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Natural resistance to experimental feline infectious peritonitis virus infection is decreased rather than increased by positive genetic selection. Vet Immunol Immunopathol 2016; 171:17-20. [PMID: 26964713 PMCID: PMC7112786 DOI: 10.1016/j.vetimm.2016.01.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2015] [Revised: 01/10/2016] [Accepted: 01/11/2016] [Indexed: 11/23/2022]
Abstract
Laboratory cats resistant to primary FIPV infection were purposely inbred. P, F1 and F1/P backcross cats were tested for resistance to primary and secondary FIPV exposures. Resistance to primary and secondary FIPV infection decreased as a result of inbreeding. Loss of heterozygosity is a risk factor for FIP. Resistance to FIPV infection is genetically complex.
A previous study demonstrated the existence of a natural resistance to feline infectious peritonitis virus (FIPV) among 36% of randomly bred laboratory cats. A genome wide association study (GWAS) on this population suggested that resistance was polygenic but failed to identify any strong specific associations. In order to enhance the power of GWAS or whole genome sequencing to identify strong genetic associations, a decision was made to positively select for resistance over three generations. The inbreeding experiment began with a genetically related parental (P) population consisting of three toms and four queens identified from among the survivors of the earlier study and belonging to a closely related subgroup (B). The subsequent effects of inbreeding were measured using 42 genome-wide STR markers. P generation cats produced 57 first filial (F1) kittens, only five of which (9.0%) demonstrated a natural resistance to FIPV infection. One of these five F1 survivors was then used to produce six F1/P-backcrosses kittens, only one of which proved resistant to FIP. Six of eight of the F1 and F1/P survivors succumbed to a secondary exposure 4–12 months later. Therefore, survival after both primary and secondary infection was decreased rather than increased by positive selection for resistance. The common genetic factor associated with this diminished resistance was a loss of heterozygosity.
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Forsberg SKG, Kierczak M, Ljungvall I, Merveille AC, Gouni V, Wiberg M, Lundgren Willesen J, Hanås S, Lequarré AS, Mejer Sørensen L, Tiret L, McEntee K, Seppälä E, Koch J, Battaille G, Lohi H, Fredholm M, Chetboul V, Häggström J, Carlborg Ö, Lindblad-Toh K, Höglund K. The Shepherds' Tale: A Genome-Wide Study across 9 Dog Breeds Implicates Two Loci in the Regulation of Fructosamine Serum Concentration in Belgian Shepherds. PLoS One 2015; 10:e0123173. [PMID: 25970163 PMCID: PMC4430432 DOI: 10.1371/journal.pone.0123173] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 02/10/2015] [Indexed: 01/24/2023] Open
Abstract
Diabetes mellitus is a serious health problem in both dogs and humans. Certain dog breeds show high prevalence of the disease, whereas other breeds are at low risk. Fructosamine and glycated haemoglobin (HbA1c) are two major biomarkers of glycaemia, where serum concentrations reflect glucose turnover over the past few weeks to months. In this study, we searched for genetic factors influencing variation in serum fructosamine concentration in healthy dogs using data from nine dog breeds. Considering all breeds together, we did not find any genome-wide significant associations to fructosamine serum concentration. However, by performing breed-specific analyses we revealed an association on chromosome 3 (pcorrected ≈ 1:68 × 10-6) in Belgian shepherd dogs of the Malinois subtype. The associated region and its close neighbourhood harbours interesting candidate genes such as LETM1 and GAPDH that are important in glucose metabolism and have previously been implicated in the aetiology of diabetes mellitus. To further explore the genetics of this breed specificity, we screened the genome for reduced heterozygosity stretches private to the Belgian shepherd breed. This revealed a region with reduced heterozygosity that shows a statistically significant interaction (p = 0.025) with the association region on chromosome 3. This region also harbours some interesting candidate genes and regulatory regions but the exact mechanisms underlying the interaction are still unknown. Nevertheless, this finding provides a plausible explanation for breed-specific genetic effects for complex traits in dogs. Shepherd breeds are at low risk of developing diabetes mellitus. The findings in Belgian shepherds could be connected to a protective mechanism against the disease. Further insight into the regulation of glucose metabolism could improve diagnostic and therapeutic methods for diabetes mellitus.
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Affiliation(s)
- Simon K. G. Forsberg
- Computational Genetics Section, Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
- * E-mail: (SKGF), (MK), (KH)
| | - Marcin Kierczak
- Computational Genetics Section, Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Science for Life Laboratory & Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- * E-mail: (SKGF), (MK), (KH)
| | - Ingrid Ljungvall
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anne-Christine Merveille
- Department of Clinical Sciences, Faculty of Veterinary Medicine, University of Liège, Liège Belgium
| | - Vassiliki Gouni
- Université Paris-Est, Ecole Nationale Vétérinaire d’Alfort, Unité de Cardiologie d’Alfort (UCA), Centre Hospitalier Universitaire Vétérinaire d’Alfort, Maisons-Alfort, France
| | - Maria Wiberg
- Department of Equine and Small Animal Medicine, Faculty of Veterinary Medicine, University of Helsinki, Helsinki, Finland
| | - Jakob Lundgren Willesen
- Department of Veterinary Clinical and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Sofia Hanås
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Evidensia, Animal Clinic Västerås, Västerås, Sweden
| | - Anne-Sophie Lequarré
- Department of Clinical Sciences, Faculty of Veterinary Medicine, University of Liège, Liège Belgium
| | - Louise Mejer Sørensen
- Department of Veterinary Clinical and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Laurent Tiret
- INRA, UMR955 de Génétique Fonctionnelle et Médicale, Maisons-Alfort, France
- Université Paris-Est Créteil, CNM project, Ecole Nationale Vétérinaire d’Alfort, Maisons-Alfort, France
| | - Kathleen McEntee
- Department of Clinical Sciences, Faculty of Veterinary Medicine, University of Liège, Liège Belgium
- Laboratory of Physiology, Faculty of Medicine, Université Libre de Bruxelles, Bruxelles, Belgium
| | - Eija Seppälä
- Department of Veterinary Biosciences, Research Program in Molecular Neurology Research Programs Unit, University of Helsinki, Helsinki, Finland
- Folkhälsan Institute of Genetics, Helsinki, Finland
- Department of Medical Genetics, University of Helsinki, Helsinki, Finland
| | - Jørgen Koch
- Department of Veterinary Clinical and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Géraldine Battaille
- Department of Clinical Sciences, Faculty of Veterinary Medicine, University of Liège, Liège Belgium
| | - Hannes Lohi
- Department of Veterinary Biosciences, Research Program in Molecular Neurology Research Programs Unit, University of Helsinki, Helsinki, Finland
- Folkhälsan Institute of Genetics, Helsinki, Finland
| | - Merete Fredholm
- Department of Veterinary Clinical and Animal Sciences, Faculty of Health and Medical Sciences, University of Copenhagen, Copenhagen, Denmark
| | - Valerie Chetboul
- Université Paris-Est, Ecole Nationale Vétérinaire d’Alfort, Unité de Cardiologie d’Alfort (UCA), Centre Hospitalier Universitaire Vétérinaire d’Alfort, Maisons-Alfort, France
- INSERM, U955, Equipe 03, Créteil, France
| | - Jens Häggström
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Örjan Carlborg
- Computational Genetics Section, Department of Clinical Sciences, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Kerstin Lindblad-Toh
- Science for Life Laboratory & Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, Sweden
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
| | - Katja Höglund
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden
- * E-mail: (SKGF), (MK), (KH)
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Andersson L. Molecular consequences of animal breeding. Curr Opin Genet Dev 2013; 23:295-301. [PMID: 23601626 DOI: 10.1016/j.gde.2013.02.014] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2012] [Revised: 02/11/2013] [Accepted: 02/25/2013] [Indexed: 01/02/2023]
Abstract
The phenotypic diversity in domestic animals provides a unique opportunity to study genotype-phenotype relationships. The identification of causal mutations provides an insight into what types of mutations have contributed to phenotypic evolution in domestic animals. Whole genome sequencing has revealed that fixation of null alleles that inactivate genes, which are essential under natural conditions but disadvantageous on the farm, has not been a common mechanism for genetic adaptation in domestic animals. Numerous examples have been revealed where structural changes cause specific phenotypic effects by altering transcriptional regulation. An emerging feature is also the evolution of alleles by the accumulation of several consecutive mutations which affect gene function.
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Affiliation(s)
- Leif Andersson
- Science for Life Laboratory, Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, SE-75123 Uppsala, Sweden.
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Identification of genomic regions associated with phenotypic variation between dog breeds using selection mapping. PLoS Genet 2011; 7:e1002316. [PMID: 22022279 PMCID: PMC3192833 DOI: 10.1371/journal.pgen.1002316] [Citation(s) in RCA: 273] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2011] [Accepted: 07/30/2011] [Indexed: 12/30/2022] Open
Abstract
The extraordinary phenotypic diversity of dog breeds has been sculpted by a unique population history accompanied by selection for novel and desirable traits. Here we perform a comprehensive analysis using multiple test statistics to identify regions under selection in 509 dogs from 46 diverse breeds using a newly developed high-density genotyping array consisting of >170,000 evenly spaced SNPs. We first identify 44 genomic regions exhibiting extreme differentiation across multiple breeds. Genetic variation in these regions correlates with variation in several phenotypic traits that vary between breeds, and we identify novel associations with both morphological and behavioral traits. We next scan the genome for signatures of selective sweeps in single breeds, characterized by long regions of reduced heterozygosity and fixation of extended haplotypes. These scans identify hundreds of regions, including 22 blocks of homozygosity longer than one megabase in certain breeds. Candidate selection loci are strongly enriched for developmental genes. We chose one highly differentiated region, associated with body size and ear morphology, and characterized it using high-throughput sequencing to provide a list of variants that may directly affect these traits. This study provides a catalogue of genomic regions showing extreme reduction in genetic variation or population differentiation in dogs, including many linked to phenotypic variation. The many blocks of reduced haplotype diversity observed across the genome in dog breeds are the result of both selection and genetic drift, but extended blocks of homozygosity on a megabase scale appear to be best explained by selection. Further elucidation of the variants under selection will help to uncover the genetic basis of complex traits and disease. There are hundreds of dog breeds that exhibit massive differences in appearance and behavior sculpted by tightly controlled selective breeding. This large-scale natural experiment has provided an ideal resource that geneticists can use to search for genetic variants that control these differences. With this goal, we developed a high-density array that surveys variable sites at more than 170,000 positions in the dog genome and used it to analyze genetic variation in 46 breeds. We identify 44 chromosomal regions that are extremely variable between breeds and are likely to control many of the traits that vary between them, including curly tails and sociality. Many other regions also bear the signature of strong artificial selection. We characterize one such region, known to associate with body size and ear type, in detail using “next-generation” sequencing technology to identify candidate mutations that may control these traits. Our results suggest that artificial selection has targeted genes involved in development and metabolism and that it may have increased the incidence of disease in dog breeds. Knowledge of these regions will be of great importance for uncovering the genetic basis of variation between dog breeds and for finding mutations that cause disease.
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