1
|
Müller-Langhans K, Oberberger L, Zablotski Y, Engelmann S, Hoedemaker M, Kühn C, Schuberth HJ, Zerbe H, Petzl W, Meyerholz-Wohllebe MM. Cows with diverging haplotypes show differences in differential milk cell count, milk parameters and vaginal temperature after S. aureus challenge but not after E. coli challenge. BMC Vet Res 2024; 20:200. [PMID: 38745199 PMCID: PMC11094921 DOI: 10.1186/s12917-024-03996-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 03/27/2024] [Indexed: 05/16/2024] Open
Abstract
BACKGROUND In dairy cattle, mastitis causes high financial losses and impairs animal well-being. Genetic selection is used to breed cows with reduced mastitis susceptibility. Techniques such as milk cell flow cytometry may improve early mastitis diagnosis. In a highly standardized in vivo infection model, 36 half-sib cows were selected for divergent paternal Bos taurus chromosome 18 haplotypes (Q vs. q) and challenged with Escherichia coli for 24 h or Staphylococcus aureus for 96 h, after which the samples were analyzed at 12 h intervals. Vaginal temperature (VT) was recorded every three minutes. The objective of this study was to compare the differential milk cell count (DMCC), milk parameters (fat %, protein %, lactose %, pH) and VT between favorable (Q) and unfavorable (q) haplotype cows using Bayesian models to evaluate their potential as improved early indicators of differential susceptibility to mastitis. RESULTS After S. aureus challenge, compared to the Q half-sibship cows, the milk of the q cows exhibited higher PMN levels according to the DMCC (24 h, p < 0.001), a higher SCC (24 h, p < 0.01 and 36 h, p < 0.05), large cells (24 h, p < 0.05) and more dead (36 h, p < 0.001) and live cells (24 h, p < 0.01). The protein % was greater in Q milk than in q milk at 0 h (p = 0.025). In the S. aureus group, Q cows had a greater protein % (60 h, p = 0.048) and fat % (84 h, p = 0.022) than q cows. Initially, the greater VT of S. aureus-challenged q cows (0 and 12-24 h, p < 0.05) reversed to a lower VT in q cows than in Q cows (48-60 h, p < 0.05). Additionally, the following findings emphasized the validity of the model: in the S. aureus group all DMCC subpopulations (24 h-96 h, p < 0.001) and in the E. coli group nearly all DMCC subpopulations (12 h-24 h, p < 0.001) were higher in challenged quarters than in unchallenged quarters. The lactose % was lower in the milk samples of E. coli-challenged quarters than in those of S. aureus-challenged quarters (24 h, p < 0.001). Between 12 and 18 h, the VT was greater in cows challenged with E. coli than in those challenged with S. aureus (3-h interval approach, p < 0.001). CONCLUSION This in vivo infection model confirmed specific differences between Q and q cows with respect to the DMCC, milk component analysis results and VT results after S. aureus inoculation but not after E. coli challenge. However, compared with conventional milk cell analysis monitoring, e.g., the global SCC, the DMCC analysis did not provide refined phenotyping of the pathogen response.
Collapse
Affiliation(s)
- Katharina Müller-Langhans
- Clinic for Ruminants With Ambulatory Clinic and Herd Health Services, Center for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, Sonnenstrasse 16, Oberschleissheim, 85764, Germany
| | - Lisa Oberberger
- Institute for Infectious Diseases and Zoonoses, Ludwig-Maximilians-University Munich, Sonnenstrasse 24, Oberschleissheim, 85764, Germany
| | - Yury Zablotski
- Clinic for Ruminants With Ambulatory Clinic and Herd Health Services, Center for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, Sonnenstrasse 16, Oberschleissheim, 85764, Germany
| | - Susanne Engelmann
- Technical University Braunschweig, Institute for Microbiology, Inhoffenstrasse 7, Brunswick, 38124, Germany
- Helmholtz Center for Infection Research, Microbial Proteomics, Inhoffenstrasse 7, Brunswick, 38124, Germany
| | - Martina Hoedemaker
- Clinic for Cattle, University of Veterinary Medicine Hanover Foundation, Bischofsholer Damm 15, Hanover, 30173, Germany
| | - Christa Kühn
- Research Institute for Farm Animal Biology, Genome Biology, Wilhelm-Stahl-Allee 2, Dummerstorf, 18196, Germany
- Agricultural and Environmental Faculty, University Rostock, Justus-Von-Liebig-Weg 6, Rostock, 18059, Germany
- Friedrich-Loeffler-Institut, Federal Research Institute for Animal Health, Südufer 10, Greifswald-Insel Riems, 17493, Germany
| | - Hans-Joachim Schuberth
- Institute for Immunology, University of Veterinary Medicine Hanover Foundation, Bünteweg 2, Hanover, 30559, Germany
| | - Holm Zerbe
- Clinic for Ruminants With Ambulatory Clinic and Herd Health Services, Center for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, Sonnenstrasse 16, Oberschleissheim, 85764, Germany
| | - Wolfram Petzl
- Clinic for Ruminants With Ambulatory Clinic and Herd Health Services, Center for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, Sonnenstrasse 16, Oberschleissheim, 85764, Germany
| | - Marie Margarete Meyerholz-Wohllebe
- Clinic for Ruminants With Ambulatory Clinic and Herd Health Services, Center for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, Sonnenstrasse 16, Oberschleissheim, 85764, Germany.
| |
Collapse
|
2
|
Schmidtmann C, Schönherz A, Guldbrandtsen B, Marjanovic J, Calus M, Hinrichs D, Thaller G. Assessing the genetic background and genomic relatedness of red cattle populations originating from Northern Europe. Genet Sel Evol 2021; 53:23. [PMID: 33676402 PMCID: PMC7936461 DOI: 10.1186/s12711-021-00613-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 02/08/2021] [Indexed: 12/20/2022] Open
Abstract
Background Local cattle breeds need special attention, as they are valuable reservoirs of genetic diversity. Appropriate breeding decisions and adequate genomic management of numerically smaller populations are required for their conservation. At this point, the analysis of dense genome-wide marker arrays provides encompassing insights into the genomic constitution of livestock populations. We have analyzed the genetic characterization of ten cattle breeds originating from Germany, The Netherlands and Denmark belonging to the group of red dairy breeds in Northern Europe. The results are intended to provide initial evidence on whether joint genomic breeding strategies of these populations will be successful. Results Traditional Danish Red and Groningen White-Headed were the most genetically differentiated breeds and their populations showed the highest levels of inbreeding. In contrast, close genetic relationships and shared ancestry were observed for the populations of German Red and White Dual-Purpose, Dutch Meuse-Rhine-Yssel, and Dutch Deep Red breeds, reflecting their common histories. A considerable amount of gene flow from Red Holstein to German Angler and to German Red and White Dual-Purpose was revealed, which is consistent with frequent crossbreeding to improve productivity of these local breeds. In Red Holstein, marked genomic signatures of selection were reported on chromosome 18, suggesting directed selection for important breeding goal traits. Furthermore, tests for signatures of selection between Red Holstein, Red and White Dual-Purpose, and Meuse-Rhine-Yssel uncovered signals for all investigated pairs of populations. The corresponding genomic regions, which were putatively under different selection pressures, harboured various genes which are associated with traits such as milk and beef production, mastitis and female fertility. Conclusions This study provides comprehensive knowledge on the genetic constitution and genomic connectedness of divergent red cattle populations in Northern Europe. The results will help to design and optimize breeding strategies. A joint genomic evaluation including some of the breeds studied here seems feasible.
Collapse
Affiliation(s)
- Christin Schmidtmann
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University Kiel, 24098, Kiel, Germany.
| | - Anna Schönherz
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, 8830, Tjele, Denmark.,Department of Animal Science, Aarhus University, 8830, Tjele, Denmark
| | - Bernt Guldbrandtsen
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, 8830, Tjele, Denmark.,Department of Animal Sciences, Department of Animal Breeding and Husbandry, University of Bonn, 53115, Bonn, Germany
| | - Jovana Marjanovic
- Animal Breeding and Genomics, Wageningen University and Research, 6700AH, Wageningen, The Netherlands
| | - Mario Calus
- Animal Breeding and Genomics, Wageningen University and Research, 6700AH, Wageningen, The Netherlands
| | - Dirk Hinrichs
- Department of Animal Breeding, University of Kassel, 37213, Witzenhausen, Germany
| | - Georg Thaller
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University Kiel, 24098, Kiel, Germany
| |
Collapse
|
3
|
Heimes A, Brodhagen J, Weikard R, Becker D, Meyerholz MM, Petzl W, Zerbe H, Schuberth HJ, Hoedemaker M, Schmicke M, Engelmann S, Kühn C. Cows selected for divergent mastitis susceptibility display a differential liver transcriptome profile after experimental Staphylococcus aureus mammary gland inoculation. J Dairy Sci 2020; 103:6364-6373. [PMID: 32307160 DOI: 10.3168/jds.2019-17612] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Accepted: 02/15/2020] [Indexed: 01/12/2023]
Abstract
Infection and inflammation of the mammary gland, and especially prevention of mastitis, are still major challenges for the dairy industry. Different approaches have been tried to reduce the incidence of mastitis. Genetic selection of cows with lower susceptibility to mastitis promises sustainable success in this regard. Bos taurus autosome (BTA) 18, particularly the region between 43 and 59 Mb, harbors quantitative trait loci (QTL) for somatic cell score, a surrogate trait for mastitis susceptibility. Scrutinizing the molecular bases hereof, we challenged udders from half-sib heifers having inherited either favorable paternal haplotypes for somatic cell score (Q) or unfavorable haplotypes (q) with the Staphylococcus aureus pathogen. RNA sequencing was used for an in-depth analysis of challenge-related alterations in the hepatic transcriptome. Liver exerts highly relevant immune functions aside from being the key metabolic organ. Hence, a holistic approach focusing on the liver enabled us to identify challenge-related and genotype-dependent differentially expressed genes and underlying regulatory networks. In response to the S. aureus challenge, we found that heifers with Q haplotypes displayed more activated immune genes and pathways after S. aureus challenge compared with their q half-sibs. Furthermore, we found a significant enrichment of differentially expressed loci in the genomic target region on BTA18, suggesting the existence of a regionally acting regulatory element with effects on a variety of genes in this region.
Collapse
Affiliation(s)
- A Heimes
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, 18196 Dummerstorf, Germany
| | - J Brodhagen
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, 18196 Dummerstorf, Germany
| | - R Weikard
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, 18196 Dummerstorf, Germany
| | - D Becker
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, 18196 Dummerstorf, Germany
| | - M M Meyerholz
- Clinic for Ruminants with Ambulatory and Herd Health Services, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, 85764 Oberschleißheim, Germany; Immunology Unit, University of Veterinary Medicine Hannover, 30559 Hannover, Germany
| | - W Petzl
- Clinic for Ruminants with Ambulatory and Herd Health Services, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, 85764 Oberschleißheim, Germany
| | - H Zerbe
- Clinic for Ruminants with Ambulatory and Herd Health Services, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, 85764 Oberschleißheim, Germany
| | - H-J Schuberth
- Immunology Unit, University of Veterinary Medicine Hannover, 30559 Hannover, Germany
| | - M Hoedemaker
- Clinic for Cattle, University of Veterinary Medicine Hannover, 30173 Hannover, Germany
| | - M Schmicke
- Faculty of Natural Sciences III, Martin-Luther Universität Halle-Wittenberg, 06120 Halle, Germany
| | - S Engelmann
- Technical University Braunschweig, Institute for Microbiology, 38023 Braunschweig, Germany; Helmholtz Centre for Infection Research, Microbial Proteomics, 38124 Braunschweig, Germany
| | - C Kühn
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, 18196 Dummerstorf, Germany; Agricultural and Environmental Faculty, University Rostock, 18059 Rostock, Germany.
| |
Collapse
|
4
|
Association of TLR gene variants in a Czech Red Pied cattle population with reproductive traits. Vet Immunol Immunopathol 2019; 220:109997. [PMID: 31901560 DOI: 10.1016/j.vetimm.2019.109997] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2019] [Revised: 11/13/2019] [Accepted: 12/17/2019] [Indexed: 12/21/2022]
Abstract
The bovine genes TLR1, TLR2 and TLR6, which encode Toll-like receptors, key components of the innate immune system, were screened for polymorphisms in Czech Red Pied (Czech Simmental) cattle, and the different variants present in the population were tested for association with reproductive and fitness traits. Diversity was investigated in a group of 164 bulls using hybrid resequencing of pooled amplicons with PacBio technology and of pooled genomic DNA using HiSeq X-Ten technology. The validated single nucleotide polymorphisms (SNPs) were genotyped in individual animals using the primer extension technique. The association of genotypic classes of 16 polymorphisms with six phenotypic traits were estimated with one-way analysis of variance (ANOVA) and with restricted maximum likelihood (REML) algorithm. The evaluated traits included the incidence of cystic ovaries, index of early reproductive disorders, paternal and maternal indicators of calving ease, production longevity and calf vitality index. The estimated breeding values were used for combined trait quantification. Early traits, namely, cystic ovaries and early reproductive disorders, were not associated with any of the tested polymorphisms according to the general ANOVA test. By contrast, five variants of all three genes were associated with calving ease, both paternal and maternal. The production longevity correlated with two variants of TLR1 and the calf vitality index correlated with the 1044 T > C (rs68268249) polymorphism in TLR2. The false discovery rate (FDR) according to Benjamini-Hochberg was favourable for the calving ease trait (0.221) and maternal calving ease (0.214), which allows to consider the observed associations real, regardless of the error arising from the multiple comparisons. These results were supported by REML only partially, probably in view of the additivity assumption. Two mechanisms of action on calving are conceivable, either via infection resistance or via the involvement of TLR2 in signalling in the myometrium. The known formation of heterodimers by the TLR1, -2 and -6 products might be responsible for the shared pattern of action in these genes. The association of the calf vitality index with TLR2 variation might reflect the increased role of infections in calves compared to adult animals.
Collapse
|
5
|
Yan Z, Wang Z, Zhang Q, Yue S, Yin B, Jiang Y, Shi K. Identification of whole-genome significant single nucleotide polymorphisms in candidate genes associated with body conformation traits in Chinese Holstein cattle. Anim Genet 2019; 51:141-146. [PMID: 31633203 PMCID: PMC7003999 DOI: 10.1111/age.12865] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/16/2019] [Indexed: 11/29/2022]
Affiliation(s)
- Zhengui Yan
- College of Animal Science and Technology, Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Zhonghua Wang
- College of Animal Science and Technology, Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Qin Zhang
- College of Animal Science and Technology, Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Shujian Yue
- College of Animal Science and Technology, Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Bin Yin
- College of Animal Science and Technology, Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Yunliang Jiang
- College of Animal Science and Technology, Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, Shandong Agricultural University, Taian, Shandong, 271018, China
| | - Kerong Shi
- College of Animal Science and Technology, Shandong Key Laboratory of Animal Bioengineering and Disease Prevention, Shandong Agricultural University, Taian, Shandong, 271018, China
| |
Collapse
|
6
|
Meyerholz MM, Rohmeier L, Eickhoff T, Hülsebusch A, Jander S, Linden M, Macias L, Koy M, Heimes A, Gorríz-Martín L, Segelke D, Engelmann S, Schmicke M, Hoedemaker M, Petzl W, Zerbe H, Schuberth HJ, Kühn C. Genetic selection for bovine chromosome 18 haplotypes associated with divergent somatic cell score affects postpartum reproductive and metabolic performance. J Dairy Sci 2019; 102:9983-9994. [PMID: 31521359 DOI: 10.3168/jds.2018-16171] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2018] [Accepted: 07/15/2019] [Indexed: 11/19/2022]
Abstract
The susceptibility of animals to periparturient diseases has a great effect on the economic efficiency of dairy industries, on the frequency of antibiotic treatment, and on animal welfare. The use of selection for breeding cows with reduced susceptibility to diseases offers a sustainable tool to improve dairy cattle farming. Several studies have focused on the association of distinct bovine chromosome 18 genotypes or haplotypes with performance traits. The aim of this study was to test whether selection of Holstein Friesian heifers via SNP genotyping for alternative paternal chromosome 18 haplotypes associated with favorable (Q) or unfavorable (q) somatic cell scores influences postpartum reproductive and metabolic diseases. Thirty-six heifers (18 Q and 18 q) were monitored from 3 wk before calving until necropsy on d 39 (± 4 d) after calving. Health status and rectal temperature were measured daily, and body condition score and body weight were assessed once per week. Blood samples were drawn twice weekly, and levels of insulin, nonesterified fatty acids, insulin-like growth factor-I, growth hormone, and β-hydroxybutyrate were measured. Comparisons between the groups were performed using Fisher's exact test, chi-squared test, and the GLIMMIX procedure in SAS. Results showed that Q-heifers had reduced incidence of metritis compared with q-heifers and were less likely to develop fever. Serum concentrations of β-hydroxybutyrate were lower and insulin-like growth factor-I plasma concentrations were higher in Q- compared with q-heifers. However, the body condition score and withers height were comparable between haplotypes, but weight loss tended to be lower in Q-heifers compared with q-heifers. No differences between the groups were detected concerning retained fetal membranes, uterine involution, or onset of cyclicity. In conclusion, selection of chromosome 18 haplotypes associated with a reduced somatic cell score resulted in a decreased incidence of postpartum reproductive and metabolic diseases in this study. The presented data add to the existing knowledge aimed at avoiding negative consequences of genetic selection strategies in dairy cattle farming. The underlying causal mechanisms modulated by haplotypes in the targeted genomic region and immune competence necessitate further investigation.
Collapse
Affiliation(s)
- M M Meyerholz
- Clinic for Ruminants with Ambulatory and Herd Health Services, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, 85764 Oberschleißheim, Germany; Immunology Unit, University of Veterinary Medicine, 30559 Hannover, Germany.
| | - L Rohmeier
- Clinic for Ruminants with Ambulatory and Herd Health Services, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, 85764 Oberschleißheim, Germany; Clinic for Swine, Small Ruminants, Forensic Medicine and Ambulatory Service, University of Veterinary Medicine, 30173 Hannover, Germany
| | - T Eickhoff
- Immunology Unit, University of Veterinary Medicine, 30559 Hannover, Germany
| | - A Hülsebusch
- Immunology Unit, University of Veterinary Medicine, 30559 Hannover, Germany
| | - S Jander
- Immunology Unit, University of Veterinary Medicine, 30559 Hannover, Germany
| | - M Linden
- Faculty of Mathematics and Physics, Leibniz University, 30167 Hannover, Germany
| | - L Macias
- Clinic for Ruminants with Ambulatory and Herd Health Services, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, 85764 Oberschleißheim, Germany
| | - M Koy
- Immunology Unit, University of Veterinary Medicine, 30559 Hannover, Germany; Clinic for Poultry, University of Veterinary Medicine, 30559 Hannover, Germany
| | - A Heimes
- Leibniz Institute for Farm Animal Biology, Genome Biology, 18196 Dummerstorf, Germany
| | - L Gorríz-Martín
- Clinic for Cattle, University of Veterinary Medicine, 30173 Hannover, Germany
| | - D Segelke
- Vereinigte Informationssysteme Tierhaltung w.V. (VIT) Verden, 27283 Verden (Aller), Germany
| | - S Engelmann
- Institute for Microbiology, Technical University, 38106 Braunschweig, Germany; Microbial Proteomics, Helmholtz Centre for Infection Research, 38124 Braunschweig, Germany
| | - M Schmicke
- Clinic for Cattle, University of Veterinary Medicine, 30173 Hannover, Germany
| | - M Hoedemaker
- Clinic for Cattle, University of Veterinary Medicine, 30173 Hannover, Germany
| | - W Petzl
- Clinic for Ruminants with Ambulatory and Herd Health Services, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, 85764 Oberschleißheim, Germany
| | - H Zerbe
- Clinic for Ruminants with Ambulatory and Herd Health Services, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, 85764 Oberschleißheim, Germany
| | - H-J Schuberth
- Immunology Unit, University of Veterinary Medicine, 30559 Hannover, Germany
| | - Ch Kühn
- Leibniz Institute for Farm Animal Biology, Genome Biology, 18196 Dummerstorf, Germany; Agricultural and Environmental Faculty, University Rostock, 18059 Rostock, Germany
| |
Collapse
|
7
|
Heimes A, Brodhagen J, Weikard R, Hammon HM, Meyerholz MM, Petzl W, Zerbe H, Engelmann S, Schmicke M, Hoedemaker M, Schuberth HJ, Kühn C. Characterization of functional traits with focus on udder health in heifers with divergent paternally inherited haplotypes on BTA18. BMC Vet Res 2019; 15:241. [PMID: 31296208 PMCID: PMC6624885 DOI: 10.1186/s12917-019-1988-4] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2018] [Accepted: 06/30/2019] [Indexed: 11/10/2022] Open
Abstract
Background A major challenge in modern medicine and animal husbandry is the issue of antimicrobial resistance. One approach to solving this potential medical hazard is the selection of farm animals with less susceptibility to infectious diseases. Recent advances in functional genome analysis and quantitative genetics have opened the horizon to apply genetic marker information for efficiently identifying animals with preferential predisposition regarding health traits. The current study characterizes functional traits with a focus on udder health in dairy heifers. The animals were selected for having inherited alternative paternal haplotypes for a genomic region on Bos taurus chromosome (BTA) 18 genetically associated with divergent susceptibility to longevity and animal health, particularly mastitis. Results In the first weeks of lactation, the q heifers which had inherited the unfavorable (q) paternal haplotype displayed a significantly higher number of udder quarters with very low somatic cell count (< 10,000 cells / ml) compared to their paternal half-sib sisters with the favorable (Q) paternal haplotype. This might result in impaired mammary gland sentinel function towards invading pathogens. Furthermore, across the course of the first lactation, there was indication that q half-sib heifers showed higher somatic cell counts, a surrogate trait for udder health, in whole milkings compared to their paternal half-sib sisters with the favorable (Q) paternal haplotype. Moreover, heifers with the haplotype Q had a higher feed intake and higher milk yield compared to those with the q haplotype. Results of this study indicate that differences in milk production and calculated energy balance per se are not the main drivers of the genetically determined differences between the BTA18 Q and q groups of heifers. Conclusions The paternally inherited haplotype from a targeted BTA18 genomic region affect somatic cell count in udder quarters during the early postpartum period and might also contribute to further aspects of animal’s health and performance traits due to indirect effects on feed intake and metabolism. Electronic supplementary material The online version of this article (10.1186/s12917-019-1988-4) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- A Heimes
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - J Brodhagen
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - R Weikard
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - H M Hammon
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Nutritional Physiology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - M M Meyerholz
- Clinic for Ruminants with Ambulatory and Herd Health Services, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, Sonnenstr. 16, 85764, Oberschleißheim, Germany
| | - W Petzl
- Clinic for Ruminants with Ambulatory and Herd Health Services, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, Sonnenstr. 16, 85764, Oberschleißheim, Germany
| | - H Zerbe
- Clinic for Ruminants with Ambulatory and Herd Health Services, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, Sonnenstr. 16, 85764, Oberschleißheim, Germany
| | - S Engelmann
- Institute for Microbiology, Technical University Braunschweig, Postfach 3329, 38023, Braunschweig, Germany.,Microbial Proteomics, Helmholtz Centre for Infection Research, Inhoffenstraße 7, 38124, Braunschweig, Germany
| | - M Schmicke
- Clinic for Cattle, University of Veterinary Medicine Hanover, Bischofsholer Damm 15, 30173, Hanover, Germany
| | - M Hoedemaker
- Clinic for Cattle, University of Veterinary Medicine Hanover, Bischofsholer Damm 15, 30173, Hanover, Germany
| | - H-J Schuberth
- Immunology Unit, University of Veterinary Medicine Hanover, Bünteweg 2, Geb. 261, 30559, Hanover, Germany
| | - C Kühn
- Leibniz Institute for Farm Animal Biology (FBN), Institute of Genome Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany. .,Agricultural and Environmental Faculty, University Rostock, Justus-von-Liebig-Weg 6, 18059, Rostock, Germany.
| |
Collapse
|
8
|
Fang L, Jiang J, Li B, Zhou Y, Freebern E, Vanraden PM, Cole JB, Liu GE, Ma L. Genetic and epigenetic architecture of paternal origin contribute to gestation length in cattle. Commun Biol 2019; 2:100. [PMID: 30886909 PMCID: PMC6418173 DOI: 10.1038/s42003-019-0341-6] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 02/06/2019] [Indexed: 12/19/2022] Open
Abstract
The length of gestation can affect offspring health and performance. Both maternal and fetal effects contribute to gestation length; however, paternal contributions to gestation length remain elusive. Using genome-wide association study (GWAS) in 27,214 Holstein bulls with millions of gestation records, here we identify nine paternal genomic loci associated with cattle gestation length. We demonstrate that these GWAS signals are enriched in pathways relevant to embryonic development, and in differentially methylated regions between sperm samples with long and short gestation length. We reveal that gestation length shares genetic and epigenetic architecture in sperm with calving ability, body depth, and conception rate. While several candidate genes are detected in our fine-mapping analysis, we provide evidence indicating ZNF613 as a promising candidate for cattle gestation length. Collectively, our findings support that the paternal genome and epigenome can impact gestation length potentially through regulation of the embryonic development. Lingzhao Fang et al. studied the paternal genetic variants that affect gestational length in cattle. They found that paternal genes from pathways involved in embryonic development were associated with gestation length, and that these were often found in differentially methylated regions of the genome.
Collapse
Affiliation(s)
- Lingzhao Fang
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA.,Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA
| | - Jicai Jiang
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA
| | - Bingjie Li
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA
| | - Yang Zhou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Education Ministry of China, Huazhong Agricultural University, 430070, Wuhan, Hubei, China
| | - Ellen Freebern
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA
| | - Paul M Vanraden
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA
| | - John B Cole
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA
| | - George E Liu
- Animal Genomics and Improvement Laboratory, BARC, Agricultural Research Service, USDA, Beltsville, MD, 20705, USA
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD, 20742, USA.
| |
Collapse
|
9
|
Tiezzi F, Arceo ME, Cole JB, Maltecca C. Including gene networks to predict calving difficulty in Holstein, Brown Swiss and Jersey cattle. BMC Genet 2018; 19:20. [PMID: 29609562 PMCID: PMC5880070 DOI: 10.1186/s12863-018-0606-y] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Accepted: 03/15/2018] [Indexed: 11/10/2022] Open
Abstract
Background Calving difficulty or dystocia has a great economic impact in the US dairy industry. Reported risk factors associated with calving difficulty are feto-pelvic disproportion, gestation length and conformation. Different dairy cattle breeds have different incidence of calving difficulty, with Holstein having the highest dystocia rates and Jersey the lowest. Genomic selection becomes important especially for complex traits with low heritability, where the accuracy of conventional selection is lower. However, for complex traits where a large number of genes influence the phenotype, genome-wide association studies showed limitations. Biological networks could overcome some of these limitations and better capture the genetic architecture of complex traits. In this paper, we characterize Holstein, Brown Swiss and Jersey breed-specific dystocia networks and employ them in genomic predictions. Results Marker association analysis identified single nucleotide polymorphisms explaining the largest average proportion of genetic variance on BTA18 in Holstein, BTA25 in Brown Swiss, and BTA15 in Jersey. Gene networks derived from the genome-wide association included 1272 genes in Holstein, 1454 genes in Brown Swiss, and 1455 genes in Jersey. Furthermore, 256 genes in Holstein network, 275 genes in the Brown Swiss network, and 253 genes in the Jersey network were within previously reported dystocia quantitative trait loci. The across-breed network included 80 genes, with 9 genes being within previously reported dystocia quantitative trait loci. The gene-gene interactions in this network differed in the different breeds. Gene ontology enrichment analysis of genes in the networks showed Regulation of ARF GTPase was very significant (FDR ≤ 0.0098) on Holstein. Neuron morphogenesis and differentiation was the term most enriched (FDR ≤ 0.0539) on the across-breed network. Genomic prediction models enriched with network-derived relationship matrices did not outperform regular GBLUP models. Conclusions Regions identified in the genome were in the proximity of previously described quantitative trait loci that would most likely affect calving difficulty by altering the feto-pelvic proportion. Inclusion of identified networks did not increase prediction accuracy. The approach used in this paper could be extended to any instance with asymmetric distribution of phenotypes, for example, resistance to disease data. Electronic supplementary material The online version of this article (10.1186/s12863-018-0606-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Francesco Tiezzi
- Department of Animal Science, North Carolina State University, Raleigh, NC, 27695, USA
| | - Maria E Arceo
- Department of Animal Science, North Carolina State University, Raleigh, NC, 27695, USA
| | - John B Cole
- Animal Genomics and Improvement Laboratory, ARS, USDA, Beltsville, MD, 27705, USA
| | - Christian Maltecca
- Department of Animal Science, North Carolina State University, Raleigh, NC, 27695, USA.
| |
Collapse
|
10
|
Müller MP, Rothammer S, Seichter D, Russ I, Hinrichs D, Tetens J, Thaller G, Medugorac I. Genome-wide mapping of 10 calving and fertility traits in Holstein dairy cattle with special regard to chromosome 18. J Dairy Sci 2017; 100:1987-2006. [PMID: 28109604 DOI: 10.3168/jds.2016-11506] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2016] [Accepted: 11/20/2016] [Indexed: 01/07/2023]
Abstract
Over the last decades, a dramatic decrease in reproductive performance has been observed in Holstein cattle and fertility problems have become the most common reason for a cow to leave the herd. The premature removal of animals with high breeding values results in both economic and breeding losses. For efficient future Holstein breeding, the identification of loci associated with low fertility is of major interest and thus constitutes the aim of this study. To reach this aim, a genome-wide combined linkage disequilibrium and linkage analysis (cLDLA) was conducted using data on the following 10 calving and fertility traits in the form of estimated breeding values: days from first service to conception of heifers and cows, nonreturn rate on d 56 of heifers and cows, days from calving to first insemination, days open, paternal and maternal calving ease, paternal and maternal stillbirth. The animal data set contained 2,527 daughter-proven Holstein bulls from Germany that were genotyped with Illumina's BovineSNP50 BeadChip (Illumina Inc., San Diego, CA). For the cLDLA, 41,635 sliding windows of 40 adjacent single nucleotide polymorphisms (SNP) were used. At each window midpoint, a variance component analysis was executed using ASReml. The underlying mixed linear model included random quantitative trait locus (QTL) and polygenic effects. We identified 50 genome-wide significant QTL. The most significant peak was detected for direct calving ease at 59,179,424 bp on chromosome 18 (BTA18). Next, a mixed-linear model association (MLMA) analysis was conducted. A comparison of the cLDLA and MLMA results with special regard to BTA18 showed that the genome-wide most significant SNP from the MLMA was associated with the same trait and located on the same chromosome at 57,589,121 bp (i.e., about 1.5 Mb apart from the cLDLA peak). The results of 5 different cLDLA and 2 MLMA models, which included the fixed effects of either SNP or haplotypes, suggested that the cLDLA method outperformed the MLMA in accuracy and precision. The haplotype-based cLDLA method allowed for a more precise mapping and the definition of ancestral and derived QTL alleles, both of which are essential for the detection of underlying quantitative trait nucleotides.
Collapse
Affiliation(s)
- M-P Müller
- Tierzuchtforschung e.V. München, Senator-Gerauer-Str. 23, 85586 Poing, Germany; Chair of Animal Genetics and Husbandry, Ludwig-Maximilians-Universität Munich, Veterinärstr. 13, 80539 Munich, Germany
| | - S Rothammer
- Chair of Animal Genetics and Husbandry, Ludwig-Maximilians-Universität Munich, Veterinärstr. 13, 80539 Munich, Germany
| | - D Seichter
- Tierzuchtforschung e.V. München, Senator-Gerauer-Str. 23, 85586 Poing, Germany
| | - I Russ
- Tierzuchtforschung e.V. München, Senator-Gerauer-Str. 23, 85586 Poing, Germany
| | - D Hinrichs
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University, Olshausenstr. 40, 24098 Kiel, Germany
| | - J Tetens
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University, Olshausenstr. 40, 24098 Kiel, Germany
| | - G Thaller
- Tierzuchtforschung e.V. München, Senator-Gerauer-Str. 23, 85586 Poing, Germany; Institute of Animal Breeding and Husbandry, Christian-Albrechts-University, Olshausenstr. 40, 24098 Kiel, Germany
| | - I Medugorac
- Chair of Animal Genetics and Husbandry, Ludwig-Maximilians-Universität Munich, Veterinärstr. 13, 80539 Munich, Germany.
| |
Collapse
|
11
|
Aliloo H, Pryce JE, González-Recio O, Cocks BG, Hayes BJ. Validation of markers with non-additive effects on milk yield and fertility in Holstein and Jersey cows. BMC Genet 2015; 16:89. [PMID: 26193888 PMCID: PMC4509610 DOI: 10.1186/s12863-015-0241-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2015] [Accepted: 06/25/2015] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND It has been suggested that traits with low heritability, such as fertility, may have proportionately more genetic variation arising from non-additive effects than traits with higher heritability, such as milk yield. Here, we performed a large genome scan with 408,255 single nucleotide polymorphism (SNP) markers to identify chromosomal regions associated with additive, dominance and epistatic (pairwise additive × additive) variability in milk yield and a measure of fertility, calving interval, using records from a population of 7,055 Holstein cows. The results were subsequently validated in an independent set of 3,795 Jerseys. RESULTS We identified genomic regions with validated additive effects on milk yield on Bos taurus autosomes (BTA) 5, 14 and 20, whereas SNPs with suggestive additive effects on fertility were observed on BTA 5, 9, 11, 18, 22, 27, 29 and the X chromosome. We also confirmed genome regions with suggestive dominance effects for milk yield (BTA 2, 3, 5, 26 and 27) and for fertility (BTA 1, 2, 3, 7, 23, 25 and 28). A number of significant epistatic effects for milk yield on BTA 14 were found across breeds. However on close inspection, these were likely to be associated with the mutation in the diacylglycerol O-acyltransferase 1 (DGAT1) gene, given that the associations were no longer significant when the additive effect of the DGAT1 mutation was included in the epistatic model. CONCLUSIONS In general, we observed a low statistical power (high false discovery rates and small number of significant SNPs) for non-additive genetic effects compared with additive effects for both traits which could be an artefact of higher dependence on linkage disequilibrium between markers and causative mutations or smaller size of non-additive effects relative to additive effects. The results of our study suggest that individual non-additive effects make a small contribution to the genetic variation of milk yield and fertility. Although we found no individual mutation with large dominance effect for both traits under investigation, a contribution to genetic variance is still possible from a large number of small dominance effects, so methods that simultaneously incorporate genotypes across all loci are suggested to test the variance explained by dominance gene actions.
Collapse
Affiliation(s)
- Hassan Aliloo
- Biosciences Research Division, Department of Economic Development, Jobs, Transport and Resources, AgriBio, 5 Ring Road, Bundoora, VIC, 3083, Australia. .,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia. .,Dairy Futures Cooperative Research Centre (CRC), AgriBio, 5 Ring Road, Bundoora, VIC, 3083, Australia.
| | - Jennie E Pryce
- Biosciences Research Division, Department of Economic Development, Jobs, Transport and Resources, AgriBio, 5 Ring Road, Bundoora, VIC, 3083, Australia. .,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia. .,Dairy Futures Cooperative Research Centre (CRC), AgriBio, 5 Ring Road, Bundoora, VIC, 3083, Australia.
| | - Oscar González-Recio
- Biosciences Research Division, Department of Economic Development, Jobs, Transport and Resources, AgriBio, 5 Ring Road, Bundoora, VIC, 3083, Australia. .,Dairy Futures Cooperative Research Centre (CRC), AgriBio, 5 Ring Road, Bundoora, VIC, 3083, Australia.
| | - Benjamin G Cocks
- Biosciences Research Division, Department of Economic Development, Jobs, Transport and Resources, AgriBio, 5 Ring Road, Bundoora, VIC, 3083, Australia. .,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia. .,Dairy Futures Cooperative Research Centre (CRC), AgriBio, 5 Ring Road, Bundoora, VIC, 3083, Australia.
| | - Ben J Hayes
- Biosciences Research Division, Department of Economic Development, Jobs, Transport and Resources, AgriBio, 5 Ring Road, Bundoora, VIC, 3083, Australia. .,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia. .,Dairy Futures Cooperative Research Centre (CRC), AgriBio, 5 Ring Road, Bundoora, VIC, 3083, Australia.
| |
Collapse
|
12
|
Macciotta N, Dimauro C, Null D, Gaspa G, Cellesi M, Cole J. Dissection of genomic correlation matrices of US Holsteins using multivariate factor analysis. J Anim Breed Genet 2014; 132:9-20. [DOI: 10.1111/jbg.12113] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 07/03/2014] [Indexed: 11/28/2022]
Affiliation(s)
- N.P.P. Macciotta
- Dipartimento di Agraria; Sezione Scienze Zootecniche; Università di Sassari; Sassari Italy
| | - C. Dimauro
- Dipartimento di Agraria; Sezione Scienze Zootecniche; Università di Sassari; Sassari Italy
| | - D.J. Null
- Animal Genomics and Improvement Laboratory; Agricultural Research Service; USDA; Beltsville Maryland USA
| | - G. Gaspa
- Dipartimento di Agraria; Sezione Scienze Zootecniche; Università di Sassari; Sassari Italy
| | - M. Cellesi
- Dipartimento di Agraria; Sezione Scienze Zootecniche; Università di Sassari; Sassari Italy
| | - J.B. Cole
- Animal Genomics and Improvement Laboratory; Agricultural Research Service; USDA; Beltsville Maryland USA
| |
Collapse
|
13
|
Cole J, Waurich B, Wensch-Dorendorf M, Bickhart D, Swalve H. A genome-wide association study of calf birth weight in Holstein cattle using single nucleotide polymorphisms and phenotypes predicted from auxiliary traits. J Dairy Sci 2014; 97:3156-72. [DOI: 10.3168/jds.2013-7409] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2013] [Accepted: 01/28/2014] [Indexed: 02/04/2023]
|
14
|
Identification of a short region on chromosome 6 affecting direct calving ease in Piedmontese cattle breed. PLoS One 2012; 7:e50137. [PMID: 23226511 PMCID: PMC3514265 DOI: 10.1371/journal.pone.0050137] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 10/17/2012] [Indexed: 11/19/2022] Open
Abstract
Calving in cattle is affected by calf morphology and by dam characteristics. It is described by two different traits: maternal calving ease, which is the ability to generate dams with good physiological predisposition to calving, and direct calving ease, which is the ability to generate calves that are easily born. The aim of this study was to identify regions of cattle genome harboring genes possibly affecting direct calving ease in the Piedmontese cattle breed. A population of 323 bulls scored for direct calving ease (EBV) was analyzed by a medium-density SNP marker panel (54,001 SNPs) to perform a genome-wide scan. The strongest signal was detected on chromosome 6 between 37.8 and 38.7 Mb where 13 SNPs associated to direct calving ease were found. Three genes are located in this region: LAP3, encoding for a leucine aminopeptidase involved in the oxytocin hydrolysis; NCAPG, encoding for a non-SMC condensin I complex, which has been associated in cattle with fetal growth and carcass size; and LCORL, which has been associated to height in humans and cattle. To further confirm the results of the genome-wide scan we genotyped additional SNPs within these genes and analyzed their association with direct calving ease. The results of this additional analysis fully confirmed the findings of the GWAS and particularly indicated LAP3 as the most probable gene involved. Linkage Disequilibrium (LD) analysis showed high correlation between SNPs located within LAP3 and LCORL indicating a possible selection signature due either to increased fitness or breeders' selection for the trait.
Collapse
|
15
|
Höglund JK, Guldbrandtsen B, Lund MS, Sahana G. Analyzes of genome-wide association follow-up study for calving traits in dairy cattle. BMC Genet 2012; 13:71. [PMID: 22888914 PMCID: PMC3465222 DOI: 10.1186/1471-2156-13-71] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2012] [Accepted: 08/02/2012] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND There is often a pronounced disagreement between results obtained from different genome-wide association studies in cattle. There are multiple reasons for this disagreement. Particularly the presence of false positives leads to a need to validate detected QTL before they are optimally incorporated or weighted in selection decisions or further studied for causal gene. In dairy cattle progeny testing scheme new data is routinely accumulated which can be used to validate previously discovered associations. However, the data is not an independent sample and the sample size may not be sufficient to have enough power to validate previous discoveries. Here we compared two strategies to validate previously detected QTL when new data is added from the same study population. We compare analyzing a combined dataset (COMB) including all data presently available to only analyzing a validation dataset (VAL) i.e. a new dataset not previously analyzed as an independent replication. Secondly, we confirm SNP detected in the Reference population (REF) (i.e. previously analyzed dataset consists of older bulls) in the VAL dataset. RESULTS Clearly the results from the combined (COMB) dataset which had nearly twice the sample size of other two subsets allowed the detection of far more significant associations than the two smaller subsets. The number of significant SNPs in REF (older bulls) was about four times higher compare to VAL (younger bulls) though both had similar sample sizes, 2,219 and 2,039 respectively. A total of 424 SNP-trait combinations on 22 chromosomes showed genome-wide significant association involving 284 unique SNPs in the COMB dataset. In the REF data set 101 associations (73 unique SNPs) and in the VAL 24 associations (18 unique SNPs) were found genome-wide significant. Sixty-eight percent of the SNPs in the REF dataset could be confirmed in the VAL dataset. Out of 469 unique SNPs showing chromosome-wide significant association with calving traits in the REF dataset 321 could be confirmed in the VAL dataset at P < 0.05. CONCLUSIONS The follow-up study for GWAS in cattle will depend on the aim of the study. If the aim is to discover novel QTL, analyses of the COMB dataset is recommended, while in case of identification of the causal mutation underlying a QTL, confirmation of the discovered SNPs are necessary to avoid following a false positive.
Collapse
Affiliation(s)
- Johanna K Höglund
- Department of Molecular Biology and Genetics, Aarhus University, P.O. Box 50, Tjele, DK-8830, Denmark
- VikingGenetics, Ebeltoftvej 16, Assentoft, Randers, SØ, DK-8960, Denmark
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, P.O. Box 7070, Uppsala, 750 07, Sweden
| | - Bernt Guldbrandtsen
- Department of Molecular Biology and Genetics, Aarhus University, P.O. Box 50, Tjele, DK-8830, Denmark
| | - Mogens S Lund
- Department of Molecular Biology and Genetics, Aarhus University, P.O. Box 50, Tjele, DK-8830, Denmark
| | - Goutam Sahana
- Department of Molecular Biology and Genetics, Aarhus University, P.O. Box 50, Tjele, DK-8830, Denmark
| |
Collapse
|
16
|
Brand B, Hartmann A, Repsilber D, Griesbeck-Zilch B, Wellnitz O, Kühn C, Ponsuksili S, Meyer HHD, Schwerin M. Comparative expression profiling of E. coli and S. aureus inoculated primary mammary gland cells sampled from cows with different genetic predispositions for somatic cell score. Genet Sel Evol 2011; 43:24. [PMID: 21702919 PMCID: PMC3143085 DOI: 10.1186/1297-9686-43-24] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2010] [Accepted: 06/24/2011] [Indexed: 01/08/2023] Open
Abstract
Background During the past ten years many quantitative trait loci (QTL) affecting mastitis incidence and mastitis related traits like somatic cell score (SCS) were identified in cattle. However, little is known about the molecular architecture of QTL affecting mastitis susceptibility and the underlying physiological mechanisms and genes causing mastitis susceptibility. Here, a genome-wide expression analysis was conducted to analyze molecular mechanisms of mastitis susceptibility that are affected by a specific QTL for SCS on Bos taurus autosome 18 (BTA18). Thereby, some first insights were sought into the genetically determined mechanisms of mammary gland epithelial cells influencing the course of infection. Methods Primary bovine mammary gland epithelial cells (pbMEC) were sampled from the udder parenchyma of cows selected for high and low mastitis susceptibility by applying a marker-assisted selection strategy considering QTL and molecular marker information of a confirmed QTL for SCS in the telomeric region of BTA18. The cells were cultured and subsequently inoculated with heat-inactivated mastitis pathogens Escherichia coli and Staphylococcus aureus, respectively. After 1, 6 and 24 h, the cells were harvested and analyzed using the microarray expression chip technology to identify differences in mRNA expression profiles attributed to genetic predisposition, inoculation and cell culture. Results Comparative analysis of co-expression profiles clearly showed a faster and stronger response after pathogen challenge in pbMEC from less susceptible animals that inherited the favorable QTL allele 'Q' than in pbMEC from more susceptible animals that inherited the unfavorable QTL allele 'q'. Furthermore, the results highlighted RELB as a functional and positional candidate gene and related non-canonical Nf-kappaB signaling as a functional mechanism affected by the QTL. However, in both groups, inoculation resulted in up-regulation of genes associated with the Ingenuity pathways 'dendritic cell maturation' and 'acute phase response signaling', whereas cell culture affected biological processes involved in 'cellular development'. Conclusions The results indicate that the complex expression profiling of pathogen challenged pbMEC sampled from cows inheriting alternative QTL alleles is suitable to study genetically determined molecular mechanisms of mastitis susceptibility in mammary epithelial cells in vitro and to highlight the most likely functional pathways and candidate genes underlying the QTL effect.
Collapse
Affiliation(s)
- Bodo Brand
- Research Group of Functional Genomics, Leibniz Institute of Farm Animal Biology, 18196 Dummerstorf, Germany
| | | | | | | | | | | | | | | | | |
Collapse
|