in a group of 209 Holstein cows. Using a single marker association analysis and haplotype tests, we refined a region of 10.6 kb on BTA3 as being associated with MAP tissue infection and a region of 6.5 kb on BTA15 as being associated with tolerance to Johne's disease.
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Affiliation(s)
- R Zanella
- Department of Animal Sciences, Washington State University, Pullman, Washington 99164-6353, USA
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Zanella R, Settles ML, McKay SD, Schnabel R, Taylor J, Whitlock RH, Schukken Y, Van Kessel JS, Smith JM, Neibergs HL. Identification of loci associated with tolerance to Johne's disease in Holstein cattle. Anim Genet 2011; 42:28-38. [PMID: 20477805 DOI: 10.1111/j.1365-2052.2010.02076.x] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022]
Abstract
Johne's disease, caused by Mycobacterium avium subspecies paratuberculosis (Map), is a fatal disease in cattle. The objective of this study was to identify loci associated with tolerance in cows infected with Map. Tolerance was defined as a cow's fitness at a given level of Map infection intensity. Fitness was measured by Map faecal cultures, and Map infection intensity was measured by culturing four gut tissues. The quantitative phenotype of tolerance was defined by numerical indexes of cultures of peak (peak tolerance, PT) and average (average tolerance, AT) faecal and tissue Map from 245 Holstein cows. The categorical phenotype was defined as: ≥ 100 cfu Map tissue infection, and faecal shedding ≥ 75 cfu (intolerant) or <10 cfu (tolerant cows). In 94 cows, Map was identified in ≥ 1 tissue, including 44 cows with ≥ 100 Map tissue cfu and 36 with ≥ 1 faecal cfu. A genome-wide association analysis was performed after filtering, leaving genotypes for 45,789 SNPs in 90 animals for the quantitative phenotype and 16 cases and 25 controls for the categorical analysis of tolerance. rs41748405:A>C (BTA15) was associated with PT (P = 1.12 × 10(-7)) and AT (P = 2.17 × 10(-6)). Associations were identified with PT and adjacent SNPs ss61512613:A>G and ss61530518:A>G (BTA6) (P < 3.0 × 10(-5)), and with AT for ss61469568:A>G (BTA 2) (P = 3.3 × 10(-5)) and ss86284768:A>G (BTA1) (P = 3.31 × 10(-5)). For the categorical phenotype, an association was found with ss8632653:A>G (BTA6) (P < 5.0 × 10(-5)). This is the first study to identify loci associated with tolerance to Johne's disease.
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Affiliation(s)
- R Zanella
- Department of Animal Sciences, Washington State University, ASLB 210, Pullman, WA 99164, USA
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Brennan MD, Neibergs HL, Phillips K, Moseley S. Polymorphic markers for the arylsulfatase A gene reveal a greatly expanded meiotic map for the human 22q telomeric region. Genomics 2000; 63:430-2. [PMID: 10704291 DOI: 10.1006/geno.1999.6110] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Two microsatellite markers, D22S1743 and D22S1744, were developed for the arylsulfatase A (ARSA) region of chromosome 22q. Linkage analysis for 171 families, using nine reference markers covering all of 22q, placed these new markers 2.0 Kosambi cM distal to D22S526, making them more distal than any microsatellite markers currently on the Généthon or Marshfield linkage maps. Recombination between proximal markers D22S270/D22S683 and D22S446/D22S311 exhibited increased rates of female meiotic recombination compared to male recombination (P < 0.01). In contrast, the region encompassing sJCW16, D22S526, D22S1743, and D22S1744 exhibited relatively greater recombination in males (1.1 cM for females and 7.5 cM for males; chi(2); P < 0.005). These four distal markers lie in a region of hyperrecombination having a sex-averaged recombination ratio of between 8.3 (D22S1843/D22S1744) and 12 cM (sJCW16/D22S526) per megabase.
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Affiliation(s)
- M D Brennan
- Department of Biochemistry and Molecular Biology, University of Louisville Medical School, Louisville, Kentucky 40292, USA.
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Bosworth BT, Dean-Nystrom EA, Casey TA, Neibergs HL. Differentiation of F18ab+ from F18ac+ Escherichia coli by single-strand conformational polymorphism analysis of the major fimbrial subunit gene (fedA). Clin Diagn Lab Immunol 1998; 5:299-302. [PMID: 9605980 PMCID: PMC104513 DOI: 10.1128/cdli.5.3.299-302.1998] [Citation(s) in RCA: 17] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Toxin-producing Escherichia coli expressing F18 fimbriae colonizes the small intestines of weaned pigs and causes diarrhea, edema disease, or both. The F18 family is composed of two antigenic variants, F18ab and F18ac. Because many strains do not express F18 fimbriae in vitro, identification and differentiation of these two variants are difficult. Single-strand conformational polymorphism (SSCP) analysis is a rapid method for identifying genetic mutations and polymorphisms. The F18 major fimbrial subunit genes (fedA) of 138 strains were amplified by PCR, and genetic differences were detected by SSCP analysis. The SSCP analysis of the fedA gene differentiated F18ab+ strains from F18ac+ strains. Most strains classified as F18ab+ by SSCP analysis contained Shiga toxin 2e and enterotoxin genes. Most strains classified as F18ac+ by SSCP analysis contained only enterotoxin genes. The SSCP analysis was a useful method for predicting the antigenicity of F18+ E. coli and could also be used for analysis of other virulence genes in E. coli and other pathogenic bacteria.
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Affiliation(s)
- B T Bosworth
- Enteric Diseases and Food Safety Research Unit, National Animal Disease Center, USDA Agricultural Research Service, Ames, Iowa 50010, USA.
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Dietz AB, Neibergs HL, Womack JE, Kehrli ME. Rapid communication: single strand conformational polymorphism (SSCP) of bovine tumor necrosis factor alpha. J Anim Sci 1997; 75:2567. [PMID: 9303477 DOI: 10.2527/1997.7592567x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Affiliation(s)
- A B Dietz
- USDA, ARS, Metabolic Diseases and Immunology Research Unit, National Animal Disease Center, Ames, IA 50010, USA
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Hofmeister A, Neibergs HL, Pokorny RM, Galandiuk S. The natural resistance-associated macrophage protein gene is associated with Crohn's disease. Surgery 1997; 122:173-8; discussion 178-9. [PMID: 9288120 DOI: 10.1016/s0039-6060(97)90006-4] [Citation(s) in RCA: 57] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Abstract
BACKGROUND Identification of the genes causing inflammatory bowel disease (IBD) would enhance the understanding of and the treatment options for this disease. A hyperreactive immune response toward the intestinal flora has been implicated in the pathology of IBD. The natural resistance-associated macrophage protein (NRAMP) gene is believed to regulate macrophage function, especially the ability to fight intracellular pathogens. Genetic differences of NRAMP might, therefore, be associated with IBD. METHODS Two DNA markers (D2S434 and D2S1323) near NRAMP were polymerase chain reaction (PCR) amplified and genotyped with DNA from 103 patients with Crohn's disease, 85 patients with ulcerative colitis, and 98 control subjects. Clinical data were obtained for all patients. Comparisons were made by chi-squared analysis. Disease association with significant haplotypes was expressed as odds ratio. RESULTS Allele and genotype distributions were similar for both markers among all groups. Haplotype frequencies were different among Crohn's disease and control groups (p = 0.024). Two individual haplotypes of the patients with Crohn's disease were significant compared with control subjects: DA (p = 0.023; odds ratio, 0.5; 95% confidence interval, 0.3 to 0.9) and EA (p = 0.001; odds ratio, 3.5; 95% confidence interval, 1.6 to 3.2). The haplotype distribution was different within three age-of-onset groups of patients with Crohn's disease (p = 0.05). CONCLUSIONS This study is the first to report an association between the NRAMP gene and Crohn's disease.
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Affiliation(s)
- A Hofmeister
- Price Institute of Surgical Research, Department of Surgery, University of Louisville School of Medicine, Ky., USA
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Pokorny RM, Hofmeister A, Galandiuk S, Dietz AB, Cohen ND, Neibergs HL. Crohn's disease and ulcerative colitis are associated with the DNA repair gene MLH1. Ann Surg 1997; 225:718-23; discussion 723-5. [PMID: 9230812 PMCID: PMC1190876 DOI: 10.1097/00000658-199706000-00009] [Citation(s) in RCA: 32] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
OBJECTIVE The purpose of this study was to determine whether there is an association between Crohn's disease and ulcerative colitis with MLH1. SUMMARY BACKGROUND DATA Identification of genes involved in the etiology of inflammatory bowel disease may lead to the development of markers that objectively can define disease and permit therapy. The treatment of Crohn's disease of the colon and ulcerative colitis also is complicated by difficulties in differentiating the two conditions. METHODS The DNA and clinical data were obtained on 126 unrelated individuals (45 Crohn's disease, 36 ulcerative colitis, and 45 control subjects without intestinal disease). Polymerase chain reaction products were analyzed by single-strand conformation polymorphisms (MLH1 exons 9, 11, 14, 15, and 16) and polyacrylamide gel electrophoresis (markers D3S1611 and D3S1768). All comparisons were analyzed by chi square test. The association between single haplotypes and disease was expressed as relative odds. RESULTS MLH1 exons 9, 11, 14, and 16 were monomorphic. Two, four, and six alleles were detected in MLH1 exon 15, D3S1611, and D3S1768, respectively. Significant associations were observed for MLH1 exon 15/D3S1611 haplotypes AB (OR = 5.5; p = 0.007) and BA (p = 0.002) with Crohn's disease and for haplotypes AB (OR = 4.0; p = 0.042), BA (p = 0.035), and BC (OR = 6.1; p = 0.016) with ulcerative colitis. Family history of inflammatory bowel disease was associated with D3S1768/D3S1611 (p = 0.05) and MLH1 exon 15/D3S1611 haplotypes (p = 0.03). D3S1611/D3S1768 haplotype CD (OR = 11.3; p = 0.03) was associated with disease, whereas MLH1 exon 15/D3S1611 haplotype AA (OR = 0.25; p = 0.02) was protective. Comparisons of MLH1 exon 15/D3S1611 haplotypes of Crohn's colitis and patients with ulcerative colitis were significant (p = 0.037). CONCLUSIONS This study identifies a novel genetic and clinical association between MLH1 and inflammatory bowel disease.
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Affiliation(s)
- R M Pokorny
- Department of Surgery, Price Institute of Surgical Research, University of Louisville School of Medicine, Kentucky, USA
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Affiliation(s)
- R M Pokorny
- University of Louisville, Department of Surgery, KY 40292, USA
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Affiliation(s)
- H L Neibergs
- USDA, ARS, National Animal Disease Center, Ames, IA 50010-0070, USA
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Affiliation(s)
- H L Neibergs
- USDA, National Animal Disease Center, Ames, IA 50010-0070, USA
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Cohen ND, Martin LJ, Simpson RB, Wallis DE, Neibergs HL. Comparison of polymerase chain reaction and microbiological culture for detection of salmonellae in equine feces and environmental samples. Am J Vet Res 1996; 57:780-6. [PMID: 8725799] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
OBJECTIVE To compare the sensitivity of polymerase chain reaction (PCR) with microbiological culture for detecting salmonellae in equine fecal samples and equine environmental swab specimens. DESIGN Samples and specimens were tested by PCR and microbiological culture. SAMPLE POPULATION A fecal sample from each of 152 horses admitted consecutively to the clinic for evaluation by the outpatient service, 282 fecal samples from 110 hospitalized horses that had been submitted to the clinical microbiology laboratory, and 313 environmental swab specimens were examined. PROCEDURE Each sample and specimen in the study was tested, using PCR and microbiological culture. Results of PCR and culture were compared. RESULTS Significantly (P < 0.001) more fecal samples were positive by PCR than by microbiological culture. 26 of 152 (17.1%) fecal samples collected from horses admitted by the outpatient service were positive by PCR and none was positive by culture. 71 of 110 hospitalized horses were identified as positive by PCR, compared with 11 horses identified as positive by culture. All culture-positive horses were positive by PCR. Of the 11 culture-positive horses, 10 (90.9%) were identified as PCR positive after testing of the first sample submitted, compared with 7 (63.6%) by culture. All PCR-positive horses were detected after a total of 3 samples/horse were submitted, whereas as many as 5 samples/horse was required to identify all culture-positive horses. 8 of 313 environmental specimens were positive by PCR, and none was positive by culture. CONCLUSION The PCR method reported here was more sensitive, more rapid, and required submission of fewer samples or specimens than did microbiological culture for detecting salmonellae.
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Affiliation(s)
- N D Cohen
- Department of Large Animal Medicine and Surgery, College of Veterinary Medicine, Texas A&M University, College Station 77843, USA
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Cohen ND, Wallis DE, Neibergs HL, Hargis BM. Detection of Salmonella enteritidis in equine feces using the polymerase chain reaction and genus-specific oligonucleotide primers. J Vet Diagn Invest 1995; 7:219-22. [PMID: 7619905 DOI: 10.1177/104063879500700209] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023] Open
Abstract
Salmonella was identified in feces from horses, using the polymerase chain reaction (PCR) and genus-specific oligonucleotide primers. Feces from healthy horses were determined to be culture negative and PCR negative for Salmonella. Fecal samples were inoculated with known numbers of colony-forming units (CFU) of S. enteritidis. The fecal samples were enriched overnight in tetrathionate broth, and then DNA was extracted and amplified by PCR using genus-specific primers. Sensitivity of the assay extended to 10 degrees CFU Salmonella enteritidis/g feces; sensitivity of microbiologic culture with enrichment extended to 10 degrees CFU Salmonella enteritidis/g feces. Feces that were not inoculated with S. enteritidis were negative by the PCR. Detection of salmonellae in feces was possible using the PCR within 24 hours from the time of submission of samples. Because samples were enriched, isolates were available for determining antibiograms and serologic grouping or typing.
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Affiliation(s)
- N D Cohen
- Department of Large Animal Medicine & Surgery, College of Veterinary Medicine, Texas A&M University, College Station 77843, USA
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Abstract
Polymerase chain reaction (PCR) primers designed to amplify the octapeptide repeat region of the bovine prion gene were used to test the association of genotypes with bovine spongiform encephalitis (BSE) in 56 BSE-affected and 177 unaffected animals. Three alleles (A,B,C) were detected as single-strand conformation polymorphisms (SSCPs) and two alleles (1,2--representing six or five copies of the octapeptide repeat respectively) were detected as amplified double-strand fragment length polymorphisms (AMFLPs). Observed genotypes of SSCPs and AMFLPs were analysed by chi-square. The SSCP genotypes of nuclear family members of animals with BSE and BSE-affected animals were different (P < 0.001, P < 0.01) from unrelated animals of the same breed without BSE. No genotypic differences were found between the BSE-affected animals and their relatives (P > 0.469). No AMFLP genotypic differences were detected between BSE-affected animals, their relatives, unrelated animals of the same breed or animals of different breeds (P > 0.05). These data suggest that BSE-affected animals and their relatives are more likely to have the AA SSCP genotype than unrelated animals of the same breed or animals of different breeds.
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Affiliation(s)
- H L Neibergs
- Department of Veterinary Pathobiology, Texas A&M University, College Station 77843
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Cohen ND, Neibergs HL, Wallis DE, Simpson RB, McGruder ED, Hargis BM. Genus-specific detection of salmonellae in equine feces by use of the polymerase chain reaction. Am J Vet Res 1994; 55:1049-54. [PMID: 7978642] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Members of the genus Salmonella were identified in feces from horses, using the polymerase chain reaction (PCR) and genus-specific oligonucleotide primers. Feces from healthy horses were determined to be culture-negative for Salmonella spp. Fecal samples were inoculated with known numbers of colony-forming units (CFU) of S anatum, S derby, S enteritidis, S heidelberg, S newport, and S typhimurium. The DNA was extracted from fecal samples and amplified by PCR, using genus-specific primers. Sensitivity of the assay extended to 10(3) CFU of Salmonella sp/g of feces; sensitivity of microbiologic culture with enrichment extended to 10(2) CFU of Salmonella sp/g of feces. Feces that were not inoculated with Salmonella spp were negative by the PCR. Detection of Salmonellae in feces was possible, using the PCR, within 10 to 12 hours from the time of submission of samples.
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Affiliation(s)
- N D Cohen
- Department of Large Animal Medicine & Surgery, College of Veterinary Medicine, Texas A&M University, College Station 77843
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Cohen ND, Wallis DE, Neibergs HL, McElroy AP, McGruder ED, DeLoach JR, Corrier DE, Hargis BM. Comparison of the polymerase chain reaction using genus-specific oligonucleotide primers and microbiologic culture for the detection of Salmonella in drag-swabs from poultry houses. Poult Sci 1994; 73:1276-81. [PMID: 7971671 DOI: 10.3382/ps.0731276] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023] Open
Abstract
Drag-swab samples were collected from 18 poultry houses at 9 broiler farms. Fifty drag-swab samples were tested for Salmonella by microbiologic culture using selective enrichment and the polymerase chain reaction (PCR) with oligonucleotide primers specific for all members of the genus Salmonella. Drag-swab samples were tested for Salmonella using PCR before and after enrichment. Only one sample was positive by PCR prior to enrichment. Forty-seven of the drag-swabs samples tested after enrichment were positive for Salmonella using PCR, and 29 were positive by microbiologic culture. All but one of the culture-positive samples were positive by PCR; this discordant sample was classified as indeterminate by PCR. Salmonella was identified in houses from all nine farms by PCR and eight of nine farms by microbiologic culture. Salmonella was found in all 18 houses by PCR and in 15 of 18 houses by microbiologic culture. In this study, PCR was significantly (P < .001) more sensitive than culture for environmental monitoring of Salmonella using drag-swabs.
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Affiliation(s)
- N D Cohen
- Department of Large Animal Medicine and Surgery, College of Veterinary Medicine, Texas A&M University, College Station 77843
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Abstract
Three loci were physically mapped with the use of a bovine x rodent hybrid somatic cell panel. Bovine brain-specific protein eta amino chain (BSPN) and bovine microsatellites ILSTS001 (D7S3) and ILSTS011 (D14S2) were assigned to cattle syntenic groups/chromosomes U24/BTA 14, U22/BTA7, and U24/BTA 14, respectively.
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Affiliation(s)
- H L Neibergs
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station 77843
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Barendse W, Armitage SM, Kossarek LM, Shalom A, Kirkpatrick BW, Ryan AM, Clayton D, Li L, Neibergs HL, Zhang N. A genetic linkage map of the bovine genome. Nat Genet 1994; 6:227-35. [PMID: 8012383 DOI: 10.1038/ng0394-227] [Citation(s) in RCA: 353] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
A cattle genetic linkage map was constructed which marks about 90% of the expected length of the cattle genome. Over 200 DNA polymorphisms were genotyped in cattle families which comprise 295 individuals in full sibling pedigrees. One hundred and seventy-one loci were found linked to one other locus. Twenty nine of the 30 chromosome pairs are represented by at least one of the 36 linkage groups. Less than a 50 cM difference was found in the male and female genetic maps. The conserved loci on this map show as many differences in gene order compared to humans as is found between humans and mice. The conservation is consistent with the patterns of karyotypic evolution found in the rodents, primates and artiodactyls. This map will be important for localizing quantitative trait loci and provides a basis for further mapping.
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Affiliation(s)
- W Barendse
- CSIRO, Division of Tropical Animal Production, Gehrmann Laboratories, University of Queensland, Brisbane, Australia
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Cohen ND, McGruder ED, Neibergs HL, Behle RW, Wallis DE, Hargis BM. Detection of Salmonella enteritidis in feces from poultry using booster polymerase chain reaction and oligonucleotide primers specific for all members of the genus Salmonella. Poult Sci 1994; 73:354-7. [PMID: 8146085 DOI: 10.3382/ps.0730354] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Salmonella enteritidis was identified in feces from hens using the polymerase chain reaction (PCR) and oligonucleotide primers specific for all members of the genus Salmonella. Feces from specific-pathogen-free Leghorn hens were determined to be negative for Salmonella by microbiological culture and by the PCR. Fecal samples were inoculated with known numbers of colony-forming units of S. enteritidis. The DNA was extracted from fecal samples and amplified by the PCR using genus-specific primers. Salmonella were detected in all samples known to be positive; the sensitivity of the assay extended to 1 cfu of S. enteritidis/g feces. Feces that were not inoculated with Salmonella were negative. Microbiological culture was less sensitive than the PCR assay; results of culture of feces with less than 10(2) cfu/g were negative. Although S. enteritidis was used in this study, the oligonucleotide primers used in this study have been previously demonstrated to be genus-specific for Salmonella.
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Affiliation(s)
- N D Cohen
- Department of Large Animal Medicine and Surgery, College of Veterinary Medicine, Texas A&M University, College Station 77843
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Toldo SS, Fries R, Steffen P, Neibergs HL, Barendse W, Womack JE, Hetzel DJ, Stranzinger G. Physically mapped, cosmid-derived microsatellite markers as anchor loci on bovine chromosomes. Mamm Genome 1993; 4:720-7. [PMID: 8111120 DOI: 10.1007/bf00357796] [Citation(s) in RCA: 98] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
To identify physical and genetic anchor loci on bovine chromosomes, 13 cosmids, obtained after the screening of partial bovine cosmid libraries with the (CA)n microsatellite motif, were mapped by fluorescence in situ hybridization (FISH). Eleven cosmid probes yielded a specific signal on one of the bovine chromosomes and identified the following loci: D5S2, D5S3, D6S3, D8S1, D11S5, D13S1, D16S5, D17S2, D19S2, D19S3, D21S8. Two cosmids produced centromeric signals on many chromosomes. The microsatellite-containing regions were subcloned and sequenced. The sequence information revealed that the two centromeric cosmids were derived from bovine satellites 1.723 and 1.709, respectively. A cosmid located in the subtelomeric region of Chromosome (Chr) 17 (D17S2) had features of a chromosome-specific satellite. Primers were designed for eight of the nonsatellite cosmids, and seven of these microsatellites were polymorphic with between three and eight alleles on a set of outbred reference families. The polymorphic and chromosomally mapped loci can now be used to physically anchor other bovine polymorphic markers by linkage analysis. The microsatellite primers were also applied to DNA samples of a previously characterized panel of somatic hybrid cell lines, allowing the assignment of seven microsatellite loci to defined syntenic groups. These assignments confirmed earlier mapping results, revealed a probable case of false synteny, and placed two formerly unassigned syntenic groups on specific chromosomes.
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Affiliation(s)
- S S Toldo
- Department of Animal Science, Swiss Federal Institute of Technology, ETH Zentrum, Zurich
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Cohen ND, Neibergs HL, McGruder ED, Whitford HW, Behle RW, Ray PM, Hargis BM. Genus-specific detection of salmonellae using the polymerase chain reaction (PCR). J Vet Diagn Invest 1993; 5:368-71. [PMID: 8373849 DOI: 10.1177/104063879300500311] [Citation(s) in RCA: 51] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/30/2023] Open
Abstract
Oligonucleotide primers for the polymerase chain reaction (PCR) that enable genus-specific detection of members of the genus Salmonella were developed. The primers amplify a 496-bp genetic sequence of members of the genus Salmonella. Amplification of DNA extracted from all other genera of the family Enterobacteriaceae and various other gram-positive aerobic and anaerobic bacteria yielded negative results. Applications of the PCR using these genus-specific primers are discussed.
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Affiliation(s)
- N D Cohen
- Department of Large Animal Medicine and Surgery, College of Veterinary Medicine, Texas A&M University, College Station 77843
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Affiliation(s)
- H L Neibergs
- Department of Veterinary Pathobiology, College of Veterinary Medicine, Texas A&M University, College Station 77843
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Abstract
Polymerase chain reaction (PCR) primers designed to amplify bovine specific sequences of the arginine-vasopressin (ARVP), glycoprotein hormone alpha (CGA), cytochrome oxidase c subunit IV pseudogene (COXP), prochymosin (CYM), coagulation factor X (F10), inhibin beta A (INHBA), low density lipoprotein receptor (LDLR) and oxytocin (OXT) genes in hybrid cells were used in a search for single strand conformation polymorphisms. DNA from 75 animals comprising crossbred and 7 purebred breeds were analysed. ARVP, COXP, CYM, LDLR and OXT were found to be polymorphic while CGA, F10 and INHBA were not. Polymorphic regions were identified within 206 bp of exon 1 of ARVP, 582 bp of the pseudogene COXP, 253 bp of exon 9 of CYM, 519 bp of LDLR cDNA and 160 bp of the upstream regulatory region of OXT. This is the first report of bovine polymorphisms for these genes and an important step in our goal to incorporate type I comparative anchor loci into the bovine linkage map. Polymorphic loci were subsequently analysed in pedigreed full-sib families and shown to be inherited in a Mendelian fashion.
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Affiliation(s)
- H L Neibergs
- Department of Veterinary Pathobiology, Texas A&M University, College Station 77843
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