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Ablondi M, Johnsson M, Eriksson S, Sabbioni A, Viklund ÅG, Mikko S. Performance of Swedish Warmblood fragile foal syndrome carriers and breeding prospects. Genet Sel Evol 2022; 54:4. [PMID: 35062868 PMCID: PMC8783495 DOI: 10.1186/s12711-021-00693-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 12/21/2021] [Indexed: 11/30/2022] Open
Abstract
Background Warmblood fragile foal syndrome (WFFS) is a monogenetic defect caused by a recessive lethal missense point mutation in the procollagen‐lysine, 2‐oxoglutarate 5‐dioxygenase 1 gene (PLOD1, c.2032G>A). The majority of homozygous WFFS horses are aborted during gestation. Clinical signs of affected horses include fragile skin, skin and mucosa lacerations, hyperextension of the articulations, and hematomas. In spite of its harmful effect, a relatively high frequency of WFFS carriers has been found in Warmblood horses, suggesting a heterozygote advantage. Thus, in this study our aims were to: (1) estimate the frequency of WFFS carriers in the Swedish Warmblood breed (SWB), (2) estimate the effect of WFFS carrier genotype on performance traits in two SWB subpopulations bred for different disciplines, and (3) simulate the potential effects of balancing selection and different selection strategies on the frequency of carriers. Methods In total, 2288 SWB sport horses born between 1971 and 2020 were tested for the WFFS mutation and had estimated breeding values (EBV) for ten traditional evaluating and 50 linear descriptive traits. Results The frequency of WFFS carriers calculated from a pool of 511 randomly selected SWB horses born in 2017 was equal to 7.4% and ranged from 0.0 to 12.0% among the whole set of tested SWB horses, starting from 1971 till 2020. The effect of the WFFS carrier genotype was significant for several EBV mainly related to movements and dressage traits and especially for horses not bred for the show jumping discipline. Using simulation, we showed that balancing selection can maintain a recessive lethal allele in populations such as the SWB breed over generations and that the frequency is expected to slowly decrease in absence of balancing selection. Finally, we showed that selection against carrier sires can result in a more rapid decrease of the frequency of the mutant allele over time. Conclusion Further research is needed to confirm the apparent association between equine performance and the WFFS carrier genotype. Identification of such associations or new causative mutations for horse performance traits can serve as new tools in horse breeding to select for healthy, sustainable, and better performing horses. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-021-00693-4.
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Affiliation(s)
- Michela Ablondi
- Department of Veterinary Science, Università degli Studi di Parma, 43126, Parma, Italy
| | - Martin Johnsson
- Dept. of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, PO Box 7023, S-750 07, Uppsala, Sweden
| | - Susanne Eriksson
- Dept. of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, PO Box 7023, S-750 07, Uppsala, Sweden
| | - Alberto Sabbioni
- Department of Veterinary Science, Università degli Studi di Parma, 43126, Parma, Italy
| | - Åsa Gelinder Viklund
- Dept. of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, PO Box 7023, S-750 07, Uppsala, Sweden
| | - Sofia Mikko
- Dept. of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, PO Box 7023, S-750 07, Uppsala, Sweden.
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2
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Baltrušis P, Charvet CL, Halvarsson P, Mikko S, Höglund J. Using droplet digital PCR for the detection of hco-acr-8b levamisole resistance marker in H. contortus. Int J Parasitol Drugs Drug Resist 2021; 15:168-176. [PMID: 33799059 PMCID: PMC8044644 DOI: 10.1016/j.ijpddr.2021.03.002] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Revised: 03/16/2021] [Accepted: 03/16/2021] [Indexed: 11/19/2022]
Abstract
The nematode Haemonchus contortus is one of the most prevalent and pathogenic parasites in small ruminants. Although usually controlled using anthelmintics, the development of drug resistance by the parasite has become a major issue in livestock production. While the molecular detection of benzimidazole resistance in H. contortus is well developed, the molecular tools and protocols are far less advanced for the detection of levamisole resistance. The hco-acr-8 gene encodes a critical acetylcholine susceptible subunit that confers levamisole-sensitivity to the receptor. Here, we report the development of a droplet digital PCR assay as a molecular tool to detect a 63 bp deletion in the hco-acr-8 that has been previously associated with levamisole resistance. Sanger sequencing of single adult H. contortus yielded 56 high-quality consensus sequences surrounding the region containing the deletion. Based on the sequencing data, new primers and probes were designed and validated with a novel droplet digital PCR assay for the quantification of the deletion containing “resistant” allele in genomic DNA samples. Single adult worms from six phenotypically described isolates (n = 60) and from two Swedish sheep farms (n = 30) where levamisole was effective were tested. Even though a significant difference in genotype frequencies between the resistant and susceptible reference isolates was found (p = 0.01), the homozygous “resistant” genotype was observed to be abundantly present in both the susceptible isolates as well as in some Swedish H. contortus samples. Furthermore, field larval culture samples, collected pre- (n = 7) and post- (n = 6) levamisole treatment on seven Swedish sheep farms where levamisole was fully efficacious according to Fecal Egg Count Reduction Test results, were tested to evaluate the frequency of the “resistant” allele in each. Frequencies of the deletion ranged from 35 to 80% in the pre-treatment samples, whereas no amplifiable H. contortus genomic DNA was detected in the post-treatment samples. Together, these data reveal relatively high frequencies of the 63 bp deletion in the hco-acr-8 both on individual H. contortus and field larval culture scales, and cast doubt on the utility of the deletion in the hco-acr-8 as a molecular marker for levamisole resistance detection on sheep farms. Acr8b – levamisole resistance marker investigated in single worms and larval cultures. Individuals homozygous for acr8b found more commonly, even in susceptible isolates. Levamisole treatment efficacy was unaffected by increased acr8b frequencies in larvae.
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Affiliation(s)
- Paulius Baltrušis
- Department of Biomedical Sciences and Veterinary Public Health, Section for Parasitology, Swedish University of Agricultural Sciences, Uppsala, Sweden.
| | | | - Peter Halvarsson
- Department of Biomedical Sciences and Veterinary Public Health, Section for Parasitology, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Sofia Mikko
- Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Johan Höglund
- Department of Biomedical Sciences and Veterinary Public Health, Section for Parasitology, Swedish University of Agricultural Sciences, Uppsala, Sweden
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3
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Ablondi M, Eriksson S, Tetu S, Sabbioni A, Viklund Å, Mikko S. Genomic Divergence in Swedish Warmblood Horses Selected for Equestrian Disciplines. Genes (Basel) 2019; 10:E976. [PMID: 31783652 PMCID: PMC6947233 DOI: 10.3390/genes10120976] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2019] [Revised: 11/20/2019] [Accepted: 11/23/2019] [Indexed: 01/12/2023] Open
Abstract
The equestrian sport horse Swedish Warmblood (SWB) originates from versatile cavalry horses. Most modern SWB breeders have specialized their breeding either towards show jumping or dressage disciplines. The aim of this study was to explore the genomic structure of SWB horses to evaluate the presence of genomic subpopulations, and to search for signatures of selection in subgroups of SWB with high or low breeding values (EBVs) for show jumping. We analyzed high density genotype information from 380 SWB horses born in the period 2010-2011, and used Principal Coordinates Analysis and Discriminant Analysis of Principal Components to detect population stratification. Fixation index and Cross Population Extended Haplotype Homozygosity scores were used to scan the genome for potential signatures of selection. In accordance with current breeding practice, this study highlights the development of two separate breed subpopulations with putative signatures of selection in eleven chromosomes. These regions involve genes with known function in, e.g., mentality, endogenous reward system, development of connective tissues and muscles, motor control, body growth and development. This study shows genetic divergence, due to specialization towards different disciplines in SWB horses. This latter evidence can be of interest for SWB and other horse studbooks encountering specialized breeding.
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Affiliation(s)
- Michela Ablondi
- Department of Veterinary Science, University of Parma, 43126 Parma, Italy; (M.A.); (A.S.)
| | - Susanne Eriksson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, PO Box 7023, S-75007 Uppsala, Sweden; (S.E.); (S.T.); (Å.V.)
| | - Sasha Tetu
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, PO Box 7023, S-75007 Uppsala, Sweden; (S.E.); (S.T.); (Å.V.)
| | - Alberto Sabbioni
- Department of Veterinary Science, University of Parma, 43126 Parma, Italy; (M.A.); (A.S.)
| | - Åsa Viklund
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, PO Box 7023, S-75007 Uppsala, Sweden; (S.E.); (S.T.); (Å.V.)
| | - Sofia Mikko
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, PO Box 7023, S-75007 Uppsala, Sweden; (S.E.); (S.T.); (Å.V.)
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4
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Solé M, Ablondi M, Binzer-Panchal A, Velie BD, Hollfelder N, Buys N, Ducro BJ, François L, Janssens S, Schurink A, Viklund Å, Eriksson S, Isaksson A, Kultima H, Mikko S, Lindgren G. Inter- and intra-breed genome-wide copy number diversity in a large cohort of European equine breeds. BMC Genomics 2019; 20:759. [PMID: 31640551 PMCID: PMC6805398 DOI: 10.1186/s12864-019-6141-z] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2019] [Accepted: 09/25/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Copy Number Variation (CNV) is a common form of genetic variation underlying animal evolution and phenotypic diversity across a wide range of species. In the mammalian genome, high frequency of CNV differentiation between breeds may be candidates for population-specific selection. However, CNV differentiation, selection and its population genetics have been poorly explored in horses. RESULTS We investigated the patterns, population variation and gene annotation of CNV using the Axiom® Equine Genotyping Array (670,796 SNPs) from a large cohort of individuals (N = 1755) belonging to eight European horse breeds, varying from draught horses to several warmblood populations. After quality control, 152,640 SNP CNVs (individual markers), 18,800 segment CNVs (consecutive SNP CNVs of same gain/loss state or both) and 939 CNV regions (CNVRs; overlapping segment CNVs by at least 1 bp) compared to the average signal of the reference (Belgian draught horse) were identified. Our analyses showed that Equus caballus chromosome 12 (ECA12) was the most enriched in segment CNV gains and losses (~ 3% average proportion of the genome covered), but the highest number of segment CNVs were detected on ECA1 and ECA20 (regardless of size). The Friesian horses showed private SNP CNV gains (> 20% of the samples) on ECA1 and Exmoor ponies displayed private SNP CNV losses on ECA25 (> 20% of the samples). The Warmblood cluster showed private SNP CNV gains located in ECA9 and Draught cluster showed private SNP CNV losses located in ECA7. The length of the CNVRs ranged from 1 kb to 21.3 Mb. A total of 10,612 genes were annotated within the CNVRs. The PANTHER annotation of these genes showed significantly under- and overrepresented gene ontology biological terms related to cellular processes and immunity (Bonferroni P-value < 0.05). We identified 80 CNVRs overlapping with known QTL for fertility, coat colour, conformation and temperament. We also report 67 novel CNVRs. CONCLUSIONS This work revealed that CNV patterns, in the genome of some European horse breeds, occurred in specific genomic regions. The results provide support to the hypothesis that high frequency private CNVs residing in genes may potentially be responsible for the diverse phenotypes seen between horse breeds.
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Affiliation(s)
- Marina Solé
- Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.
| | - Michela Ablondi
- Department of Veterinary Science, Università di Parma, Parma, Italy
| | - Amrei Binzer-Panchal
- Department of Medical Sciences, Array and Analysis Facility, Uppsala University, Uppsala, Sweden
| | - Brandon D Velie
- Faculty of Life and Environmental Science, University of Sydney, Sydney, NSW, Australia
| | - Nina Hollfelder
- Department of Medical Sciences, Array and Analysis Facility, Uppsala University, Uppsala, Sweden
| | - Nadine Buys
- Livestock Genetics, Department of Biosystems, KU Leuven, 3001, Leuven, Belgium
| | - Bart J Ducro
- Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700 AH, Wageningen, the Netherlands
| | - Liesbeth François
- Livestock Genetics, Department of Biosystems, KU Leuven, 3001, Leuven, Belgium
| | - Steven Janssens
- Livestock Genetics, Department of Biosystems, KU Leuven, 3001, Leuven, Belgium
| | - Anouk Schurink
- Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700 AH, Wageningen, the Netherlands.,Centre for Genetic Resources, the Netherlands (CGN), Wageningen University & Research, P.O. Box 338, 6700 AH, Wageningen, the Netherlands
| | - Åsa Viklund
- Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Susanne Eriksson
- Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anders Isaksson
- Department of Medical Sciences, Array and Analysis Facility, Uppsala University, Uppsala, Sweden
| | - Hanna Kultima
- Department of Medical Sciences, Array and Analysis Facility, Uppsala University, Uppsala, Sweden
| | - Sofia Mikko
- Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Gabriella Lindgren
- Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Livestock Genetics, Department of Biosystems, KU Leuven, 3001, Leuven, Belgium
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Upadhyay M, Eriksson S, Mikko S, Strandberg E, Stålhammar H, Groenen MAM, Crooijmans RPMA, Andersson G, Johansson AM. Genomic relatedness and diversity of Swedish native cattle breeds. Genet Sel Evol 2019; 51:56. [PMID: 31578144 PMCID: PMC6775670 DOI: 10.1186/s12711-019-0496-0] [Citation(s) in RCA: 27] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Accepted: 09/13/2019] [Indexed: 01/03/2023] Open
Abstract
Background Native cattle breeds are important genetic resources given their adaptation to the local environment in which they are bred. However, the widespread use of commercial cattle breeds has resulted in a marked reduction in population size of several native cattle breeds worldwide. Therefore, conservation management of native cattle breeds requires urgent attention to avoid their extinction. To this end, we genotyped nine Swedish native cattle breeds with genome-wide 150 K single nucleotide polymorphisms (SNPs) to investigate the level of genetic diversity and relatedness between these breeds. Results We used various SNP-based approaches on this dataset to connect the demographic history with the genetic diversity and population structure of these Swedish cattle breeds. Our results suggest that the Väne and Ringamåla breeds originating from southern Sweden have experienced population isolation and have a low genetic diversity, whereas the Fjäll breed has a large founder population and a relatively high genetic diversity. Based on the shared ancestry and the constructed phylogenetic trees, we identified two major clusters in Swedish native cattle. In the first cluster, which includes Swedish mountain cattle breeds, there was little differentiation among the Fjäll, Fjällnära, Swedish Polled, and Bohus Polled breeds. The second cluster consists of breeds from southern Sweden: Väne, Ringamåla and Swedish Red. Interestingly, we also identified sub-structuring in the Fjällnära breed, which indicates different breeding practices on the farms that maintain this breed. Conclusions This study represents the first comprehensive genome-wide analysis of the genetic relatedness and diversity in Swedish native cattle breeds. Our results show that different demographic patterns such as genetic isolation and cross-breeding have shaped the genomic diversity of Swedish native cattle breeds and that the Swedish mountain breeds have retained their authentic distinct gene pool without significant contribution from any of the other European cattle breeds that were included in this study.
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Affiliation(s)
- Maulik Upadhyay
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Susanne Eriksson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.
| | - Sofia Mikko
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Erling Strandberg
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | | | - Martien A M Groenen
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | | | - Göran Andersson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anna M Johansson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
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6
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Ablondi M, Viklund Å, Lindgren G, Eriksson S, Mikko S. Signatures of selection in the genome of Swedish warmblood horses selected for sport performance. BMC Genomics 2019; 20:717. [PMID: 31533613 PMCID: PMC6751828 DOI: 10.1186/s12864-019-6079-1] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2019] [Accepted: 09/04/2019] [Indexed: 01/09/2023] Open
Abstract
Background A growing demand for improved physical skills and mental attitude in modern sport horses has led to strong selection for performance in many warmblood studbooks. The aim of this study was to detect genomic regions with low diversity, and therefore potentially under selection, in Swedish Warmblood horses (SWB) by analysing high-density SNP data. To investigate if such signatures could be the result of selection for equestrian sport performance, we compared our SWB SNP data with those from Exmoor ponies, a horse breed not selected for sport performance traits. Results The genomic scan for homozygous regions identified long runs of homozygosity (ROH) shared by more than 85% of the genotyped SWB individuals. Such ROH were located on ECA4, ECA6, ECA7, ECA10 and ECA17. Long ROH were instead distributed evenly across the genome of Exmoor ponies in 77% of the chromosomes. Two population differentiation tests (FST and XP-EHH) revealed signatures of selection on ECA1, ECA4, and ECA6 in SWB horses. Conclusions Genes related to behaviour, physical abilities and fertility, appear to be targets of selection in the SWB breed. This study provides a genome-wide map of selection signatures in SWB horses, and ground for further functional studies to unravel the biological mechanisms behind complex traits in horses.
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Affiliation(s)
- Michela Ablondi
- Dept. of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, PO Box 7023, S-750 07, Uppsala, Sweden.,Department of Veterinary Science, Università degli Studi di Parma, 43126, Parma, Italy
| | - Åsa Viklund
- Dept. of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, PO Box 7023, S-750 07, Uppsala, Sweden
| | - Gabriella Lindgren
- Dept. of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, PO Box 7023, S-750 07, Uppsala, Sweden.,Livestock Genetics, Department of Biosystems, Leuven, KU, Belgium
| | - Susanne Eriksson
- Dept. of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, PO Box 7023, S-750 07, Uppsala, Sweden
| | - Sofia Mikko
- Dept. of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, PO Box 7023, S-750 07, Uppsala, Sweden.
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Rochus CM, Westberg Sunesson K, Jonas E, Mikko S, Johansson AM. Mutations in ASIP and MC1R: dominant black and recessive black alleles segregate in native Swedish sheep populations. Anim Genet 2019; 50:712-717. [PMID: 31475378 DOI: 10.1111/age.12837] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/08/2019] [Indexed: 01/03/2023]
Abstract
By studying genes associated with coat colour, we can understand the role of these genes in pigmentation but also gain insight into selection history. North European short-tailed sheep, including Swedish breeds, have variation in their coat colour, making them good models to expand current knowledge of mutations associated with coat colour in sheep. We studied ASIP and MC1R, two genes with known roles in pigmentation, and their association with black coat colour. We did this by sequencing the coding regions of ASIP in 149 animals and MC1R in 129 animals from seven native Swedish sheep breeds in individuals with black, white or grey fleece. Previously known mutations in ASIP [recessive black allele: g.100_105del (D5 ) and/or g.5172T>A] were associated with black coat colour in Klövsjö and Roslag sheep breeds and mutations in both ASIP and MC1R (dominant black allele: c.218T>A and/or c.361G>A) were associated with black coat colour in Swedish Finewool. In Gotland, Gute, Värmland and Helsinge sheep breeds, coat colour inheritance was more complex: only 11 of 16 individuals with black fleece had genotypes that could explain their black colour. These breeds have grey individuals in their populations, and grey is believed to be a result of mutations and allelic copy number variation within the ASIP duplication, which could be a possible explanation for the lack of a clear inheritance pattern in these breeds. Finally, we found a novel missense mutation in MC1R (c.452G>A) in Gotland, Gute and Värmland sheep and evidence of a duplication of MC1R in Gotland sheep.
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Affiliation(s)
- C M Rochus
- Department of Animal Breeding and Genetics, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Box 7923, SE-75007, Uppsala, Sweden.,UFR Génétique, Élevage et Reproduction, Sciences de la Vie et Santé, AgroParisTech, Université Paris Saclay, 16 rue Claude Bernard, F-75231, Paris Cedex 05, France.,Génétique Physiologie Systèmes d'Elevage, Animal Genetics Division, INRA, 24 chemin de Borde-Rouge-Auzeville Tolosane, F-31326 Castanet-Tolosan, France
| | - K Westberg Sunesson
- Department of Animal Breeding and Genetics, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Box 7923, SE-75007, Uppsala, Sweden
| | - E Jonas
- Department of Animal Breeding and Genetics, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Box 7923, SE-75007, Uppsala, Sweden
| | - S Mikko
- Department of Animal Breeding and Genetics, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Box 7923, SE-75007, Uppsala, Sweden
| | - A M Johansson
- Department of Animal Breeding and Genetics, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences, Box 7923, SE-75007, Uppsala, Sweden
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Staiger EA, Almén MS, Promerová M, Brooks S, Cothran EG, Imsland F, Jäderkvist Fegraeus K, Lindgren G, Mehrabani Yeganeh H, Mikko S, Vega-Pla JL, Tozaki T, Rubin CJ, Andersson L. The evolutionary history of theDMRT3‘Gait keeper’ haplotype. Anim Genet 2017; 48:551-559. [DOI: 10.1111/age.12580] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/25/2017] [Indexed: 01/25/2023]
Affiliation(s)
- E. A. Staiger
- Department of Medical Biochemistry and Microbiology; Uppsala University; SE-75123 Uppsala Sweden
| | - M. S. Almén
- Department of Medical Biochemistry and Microbiology; Uppsala University; SE-75123 Uppsala Sweden
| | - M. Promerová
- Department of Medical Biochemistry and Microbiology; Uppsala University; SE-75123 Uppsala Sweden
| | - S. Brooks
- Department of Animal Science; University of Florida; Gainesville FL 32611-0910 USA
| | - E. G. Cothran
- Department of Veterinary Integrative Biosciences; College of Veterinary Medicine and Biomedical Sciences; Texas A&M University; College Station TX 77843-4458 USA
| | - F. Imsland
- Department of Medical Biochemistry and Microbiology; Uppsala University; SE-75123 Uppsala Sweden
| | - K. Jäderkvist Fegraeus
- Department of Animal Breeding and Genetics; Swedish University of Agricultural Sciences; SE-75007 Uppsala Sweden
| | - G. Lindgren
- Department of Animal Breeding and Genetics; Swedish University of Agricultural Sciences; SE-75007 Uppsala Sweden
| | | | - S. Mikko
- Department of Animal Breeding and Genetics; Swedish University of Agricultural Sciences; SE-75007 Uppsala Sweden
| | - J. L. Vega-Pla
- Laboratorio de Investigación Aplicada; Cría Caballar de las Fuerzas Armadas; 14080 Cordoba Spain
| | - T. Tozaki
- Genetic Analysis Department; Laboratory of Racing Chemistry; Tochigi 320-0851 Utsunomiya Japan
| | - C. J. Rubin
- Department of Medical Biochemistry and Microbiology; Uppsala University; SE-75123 Uppsala Sweden
| | - L. Andersson
- Department of Medical Biochemistry and Microbiology; Uppsala University; SE-75123 Uppsala Sweden
- Department of Veterinary Integrative Biosciences; College of Veterinary Medicine and Biomedical Sciences; Texas A&M University; College Station TX 77843-4458 USA
- Department of Animal Breeding and Genetics; Swedish University of Agricultural Sciences; SE-75007 Uppsala Sweden
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9
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Viļuma A, Mikko S, Hahn D, Skow L, Andersson G, Bergström TF. Genomic structure of the horse major histocompatibility complex class II region resolved using PacBio long-read sequencing technology. Sci Rep 2017; 7:45518. [PMID: 28361880 PMCID: PMC5374520 DOI: 10.1038/srep45518] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 02/27/2017] [Indexed: 11/10/2022] Open
Abstract
The mammalian Major Histocompatibility Complex (MHC) region contains several gene families characterized by highly polymorphic loci with extensive nucleotide diversity, copy number variation of paralogous genes, and long repetitive sequences. This structural complexity has made it difficult to construct a reliable reference sequence of the horse MHC region. In this study, we used long-read single molecule, real-time (SMRT) sequencing technology from Pacific Biosciences (PacBio) to sequence eight Bacterial Artificial Chromosome (BAC) clones spanning the horse MHC class II region. The final assembly resulted in a 1,165,328 bp continuous gap free sequence with 35 manually curated genomic loci of which 23 were considered to be functional and 12 to be pseudogenes. In comparison to the MHC class II region in other mammals, the corresponding region in horse shows extraordinary copy number variation and different relative location and directionality of the Eqca-DRB, -DQA, -DQB and -DOB loci. This is the first long-read sequence assembly of the horse MHC class II region with rigorous manual gene annotation, and it will serve as an important resource for association studies of immune-mediated equine diseases and for evolutionary analysis of genetic diversity in this region.
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Affiliation(s)
- Agnese Viļuma
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences (SLU), Box 7023, 750 07 Uppsala, Sweden
| | - Sofia Mikko
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences (SLU), Box 7023, 750 07 Uppsala, Sweden
| | - Daniela Hahn
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences (SLU), Box 7023, 750 07 Uppsala, Sweden
| | - Loren Skow
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843, USA
| | - Göran Andersson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences (SLU), Box 7023, 750 07 Uppsala, Sweden
| | - Tomas F Bergström
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences (SLU), Box 7023, 750 07 Uppsala, Sweden
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Viluma A, Mikko S, Bergström TF, Andersson G. P4006 Equine major histocompatibility complex class II region: Long-read sequencing and annotation of nine bacterial artificial chromosome clones. J Anim Sci 2016. [DOI: 10.2527/jas2016.94supplement482x] [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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Velie BD, Shrestha M, Francois L, Schurink A, Stinckens A, Blott S, Ducro BJ, Mikko S, Thomas R, Sundquist M, Eriksson S, Buys N, Lindgren G. P6017 A high density genome-wide scan for genetic risk factors of insect bite hypersensitivity (IBH): A Horsegene Project Initiative. J Anim Sci 2016. [DOI: 10.2527/jas2016.94supplement4156a] [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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François L, Jäderkvist Fegraeus K, Eriksson S, Andersson LS, Tesfayonas YG, Viluma A, Imsland F, Buys N, Mikko S, Lindgren G, Velie BD. Conformation Traits and Gaits in the Icelandic Horse are Associated with Genetic Variants in Myostatin (MSTN). J Hered 2016; 107:431-7. [PMID: 27208149 DOI: 10.1093/jhered/esw031] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2016] [Accepted: 05/11/2016] [Indexed: 11/13/2022] Open
Abstract
Many genes are known to have an influence on conformation and performance traits; however, the role of one gene, Myostatin (MSTN), has been highlighted in recent studies on horses. Myostatin acts as a repressor in the development and regulation of differentiation and proliferative growth of skeletal muscle. Several studies have examined the link between MSTN, conformation, and performance in racing breeds, but no studies have investigated the relationship in Icelandic horses. Icelandic horses, a highly unique breed, are known both for their robust and compact conformation as well as their additional gaits tölt and pace. Three SNPs (g.65868604G>T [PR8604], g.66493737C>T [PR3737], and g.66495826A>G [PR5826]) flanking or within equine MSTN were genotyped in 195 Icelandic horses. The SNPs and haplotypes were analyzed for association with official estimated breeding values (EBV) for conformation traits (n = 11) and gaits (n = 5). The EBV for neck, withers, and shoulders was significantly associated with both PR8604 and PR3737 (P < 0.05). PR8604 was also associated with EBV for total conformation (P = 0.05). These associations were all supported by the haplotype analysis. However, while SNP PR5826 showed a significant association with EBVs for leg stance and hooves (P < 0.05), haplotype analyses for these traits failed to fully support these associations. This study demonstrates the possible role of MSTN on both the form and function of horses from non-racing breeds. Further analysis of Icelandic horses as well as other non-racing breeds would be beneficial and likely help to completely understand the influence of MSTN on conformation and performance in horses.
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Affiliation(s)
- Liesbeth François
- From the Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden (François, Jäderkvist Fegraeus, Eriksson, Andersson, Tesfayonas, Viluma, Mikko, Lindgren, and Velie); KU Leuven, Department of Biosystems, Livestock Genetics, Leuven 3001, Belgium (François and Buys); and Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden (Imsland)
| | - Kim Jäderkvist Fegraeus
- From the Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden (François, Jäderkvist Fegraeus, Eriksson, Andersson, Tesfayonas, Viluma, Mikko, Lindgren, and Velie); KU Leuven, Department of Biosystems, Livestock Genetics, Leuven 3001, Belgium (François and Buys); and Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden (Imsland)
| | - Susanne Eriksson
- From the Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden (François, Jäderkvist Fegraeus, Eriksson, Andersson, Tesfayonas, Viluma, Mikko, Lindgren, and Velie); KU Leuven, Department of Biosystems, Livestock Genetics, Leuven 3001, Belgium (François and Buys); and Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden (Imsland)
| | - Lisa S Andersson
- From the Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden (François, Jäderkvist Fegraeus, Eriksson, Andersson, Tesfayonas, Viluma, Mikko, Lindgren, and Velie); KU Leuven, Department of Biosystems, Livestock Genetics, Leuven 3001, Belgium (François and Buys); and Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden (Imsland)
| | - Yohannes G Tesfayonas
- From the Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden (François, Jäderkvist Fegraeus, Eriksson, Andersson, Tesfayonas, Viluma, Mikko, Lindgren, and Velie); KU Leuven, Department of Biosystems, Livestock Genetics, Leuven 3001, Belgium (François and Buys); and Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden (Imsland)
| | - Agnese Viluma
- From the Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden (François, Jäderkvist Fegraeus, Eriksson, Andersson, Tesfayonas, Viluma, Mikko, Lindgren, and Velie); KU Leuven, Department of Biosystems, Livestock Genetics, Leuven 3001, Belgium (François and Buys); and Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden (Imsland)
| | - Freyja Imsland
- From the Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden (François, Jäderkvist Fegraeus, Eriksson, Andersson, Tesfayonas, Viluma, Mikko, Lindgren, and Velie); KU Leuven, Department of Biosystems, Livestock Genetics, Leuven 3001, Belgium (François and Buys); and Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden (Imsland)
| | - Nadine Buys
- From the Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden (François, Jäderkvist Fegraeus, Eriksson, Andersson, Tesfayonas, Viluma, Mikko, Lindgren, and Velie); KU Leuven, Department of Biosystems, Livestock Genetics, Leuven 3001, Belgium (François and Buys); and Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden (Imsland)
| | - Sofia Mikko
- From the Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden (François, Jäderkvist Fegraeus, Eriksson, Andersson, Tesfayonas, Viluma, Mikko, Lindgren, and Velie); KU Leuven, Department of Biosystems, Livestock Genetics, Leuven 3001, Belgium (François and Buys); and Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden (Imsland)
| | - Gabriella Lindgren
- From the Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden (François, Jäderkvist Fegraeus, Eriksson, Andersson, Tesfayonas, Viluma, Mikko, Lindgren, and Velie); KU Leuven, Department of Biosystems, Livestock Genetics, Leuven 3001, Belgium (François and Buys); and Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden (Imsland)
| | - Brandon D Velie
- From the Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 750 07 Uppsala, Sweden (François, Jäderkvist Fegraeus, Eriksson, Andersson, Tesfayonas, Viluma, Mikko, Lindgren, and Velie); KU Leuven, Department of Biosystems, Livestock Genetics, Leuven 3001, Belgium (François and Buys); and Science for Life Laboratory Uppsala, Department of Medical Biochemistry and Microbiology, Uppsala University, 751 23 Uppsala, Sweden (Imsland)
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Velie BD, Shrestha M, Franҫois L, Schurink A, Tesfayonas YG, Stinckens A, Blott S, Ducro BJ, Mikko S, Thomas R, Swinburne JE, Sundqvist M, Eriksson S, Buys N, Lindgren G. Using an Inbred Horse Breed in a High Density Genome-Wide Scan for Genetic Risk Factors of Insect Bite Hypersensitivity (IBH). PLoS One 2016; 11:e0152966. [PMID: 27070818 PMCID: PMC4829256 DOI: 10.1371/journal.pone.0152966] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [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: 10/20/2015] [Accepted: 03/22/2016] [Indexed: 11/19/2022] Open
Abstract
While susceptibility to hypersensitive reactions is a common problem amongst humans and animals alike, the population structure of certain animal species and breeds provides a more advantageous route to better understanding the biology underpinning these conditions. The current study uses Exmoor ponies, a highly inbred breed of horse known to frequently suffer from insect bite hypersensitivity, to identify genomic regions associated with a type I and type IV hypersensitive reaction. A total of 110 cases and 170 controls were genotyped on the 670K Axiom Equine Genotyping Array. Quality control resulted in 452,457 SNPs and 268 individuals being tested for association. Genome-wide association analyses were performed using the GenABEL package in R and resulted in the identification of two regions of interest on Chromosome 8. The first region contained the most significant SNP identified, which was located in an intron of the DCC netrin 1 receptor gene. The second region identified contained multiple top SNPs and encompassed the PIGN, KIAA1468, TNFRSF11A, ZCCHC2, and PHLPP1 genes. Although additional studies will be needed to validate the importance of these regions in horses and the relevance of these regions in other species, the knowledge gained from the current study has the potential to be a step forward in unraveling the complex nature of hypersensitive reactions.
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Affiliation(s)
- Brandon D. Velie
- Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- * E-mail:
| | - Merina Shrestha
- Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Liesbeth Franҫois
- Research Group Livestock Genetics, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Anouk Schurink
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, the Netherlands
| | - Yohannes G. Tesfayonas
- Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anneleen Stinckens
- Research Group Livestock Genetics, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Sarah Blott
- School of Veterinary Medicine & Science, University of Nottingham, Leicestershire, United Kingdom
| | - Bart J. Ducro
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, the Netherlands
| | - Sofia Mikko
- Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ruth Thomas
- Exmoor Pony Society, Cullompton, United Kingdom
| | - June E. Swinburne
- Animal DNA Diagnostics Ltd, Cambridgeshire, United Kingdom
- Animal Health Trust, Newmarket, United Kingdom
| | | | - Susanne Eriksson
- Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Nadine Buys
- Research Group Livestock Genetics, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Gabriella Lindgren
- Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Viluma A, Sayyab S, Mikko S, Andersson G, Bergström TF. Evaluation of whole-genome sequencing of four Chinese crested dogs for variant detection using the ion proton system. Canine Genet Epidemiol 2015; 2:16. [PMID: 26457193 PMCID: PMC4599337 DOI: 10.1186/s40575-015-0029-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2015] [Accepted: 09/09/2015] [Indexed: 12/21/2022] Open
Abstract
Background Next generation sequencing (NGS) has traditionally been performed by large genome centers, but in recent years, the costs for whole-genome sequencing (WGS) have decreased substantially. With the introduction of smaller and less expensive “desktop” systems, NGS is now moving into the general laboratory. To evaluate the Ion Proton system for WGS we sequenced four Chinese Crested dogs and analyzed the data quality in terms of genome and exome coverage, the number of detected single nucleotide variants (SNVs) and insertions and deletions (INDELs) and the genotype concordance with the Illumina HD canine SNP array. For each of the four dogs, a 200 bp fragment library was constructed from genomic DNA and sequenced on two Ion PI chips per dog to reach mean coverage of 6–8x of the canine genome (genome size ≈ 2.4 Gb). Results On average, each Ion PI chip yielded approximately 73.3 million reads with a mean read length of 130 bp (~9.5 Gb sequence data) of which 98.5 % could be aligned to the canine reference genome (CanFam3.1). By sequencing a single dog using one fragment library and two Ion PI chips, on average 80 % of the genome and 77 % exome was covered by at least four reads. After removing duplicate reads (20.7 %) the mean coverage across the whole genome was 6x. Using sequence data from all four individuals (four fragment libraries and eight Ion PI chips) the genome and exome coverage could be further increased to 97.2 and 94.3 %, respectively. We detected 4.83 million unique SNPs and 6.10 million unique INDEL positions across all individuals. A comparison between SNP genotypes detected with the WGS and the 170 K Illumina HD canine SNP array showed 90 % concordance. Conclusions We have evaluated whole-genome sequencing on the Ion Proton system for genetic variant detection in four Chinese crested dogs. Even though INDEL calling with Ion Proton data is challenging due to specific platform errors, in case of SNP calling it can serve as an alternative to other next-generation sequencing platforms and SNP genotyping arrays, in studies aiming to identify causative mutations for rare monogenic diseases. In addition, we have identified new genetic variants of the Chinese Crested dog that will contribute to further whole-genome sequencing studies aimed to identify mutations associated with monogenic diseases with autosomal recessive inheritance. Electronic supplementary material The online version of this article (doi:10.1186/s40575-015-0029-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Agnese Viluma
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Shumaila Sayyab
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Sofia Mikko
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Göran Andersson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Tomas F Bergström
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Velie BD, Jäderkvist K, Imsland F, Viluma A, Andersson LS, Mikko S, Eriksson S, Lindgren G. Frequencies of polymorphisms in myostatin vary in Icelandic horses according to the use of the horses. Anim Genet 2015; 46:467-8. [PMID: 26095686 DOI: 10.1111/age.12315] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/05/2015] [Indexed: 11/28/2022]
Affiliation(s)
- Brandon D Velie
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, 750 07, Sweden
| | - Kim Jäderkvist
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, 750 07, Sweden
| | - Freyja Imsland
- Department of Medical Biochemistry and Microbiology, Uppsala University, Uppsala, 751 24, Sweden
| | - Agnese Viluma
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, 750 07, Sweden
| | - Lisa S Andersson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, 750 07, Sweden
| | - Sofia Mikko
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, 750 07, Sweden
| | - Susanne Eriksson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, 750 07, Sweden
| | - Gabriella Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, 750 07, Sweden
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Abebe AS, Mikko S, Johansson AM. Genetic diversity of five local Swedish chicken breeds detected by microsatellite markers. PLoS One 2015; 10:e0120580. [PMID: 25855978 PMCID: PMC4391840 DOI: 10.1371/journal.pone.0120580] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2014] [Accepted: 01/27/2015] [Indexed: 11/19/2022] Open
Abstract
This study aimed at investigating the genetic diversity, relationship and population structure of 110 local Swedish chickens derived from five breeds (Gotlandshöna, Hedemorahöna, Öländsk dvärghöna, Skånsk blommehöna, and Bohuslän- Dals svarthöna, in the rest of the paper the shorter name Svarthöna is used) using 24 microsatellite markers. In total, one hundred thirteen alleles were detected in all populations, with a mean of 4.7 alleles per locus. For the five chicken breeds, the observed and expected heterozygosity ranged from 0.225 to 0.408 and from 0.231 to 0.515, with the lowest scores for the Svarthöna and the highest scores for the Skånsk blommehöna breeds, respectively. Similarly, the average within breed molecular kinship varied from 0.496 to 0.745, showing high coancestry, with Skånsk blommehöna having the lowest and Svarthöna the highest coancestry. Furthermore, all breeds showed significant deviations from Hardy-Weinberg expectations. Across the five breeds, the global heterozygosity deficit (FIT) was 0.545, population differentiation index (FST) was 0.440, and the global inbreeding of individuals within breed (FIS) was 0.187. The phylogenetic relationships of chickens were examined using neighbor-joining trees constructed at the level of breeds and individual samples. The neighbor-joining tree constructed at breed level revealed two main clusters, with Hedemorahöna and Öländsk dvärghöna breeds in one cluster, and Gotlandshöna and Svarthöna breeds in the second cluster leaving the Skånsk blommehöna in the middle. Based on the results of the STRUCTURE analysis, the most likely number of clustering of the five breeds was at K = 4, with Hedemorahöna, Gotlandshöna and Svarthöna breeds forming their own distinct clusters, while Öländsk dvärghöna and Skånsk blommehöna breeds clustered together. Losses in the overall genetic diversity of local Swedish chickens due to breeds extinction varied from -1.46% to -6.723%. The results of the current study can be used as baseline genetic information for genetic conservation program, for instance, to control inbreeding and to implement further genetic studies in local Swedish chickens.
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Affiliation(s)
- Abiye Shenkut Abebe
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Sofia Mikko
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anna M. Johansson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- * E-mail:
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18
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Jäderkvist K, Andersson LS, Johansson AM, Árnason T, Mikko S, Eriksson S, Andersson L, Lindgren G. The DMRT3 'Gait keeper' mutation affects performance of Nordic and Standardbred trotters. J Anim Sci 2014; 92:4279-86. [PMID: 25085403 DOI: 10.2527/jas.2014-7803] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
In a previous study it was shown that a nonsense mutation in the DMRT3 gene alters the pattern of locomotion in horses and that this mutation has a strong positive impact on trotting performance of Standardbreds. One aim of this study was to test if racing performance and trotting technique in the Nordic (Coldblood) trotters are also influenced by the DMRT3 genotype. Another aim was to further investigate the effect of the mutation on performance in Standardbreds, by using a within-family analysis and genotype-phenotype correlations in a larger horse material than in the previous study. We genotyped 427 Nordic trotters and 621 Standardbreds for the DMRT3 nonsense mutation and a SNP in strong linkage disequilibrium with it. In Nordic trotters, we show that horses homozygous for the DMRT3 mutation (A) had significantly higher EBV for trotting performance traits than heterozygous (CA) or homozygous wild-type (CC) horses (P = 0.001). Furthermore, AA homozygotes had a higher proportion of victories and top 3 placings than horses heterozygous or homozygous wild-type, when analyzing performance data for the period 3 to 6 yr of age (P = 0.06 and P = 0.05, respectively). Another finding in the Nordic trotters was that the DMRT3 mutation influenced trotting technique (P = 2.1 × 10(-8)). Standardbred horses homozygous AA had significantly higher EBV for all traits than horses with at least 1 wild-type allele (CA and CC; P = 1.6 × 10(-16)). In a within-family analysis of Standardbreds, we found significant differences in several traits (e.g., earnings, P = 0.002; number of entered races, P = 0.004; and fraction of offspring that entered races, P = 0.002) among paternal half-sibs with genotype AA or CA sired by a CA stallion. For most traits, we found significant differences at young ages. For Nordic trotters, most of the results were significant at 3 yr of age but not for the older ages, and for the Standardbreds most of the results for the ages 3 to 5 were significant. For Nordic trotters, the proportion of victories and placings were the only traits that were significant for other ages than 3 yr.
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Affiliation(s)
- K Jäderkvist
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden
| | - L S Andersson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden
| | - A M Johansson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden
| | - T Árnason
- IHBC AB, Knubbo, SE-744 94 Morgongåva, Sweden
| | - S Mikko
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden
| | - S Eriksson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden
| | - L Andersson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden Department of Medical Biochemistry and Microbiology, Uppsala University, SE-751 23, Uppsala, Sweden
| | - G Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-750 07, Uppsala, Sweden
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Promerová M, Andersson LS, Juras R, Penedo MCT, Reissmann M, Tozaki T, Bellone R, Dunner S, Hořín P, Imsland F, Imsland P, Mikko S, Modrý D, Roed KH, Schwochow D, Vega-Pla JL, Mehrabani-Yeganeh H, Yousefi-Mashouf N, G Cothran E, Lindgren G, Andersson L. Worldwide frequency distribution of the 'Gait keeper' mutation in the DMRT3 gene. Anim Genet 2014; 45:274-82. [PMID: 24444049 DOI: 10.1111/age.12120] [Citation(s) in RCA: 64] [Impact Index Per Article: 6.4] [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: 11/19/2013] [Indexed: 01/24/2023]
Abstract
For centuries, domestic horses have represented an important means of transport and served as working and companion animals. Although their role in transportation is less important today, many horse breeds are still subject to intense selection based on their pattern of locomotion. A striking example of such a selected trait is the ability of a horse to perform additional gaits other than the common walk, trot and gallop. Those could be four-beat ambling gaits, which are particularly smooth and comfortable for the rider, or pace, used mainly in racing. Gaited horse breeds occur around the globe, suggesting that gaitedness is an old trait, selected for in many breeds. A recent study discovered that a nonsense mutation in DMRT3 has a major impact on gaitedness in horses and is present at a high frequency in gaited breeds and in horses bred for harness racing. Here, we report a study of the worldwide distribution of this mutation. We genotyped 4396 horses representing 141 horse breeds for the DMRT3 stop mutation. More than half (2749) of these horses also were genotyped for a SNP situated 32 kb upstream of the DMRT3 nonsense mutation because these two SNPs are in very strong linkage disequilibrium. We show that the DMRT3 mutation is present in 68 of the 141 genotyped horse breeds at a frequency ranging from 1% to 100%. We also show that the mutation is not limited to a geographical area, but is found worldwide. The breeds with a high frequency of the stop mutation (>50%) are either classified as gaited or bred for harness racing.
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Affiliation(s)
- M Promerová
- Department of Medical Biochemistry and Microbiology, Uppsala University, SE-75123, Uppsala, Sweden
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Hemberg E, Einarsson S, Jones B, Mikko S. The Origin of Amniotic Polymorphonuclear Leucocytes in the Mare. Reprod Domest Anim 2013; 48:e88-9. [DOI: 10.1111/rda.12237] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2013] [Accepted: 08/19/2013] [Indexed: 11/29/2022]
Affiliation(s)
- E Hemberg
- Herrgården; Hjortkvarn Sweden
- Department of Clinical Sciences; Faculty of Veterinary Medicine and Animal Science; Swedish University of Agricultural Sciences; Uppsala Sweden
| | - S Einarsson
- Department of Clinical Sciences; Faculty of Veterinary Medicine and Animal Science; Swedish University of Agricultural Sciences; Uppsala Sweden
| | - B Jones
- Department of Clinical Sciences; Faculty of Veterinary Medicine and Animal Science; Swedish University of Agricultural Sciences; Uppsala Sweden
| | - S Mikko
- Department of Animal Breeding and Genetics; Faculty of Veterinary Medicine and Animal Science; Swedish University of Agricultural Sciences; Uppsala Sweden
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Petersen JL, Mickelson JR, Cothran EG, Andersson LS, Axelsson J, Bailey E, Bannasch D, Binns MM, Borges AS, Brama P, da Câmara Machado A, Distl O, Felicetti M, Fox-Clipsham L, Graves KT, Guérin G, Haase B, Hasegawa T, Hemmann K, Hill EW, Leeb T, Lindgren G, Lohi H, Lopes MS, McGivney BA, Mikko S, Orr N, Penedo MCT, Piercy RJ, Raekallio M, Rieder S, Røed KH, Silvestrelli M, Swinburne J, Tozaki T, Vaudin M, M Wade C, McCue ME. Genetic diversity in the modern horse illustrated from genome-wide SNP data. PLoS One 2013; 8:e54997. [PMID: 23383025 PMCID: PMC3559798 DOI: 10.1371/journal.pone.0054997] [Citation(s) in RCA: 168] [Impact Index Per Article: 15.3] [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: 10/03/2012] [Accepted: 12/20/2012] [Indexed: 11/18/2022] Open
Abstract
Horses were domesticated from the Eurasian steppes 5,000-6,000 years ago. Since then, the use of horses for transportation, warfare, and agriculture, as well as selection for desired traits and fitness, has resulted in diverse populations distributed across the world, many of which have become or are in the process of becoming formally organized into closed, breeding populations (breeds). This report describes the use of a genome-wide set of autosomal SNPs and 814 horses from 36 breeds to provide the first detailed description of equine breed diversity. F(ST) calculations, parsimony, and distance analysis demonstrated relationships among the breeds that largely reflect geographic origins and known breed histories. Low levels of population divergence were observed between breeds that are relatively early on in the process of breed development, and between those with high levels of within-breed diversity, whether due to large population size, ongoing outcrossing, or large within-breed phenotypic diversity. Populations with low within-breed diversity included those which have experienced population bottlenecks, have been under intense selective pressure, or are closed populations with long breed histories. These results provide new insights into the relationships among and the diversity within breeds of horses. In addition these results will facilitate future genome-wide association studies and investigations into genomic targets of selection.
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Affiliation(s)
- Jessica L Petersen
- University of Minnesota, College of Veterinary Medicine, St Paul, MN, USA.
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Petersen JL, Mickelson JR, Rendahl AK, Valberg SJ, Andersson LS, Axelsson J, Bailey E, Bannasch D, Binns MM, Borges AS, Brama P, da Câmara Machado A, Capomaccio S, Cappelli K, Cothran EG, Distl O, Fox-Clipsham L, Graves KT, Guérin G, Haase B, Hasegawa T, Hemmann K, Hill EW, Leeb T, Lindgren G, Lohi H, Lopes MS, McGivney BA, Mikko S, Orr N, Penedo MCT, Piercy RJ, Raekallio M, Rieder S, Røed KH, Swinburne J, Tozaki T, Vaudin M, Wade CM, McCue ME. Genome-wide analysis reveals selection for important traits in domestic horse breeds. PLoS Genet 2013; 9:e1003211. [PMID: 23349635 PMCID: PMC3547851 DOI: 10.1371/journal.pgen.1003211] [Citation(s) in RCA: 174] [Impact Index Per Article: 15.8] [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: 08/28/2012] [Accepted: 11/15/2012] [Indexed: 02/04/2023] Open
Abstract
Intense selective pressures applied over short evolutionary time have resulted in homogeneity within, but substantial variation among, horse breeds. Utilizing this population structure, 744 individuals from 33 breeds, and a 54,000 SNP genotyping array, breed-specific targets of selection were identified using an F(ST)-based statistic calculated in 500-kb windows across the genome. A 5.5-Mb region of ECA18, in which the myostatin (MSTN) gene was centered, contained the highest signature of selection in both the Paint and Quarter Horse. Gene sequencing and histological analysis of gluteal muscle biopsies showed a promoter variant and intronic SNP of MSTN were each significantly associated with higher Type 2B and lower Type 1 muscle fiber proportions in the Quarter Horse, demonstrating a functional consequence of selection at this locus. Signatures of selection on ECA23 in all gaited breeds in the sample led to the identification of a shared, 186-kb haplotype including two doublesex related mab transcription factor genes (DMRT2 and 3). The recent identification of a DMRT3 mutation within this haplotype, which appears necessary for the ability to perform alternative gaits, provides further evidence for selection at this locus. Finally, putative loci for the determination of size were identified in the draft breeds and the Miniature horse on ECA11, as well as when signatures of selection surrounding candidate genes at other loci were examined. This work provides further evidence of the importance of MSTN in racing breeds, provides strong evidence for selection upon gait and size, and illustrates the potential for population-based techniques to find genomic regions driving important phenotypes in the modern horse.
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Affiliation(s)
- Jessica L Petersen
- College of Veterinary Medicine, University of Minnesota, St. Paul, Minnesota, USA.
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Sundström E, Imsland F, Mikko S, Wade C, Sigurdsson S, Pielberg GR, Golovko A, Curik I, Seltenhammer MH, Sölkner J, Lindblad-Toh K, Andersson L. Copy number expansion of the STX17 duplication in melanoma tissue from Grey horses. BMC Genomics 2012; 13:365. [PMID: 22857264 PMCID: PMC3443021 DOI: 10.1186/1471-2164-13-365] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2012] [Accepted: 07/18/2012] [Indexed: 01/11/2023] Open
Abstract
Background Greying with age in horses is an autosomal dominant trait, associated with loss of hair pigmentation, melanoma and vitiligo-like depigmentation. We recently identified a 4.6 kb duplication in STX17 to be associated with the phenotype. The aims of this study were to investigate if the duplication in Grey horses shows copy number variation and to exclude that any other polymorphism is uniquely associated with the Grey mutation. Results We found little evidence for copy number expansion of the duplicated sequence in blood DNA from Grey horses. In contrast, clear evidence for copy number expansions was indicated in five out of eight tested melanoma tissues or melanoma cell lines. A tendency of a higher copy number in aggressive tumours was also found. Massively parallel resequencing of the ~350 kb Grey haplotype did not reveal any additional mutations perfectly associated with the phenotype, confirming the duplication as the true causative mutation. We identified three SNP alleles that were present in a subset of Grey haplotypes within the 350 kb region that shows complete linkage disequilibrium with the causative mutation. Thus, these three nucleotide substitutions must have occurred subsequent to the duplication, consistent with our interpretation that the Grey mutation arose more than 2,000 years before present. Conclusions These results suggest that the mutation acts as a melanoma-driving regulatory element. The elucidation of the mechanistic features of the duplication will be of considerable interest for the characterization of these horse melanomas as well as for the field of human melanoma research.
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Affiliation(s)
- Elisabeth Sundström
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Wik L, Mikko S, Klingeborn M, Stéen M, Simonsson M, Linné T. Polymorphisms and variants in the prion protein sequence of European moose (Alces alces), reindeer (Rangifer tarandus), roe deer (Capreolus capreolus) and fallow deer (Dama dama) in Scandinavia. Prion 2012; 6:256-60. [PMID: 22441661 DOI: 10.4161/pri.19641] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
The prion protein (PrP) sequence of European moose, reindeer, roe deer and fallow deer in Scandinavia has high homology to the PrP sequence of North American cervids. Variants in the European moose PrP sequence were found at amino acid position 109 as K or Q. The 109Q variant is unique in the PrP sequence of vertebrates. During the 1980s a wasting syndrome in Swedish moose, Moose Wasting Syndrome (MWS), was described. SNP analysis demonstrated a difference in the observed genotype proportions of the heterozygous Q/K and homozygous Q/Q variants in the MWS animals compared with the healthy animals. In MWS moose the allele frequencies for 109K and 109Q were 0.73 and 0.27, respectively, and for healthy animals 0.69 and 0.31. Both alleles were seen as heterozygotes and homozygotes. In reindeer, PrP sequence variation was demonstrated at codon 176 as D or N and codon 225 as S or Y. The PrP sequences in roe deer and fallow deer were identical with published GenBank sequences.
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Affiliation(s)
- Lotta Wik
- Division of Immunology, Department of Biomedical Sciences and Veterinary Public Health, Faculty of Veterinary Medicine and Animal Science, Swedish University of Agricultural Sciences; Uppsala, Sweden
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Andersson LS, Swinburne JE, Meadows JRS, Broström H, Eriksson S, Fikse WF, Frey R, Sundquist M, Tseng CT, Mikko S, Lindgren G. Erratum to: The same ELA class II risk factors confer equine insect bite hypersensitivity in two distinct populations. Immunogenetics 2011. [PMCID: PMC3462919 DOI: 10.1007/s00251-011-0592-y] [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] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- Lisa S. Andersson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 597, SE-751 24 Uppsala, Sweden
| | - June E. Swinburne
- Centre for Preventive Medicine, Animal Health Trust, Lanwades Park, Kentford, Newmarket, Suffolk, CB7 8UU UK
| | - Jennifer R. S. Meadows
- Department of Medical Biochemistry and Microbiology, Uppsala University, Box 582, SE-751 24 Uppsala, Sweden
| | - Hans Broström
- Department of Clinical Sciences, Swedish University of Agricultural Sciences, Box 7054, SE-750 07 Uppsala, Sweden
| | - Susanne Eriksson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, SE-750 07 Uppsala, Sweden
| | - W. Freddy Fikse
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, SE-750 07 Uppsala, Sweden
| | - Rebecka Frey
- Norsholms Animal Hospital, Biskop Henriksv. 6, SE-602 37 Norrköping, Sweden
| | - Marie Sundquist
- Östra Greda Research Group, Vialmv. 5, SE-387 91 Borgholm, Sweden
| | - Chia T. Tseng
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY 14853 USA
| | - Sofia Mikko
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 7023, SE-750 07 Uppsala, Sweden
| | - Gabriella Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 597, SE-751 24 Uppsala, Sweden
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Andersson LS, Swinburne JE, Meadows JRS, Broström H, Eriksson S, Fikse WF, Frey R, Sundquist M, Tseng CT, Mikko S, Lindgren G. The same ELA class II risk factors confer equine insect bite hypersensitivity in two distinct populations. Immunogenetics 2011; 64:201-8. [PMID: 21947540 PMCID: PMC3276761 DOI: 10.1007/s00251-011-0573-1] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Accepted: 09/09/2011] [Indexed: 11/15/2022]
Abstract
Insect bite hypersensitivity (IBH) is a chronic allergic dermatitis common in horses. Affected horses mainly react against antigens present in the saliva from the biting midges, Culicoides ssp, and occasionally black flies, Simulium ssp. Because of this insect dependency, the disease is clearly seasonal and prevalence varies between geographical locations. For two distinct horse breeds, we genotyped four microsatellite markers positioned within the MHC class II region and sequenced the highly polymorphic exons two from DRA and DRB3, respectively. Initially, 94 IBH-affected and 93 unaffected Swedish born Icelandic horses were tested for genetic association. These horses had previously been genotyped on the Illumina Equine SNP50 BeadChip, which made it possible to ensure that our study did not suffer from the effects of stratification. The second population consisted of 106 unaffected and 80 IBH-affected Exmoor ponies. We show that variants in the MHC class II region are associated with disease susceptibility (praw = 2.34 × 10−5), with the same allele (COR112:274) associated in two separate populations. In addition, we combined microsatellite and sequencing data in order to investigate the pattern of homozygosity and show that homozygosity across the entire MHC class II region is associated with a higher risk of developing IBH (p = 0.0013). To our knowledge this is the first time in any atopic dermatitis suffering species, including man, where the same risk allele has been identified in two distinct populations.
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Affiliation(s)
- Lisa S Andersson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 597, SE-751 24, Uppsala, Sweden
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Andersson LS, Högström C, Mikko S, Eriksson S, Grandinson K, Broström H, Frey R, Sundquist M, Lindgren G. Polymorphisms inSPINK5do not associate with insect bite hypersensitivity in Icelandic horses born in Sweden. Anim Genet 2009; 40:790-1. [DOI: 10.1111/j.1365-2052.2009.01890.x] [Citation(s) in RCA: 4] [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: 11/26/2022]
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Mohamad K, Olsson M, van Tol HTA, Mikko S, Vlamings BH, Andersson G, Rodríguez-Martínez H, Purwantara B, Paling RW, Colenbrander B, Lenstra JA. On the origin of Indonesian cattle. PLoS One 2009; 4:e5490. [PMID: 19436739 PMCID: PMC2677627 DOI: 10.1371/journal.pone.0005490] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2009] [Accepted: 04/14/2009] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Two bovine species contribute to the Indonesian livestock, zebu (Bos indicus) and banteng (Bos javanicus), respectively. Although male hybrid offspring of these species is not fertile, Indonesian cattle breeds are supposed to be of mixed species origin. However, this has not been documented and is so far only supported by preliminary molecular analysis. METHODS AND FINDINGS Analysis of mitochondrial, Y-chromosomal and microsatellite DNA showed a banteng introgression of 10-16% in Indonesian zebu breeds. East-Javanese Madura and Galekan cattle have higher levels of autosomal banteng introgression (20-30%) and combine a zebu paternal lineage with a predominant (Madura) or even complete (Galekan) maternal banteng origin. Two Madura bulls carried taurine Y-chromosomal haplotypes, presumably of French Limousin origin. In contrast, we did not find evidence for zebu introgression in five populations of the Bali cattle, a domestic form of the banteng. CONCLUSIONS Because of their unique species composition Indonesian cattle represent a valuable genetic resource, which potentially may also be exploited in other tropical regions.
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Affiliation(s)
- Kusdiantoro Mohamad
- Faculty of Veterinary Medicine, Bogor Agricultural University, Bogor, Indonesia
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Mia Olsson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
- Department of Microbiology and Medical Biochemistry, Uppsala University, Uppsala, Sweden
| | | | - Sofia Mikko
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Bart H. Vlamings
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Göran Andersson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | | | - Bambang Purwantara
- Faculty of Veterinary Medicine, Bogor Agricultural University, Bogor, Indonesia
| | - Robert W. Paling
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Ben Colenbrander
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Johannes A. Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
- * E-mail: J.A.
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Brunberg E, Andersson L, Cothran G, Sandberg K, Mikko S, Lindgren G. A missense mutation in PMEL17 is associated with the Silver coat color in the horse. BMC Genet 2006; 7:46. [PMID: 17029645 PMCID: PMC1617113 DOI: 10.1186/1471-2156-7-46] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2006] [Accepted: 10/09/2006] [Indexed: 11/24/2022] Open
Abstract
Background The Silver coat color, also called Silver dapple, in the horse is characterized by dilution of the black pigment in the hair. This phenotype shows an autosomal dominant inheritance. The effect of the mutation is most visible in the long hairs of the mane and tail, which are diluted to a mixture of white and gray hairs. Herein we describe the identification of the responsible gene and a missense mutation associated with the Silver phenotype. Results Segregation data on the Silver locus (Z) were obtained within one half-sib family that consisted of a heterozygous Silver colored stallion with 34 offspring and their 29 non-Silver dams. We typed 41 genetic markers well spread over the horse genome, including one single microsatellite marker (TKY284) close to the candidate gene PMEL17 on horse chromosome 6 (ECA6q23). Significant linkage was found between the Silver phenotype and TKY284 (θ = 0, z = 9.0). DNA sequencing of PMEL17 in Silver and non-Silver horses revealed a missense mutation in exon 11 changing the second amino acid in the cytoplasmic region from arginine to cysteine (Arg618Cys). This mutation showed complete association with the Silver phenotype across multiple horse breeds, and was not found among non-Silver horses with one clear exception; a chestnut colored individual that had several Silver offspring when mated to different non-Silver stallions also carried the exon 11 mutation. In total, 64 Silver horses from six breeds and 85 non-Silver horses from 14 breeds were tested for the exon 11 mutation. One additional mutation located in intron 9, only 759 bases from the missense mutation, also showed complete association with the Silver phenotype. However, as one could expect to find several non-causative mutations completely associated with the Silver mutation, we argue that the missense mutation is more likely to be causative. Conclusion The present study shows that PMEL17 causes the Silver coat color in the horse and enable genetic testing for this trait.
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Affiliation(s)
- Emma Brunberg
- Dept of Medical Biochemistry and Microbiology, Uppsala University, SE-751 24 Uppsala, Sweden.
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Abstract
Grey horses are born coloured, turn progressively grey and often develop melanomas late in life. Grey shows an autosomal dominant inheritance and the locus has previously been mapped to horse chromosome 25 (ECA25), around the TXN gene. We have now developed eight new single nucleotide polymorphisms (SNPs) associated with genes on ECA25 using information on the linear order of genes on human chromosome 9q, as well as the human and mouse coding sequences. These SNPs were mapped in relation to the Grey locus using more than 300 progeny from matings between two Swedish Warmblood grey stallions and non-grey mares. Grey was firmly assigned to an interval with flanking markers NANS and ABCA1. This corresponds to a region of approximately 6.9 Mb on human chromosome 9q. Furthermore, no recombination was observed between Grey, TGFBR1 and TMEFF1, the last two being 1.4 Mb apart in human. There are no obvious candidate genes in this region and none of the genes has been associated with pigmentation disorders or melanoma development, suggesting that the grey phenotype is caused by a mutation in a novel gene.
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Affiliation(s)
- G Pielberg
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Abstract
The neuropeptide Y (NPY) receptor subtypes Y1 and Y5 are involved in the regulation of feeding and several other physiological functions in mammals. To increase our understanding of the origin and mechanisms of the complex NPY system, we report here the cloning and pharmacological characterization of receptors Y1 and Y5 in the first non-mammal, chicken (Gallus gallus). The receptors display 80-83% and 64-72% amino acid sequence identity, respectively, with their mammalian orthologues. The three endogenous ligands NPY, peptide YY (PYY) and pancreatic polypeptide (PP) have similar affinities as in mammals, i.e. NPY and PYY have subnanomolar affinity for both receptors whereas chicken PP bound with nanomolar affinity to Y5 but not to Y1. A notable difference to mammalian receptor subtypes is that the Y1 antagonist SR120819A does not bind chicken Y1, whereas BIBP3226 does. The Y5 antagonist CGP71863A binds to the chicken Y5 receptor. Anatomically, both Y1 and Y5 have high mRNA expression levels in the infundibular nucleus which is the homologous structure of the hypothalamic arcuate nucleus in mammals. These results suggest that some of the selective Y1 and Y5 antagonists developed in mammals can be used to study appetite regulation in chicken.
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Affiliation(s)
- Sara K S Holmberg
- Department of Neuroscience, Unit of Pharmacology, Uppsala University, Uppsala, Sweden
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van Haeringen WA, Gwakisa PS, Mikko S, Eythorsdottir E, Holm LE, Olsaker I, Outteridge P, Andersson L. Heterozygosity excess at the cattle DRB locus revealed by large scale genotyping of two closely linked microsatellites. Anim Genet 1999; 30:169-76. [PMID: 10442977 DOI: 10.1046/j.1365-2052.1999.00436.x] [Citation(s) in RCA: 11] [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: 11/20/2022]
Abstract
A method for MHC DRB typing in cattle based on two closely linked and highly polymorphic microsatellites is described. The two microsatellites DRBP1ms and DRB3ms are located in intron 2 of the corresponding DRB gene. The very strong linkage disequilibrium between the two loci made it possible to establish DRB microsatellite haplotypes. The typing results with this method on reference samples followed closely that obtained with RFLP and direct sequence analysis of DRB3 exon 2. The method is well suited for large scale genotyping and was successfully applied for typing more than 600 unrelated animals representing 23 breeds. The data were used to test whether the observed DRB allele frequency distributions were consistent with that expected for selectively neutral alleles in populations at mutation-drift equilibrium. A significant heterozygosity excess was detected and there was an obvious trend across breeds towards a more even allele frequency distribution than expected. The deviation may be due to balancing selection acting on the DRB locus or by recent population bottlenecks.
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Affiliation(s)
- W A van Haeringen
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Abstract
Genetic polymorphism at Mhc class II DRB loci was investigated in samples of musk-ox from Canada and Greenland; moose from Sweden, Norway, Canada, and Alaska; roe deer from Norway and Sweden; reindeer from Svalbard and Norway; fallow deer from Norway and Sweden; and red deer from Norway. The results were compared with published data on cattle, bison, goat, sheep, and red deer. Cattle-specific primers amplified a single DRB locus in all species except fallow deer and red deer, in which two loci were found. Single strand conformation polymorphism analysis and DNA sequence analysis were employed to detect genetic polymorphism. Complete monomorphism was found in musk-ox and fallow deer. Limited polymorphism was found in the moose, roe deer, and reindeer from Svalbard, whereas intermediate to extensive DRB diversity was present in reindeer from Norway and in bison, sheep, goat, cattle, and red deer. The restricted Mhc diversity in moose, roe deer, and fallow deer is notable in relation to the dramatic population expansion of moose and roe deer in Sweden during this century and since fallow deer is used for meat and game production with good results and without any marked disease problems. The results question the view that species or populations with restricted Mhc diversity have poor resistance to infectious diseases. A phylogenetic tree analysis revealed a clustering of DRB sequences within species rather than within allelic lineages across species. The results suggest trans-species persistence of polymorphic sequence motifs rather than of allelic lineages.
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Affiliation(s)
- S Mikko
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Abstract
One of the most common cattle major histocompatibility complex DRB3 alleles, *0201, includes a deletion of codon 65 encoding one residue in the alpha-helical chain. The mutation is functionally interesting and is likely to influence peptide binding. Exon 2 of two additional del65 alleles, *3301 and *4101, have now been sequenced with the aim to investigate the evolutionary relationship of this allelic group. Despite a fairly large genetic distance between the three alleles (11-17 nucleotide substitutions causing 8-11 amino acid substitutions) we found clear indications of a common ancestry. The alpha-helical region was very similar or identical among the alleles whereas the beta-strand region was quite divergent. The results indicated that interallelic recombination has contributed to the diversification of the del65 group. Deletion of codon 65 has also been found in a roe deer DRB1 allele and a cattle DQB3 allele. Sequence comparisons of the cattle and roe deer DRB del65 alleles refuted the possibility of a trans-species persistence of a del65 allelic lineage but the two species may share a short ancestral sequence motif including del65. In addition to del65, the cattle DQB3 allele did not show any striking sequence similarities to the DRB alleles.
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Affiliation(s)
- S Mikko
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Box 597, S-751 24 Uppsala, Sweden
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Abstract
The degree of genetic polymorphism at the DRB3 locus in the major histocompatibility complex (Mhc) of the North American bison was investigated by PCR and DNA sequence analysis. Nine different alleles were characterized in a selected sample of 20 animals. The genetic distances between alleles were as large as usually found at highly polymorphic Mhc loci in other species. A comparative analysis of the DRB3 polymorphism in bison and cattle revealed an extensive sharing of sequence motifs. The result clearly shows a transspecies persistence of DRB3 allelic lineages in the two species. Consequently a significant amount of Mhc polymorphism has been maintained through the population bottleneck that bison experienced in the late nineteenth century. An analysis of the pattern of sequence polymorphism among bison and cattle DRB3 alleles strongly suggested that interallelic recombination has contributed significantly to the generation of allelic diversity at this locus.
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Affiliation(s)
- S Mikko
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Russell GC, Davies CJ, Andersson L, Mikko S, Ellis SA, Hensen EJ, Lewin HA, Muggli-Cockett NE, Poel JJVD. BoLA class II nucleotide sequences, 1996: report of the ISAG BoLA Nomenclature Committee. Anim Genet 1997. [DOI: 10.1111/j.1365-2052.1997.00107.x] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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Davies CJ, Andersson L, Mikko S, Ellis SA, Hensen EJ, Lewin HA, Muggli-Cockett NE, Poel JJVD, Russell GC. Nomenclature for factors of the BoLA system, 1996: report of the ISAG BoLA Nomenclature Committee. Anim Genet 1997. [DOI: 10.1111/j.1365-2052.1997.00106.x] [Citation(s) in RCA: 82] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Nilsson PR, Marsh SGE, Joosten I, Nieuwland MGB, Hensen EJ, Grosfeld-Stulemeyer MC, Mikko S, Gelhaus A, Schreuder GMT. THE SPECIFICITY OF ANTI-HLA CLASS II MONOCLONAL ANTIBODIES IN CATTLE. ACTA ACUST UNITED AC 1997; 24:211-223. [PMID: 28984421 DOI: 10.1111/j.1365-2370.1997.00262.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
At the Eleventh International HLA Histocompatibility Workshop, numerous anti-HLA class II monoclonal antibodies (mAb) were tested. For several of the polymorphic mAb, one epitope for binding has been mapped within the antigen-binding site of the class II molecules. Screening of the available bovine DRB3 and DQB exon 2 sequences revealed that some of the key amino acid (AA) motifs of these epitopes were present in cattle as well, and the question was raised whether this sharing of key AA motifs might cause interspecies cross-reactivity. Eight polymorphic anti-HLA class II mAb (seven anti-HLA DRB1 and one anti-HLA DQB) were selected for analysis of their reactivity towards bovine lymphocytes. In addition, the monomorphic anti-HLA class II mAb, 7.5.10.1, was selected for analysis, as this mAb was described to detect class II polymorphism in cattle. Flow cytometry and lymphocyte microcytotoxicity testing revealed that five of the polymorphic anti-HLA mAb were reactive with bovine lymphocytes. Furthermore, the anti-bovine reactivity of 7.5.10.1 was confirmed. These findings were supported by biochemical analysis. The anti-bovine reaction of the anti-HLA mAb did not correspond with the expected reaction, which was based on the presence of the AA, postulated to be responsible for recognition. Therefore, we suggest that the patterns of reactivity of the anti-HLA mAb are not always determined by one epitope.
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Affiliation(s)
- Ph R Nilsson
- Department of Animal Husbandry and ,Department of Experimental Animal Morphology and Cell Biology, Agricultural University, Wageningen, the Netherlands; ,Anthony Nolan Research Institute, Royal Free Hospital, London, UK; ,Transplantation Serology Laboratory, University Hospital Nijmegen, Nijmegen, the Netherlands; ,Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, University of Utrecht, Utrecht, the Netherlands; ,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden; ,Department of Molecular Biology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany; and ,Department of Immunohaematology and Bloodbank, University Hospital, Leiden, the Netherlands
| | - S G E Marsh
- Department of Animal Husbandry and ,Department of Experimental Animal Morphology and Cell Biology, Agricultural University, Wageningen, the Netherlands; ,Anthony Nolan Research Institute, Royal Free Hospital, London, UK; ,Transplantation Serology Laboratory, University Hospital Nijmegen, Nijmegen, the Netherlands; ,Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, University of Utrecht, Utrecht, the Netherlands; ,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden; ,Department of Molecular Biology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany; and ,Department of Immunohaematology and Bloodbank, University Hospital, Leiden, the Netherlands
| | - I Joosten
- Department of Animal Husbandry and ,Department of Experimental Animal Morphology and Cell Biology, Agricultural University, Wageningen, the Netherlands; ,Anthony Nolan Research Institute, Royal Free Hospital, London, UK; ,Transplantation Serology Laboratory, University Hospital Nijmegen, Nijmegen, the Netherlands; ,Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, University of Utrecht, Utrecht, the Netherlands; ,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden; ,Department of Molecular Biology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany; and ,Department of Immunohaematology and Bloodbank, University Hospital, Leiden, the Netherlands
| | - M G B Nieuwland
- Department of Animal Husbandry and ,Department of Experimental Animal Morphology and Cell Biology, Agricultural University, Wageningen, the Netherlands; ,Anthony Nolan Research Institute, Royal Free Hospital, London, UK; ,Transplantation Serology Laboratory, University Hospital Nijmegen, Nijmegen, the Netherlands; ,Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, University of Utrecht, Utrecht, the Netherlands; ,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden; ,Department of Molecular Biology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany; and ,Department of Immunohaematology and Bloodbank, University Hospital, Leiden, the Netherlands
| | - E J Hensen
- Department of Animal Husbandry and ,Department of Experimental Animal Morphology and Cell Biology, Agricultural University, Wageningen, the Netherlands; ,Anthony Nolan Research Institute, Royal Free Hospital, London, UK; ,Transplantation Serology Laboratory, University Hospital Nijmegen, Nijmegen, the Netherlands; ,Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, University of Utrecht, Utrecht, the Netherlands; ,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden; ,Department of Molecular Biology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany; and ,Department of Immunohaematology and Bloodbank, University Hospital, Leiden, the Netherlands
| | - M C Grosfeld-Stulemeyer
- Department of Animal Husbandry and ,Department of Experimental Animal Morphology and Cell Biology, Agricultural University, Wageningen, the Netherlands; ,Anthony Nolan Research Institute, Royal Free Hospital, London, UK; ,Transplantation Serology Laboratory, University Hospital Nijmegen, Nijmegen, the Netherlands; ,Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, University of Utrecht, Utrecht, the Netherlands; ,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden; ,Department of Molecular Biology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany; and ,Department of Immunohaematology and Bloodbank, University Hospital, Leiden, the Netherlands
| | - S Mikko
- Department of Animal Husbandry and ,Department of Experimental Animal Morphology and Cell Biology, Agricultural University, Wageningen, the Netherlands; ,Anthony Nolan Research Institute, Royal Free Hospital, London, UK; ,Transplantation Serology Laboratory, University Hospital Nijmegen, Nijmegen, the Netherlands; ,Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, University of Utrecht, Utrecht, the Netherlands; ,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden; ,Department of Molecular Biology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany; and ,Department of Immunohaematology and Bloodbank, University Hospital, Leiden, the Netherlands
| | - A Gelhaus
- Department of Animal Husbandry and ,Department of Experimental Animal Morphology and Cell Biology, Agricultural University, Wageningen, the Netherlands; ,Anthony Nolan Research Institute, Royal Free Hospital, London, UK; ,Transplantation Serology Laboratory, University Hospital Nijmegen, Nijmegen, the Netherlands; ,Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, University of Utrecht, Utrecht, the Netherlands; ,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden; ,Department of Molecular Biology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany; and ,Department of Immunohaematology and Bloodbank, University Hospital, Leiden, the Netherlands
| | - G M Th Schreuder
- Department of Animal Husbandry and ,Department of Experimental Animal Morphology and Cell Biology, Agricultural University, Wageningen, the Netherlands; ,Anthony Nolan Research Institute, Royal Free Hospital, London, UK; ,Transplantation Serology Laboratory, University Hospital Nijmegen, Nijmegen, the Netherlands; ,Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, University of Utrecht, Utrecht, the Netherlands; ,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden; ,Department of Molecular Biology, Bernhard Nocht Institute for Tropical Medicine, Hamburg, Germany; and ,Department of Immunohaematology and Bloodbank, University Hospital, Leiden, the Netherlands
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Nilsson PR, Marsh SG, Joosten I, Nieuwland MG, Hensen EJ, Grosfeld-Stulemeyer MC, Mikko S, Gelhaus A, Schreuder GM. The specificity of anti-HLA class II monoclonal antibodies in cattle. Eur J Immunogenet 1997; 24:211-23. [PMID: 9226127] [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] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Abstract
At the Eleventh International HLA Histocompatibility Workshop, numerous anti-HLA class II monoclonal antibodies (mAb) were tested. For several of the polymorphic mAb, one epitope for binding has been mapped within the antigen-binding site of the class II molecules. Screening of the available bovine DRB3 and DQB exon 2 sequences revealed that some of the key amino acid (AA) motifs of these epitopes were present in cattle as well, and the question was raised whether this sharing of key AA motifs might cause interspecies cross-reactivity. Eight polymorphic anti-HLA class II mAb (seven anti-HLA DRB1 and one anti-HLA DQB) were selected for analysis of their reactivity towards bovine lymphocytes. In addition, the monomorphic anti-HLA class II mAb, 7.5.10.1, was selected for analysis, as this mAb was described to detect class II polymorphism in cattle. Flow cytometry and lymphocyte microcytotoxicity testing revealed that five of the polymorphic anti-HLA mAb were reactive with bovine lymphocytes. Furthermore, the anti-bovine reactivity of 7.5.10.1 was confirmed. These findings were supported by biochemical analysis. The anti-bovine reaction of the anti-HLA mAb did not correspond with the expected reaction, which was based on the presence of the AA, postulated to be responsible for recognition. Therefore, we suggest that the patterns of reactivity of the anti-HLA mAb are not always determined by one epitope.
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Affiliation(s)
- P R Nilsson
- Department of Animal Husbandry, Agricultural University, Wageningen, The Netherlands
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Outteridge PM, Andersson L, Douch PG, Green RS, Gwakisa PS, Hohenhaus MA, Mikko S. The PCR typing of MHC-DRB genes in the sheep using primers for an intronic microsatellite: application to nematode parasite resistance. Immunol Cell Biol 1996; 74:330-6. [PMID: 8872183 DOI: 10.1038/icb.1996.59] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [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: 02/02/2023]
Abstract
The strong association between polymorphisms in an intronic microsatellite and the coding sequences for (BoLA)-DRB3 genes, previously described for demonstrating alleles of class II major histocompatibility complex (MHC) in the cow, was examined in sheep to see if similar polymorphisms could be demonstrated in the DRB region of the MHC. The bovine primes LA53 and LA54, previously used to amplify the bovine DRB3 microsatellites, were used with DNA from Australian sheep, eight DRB alleles were identified by length polymorphisms of polymerase chain reaction (PCR) products amplified from the DRB microsatellite region. Incomplete amplification of both alleles was sometimes found for sheep DNA samples using bovine primers, so a modified primer (LA53b) was used, and found to amplify the microsatellite next to intron 2 of the MHC more reliably than the LA53 primer. Two additional primers (LA31 and LA32), used in amplification of the exon 2 region of bovine DRB3, were used in the sheep, and the PCR products were analysed by single-stranded conformation polymorphism (SSCP). These primers successfully amplified the variable region of the ovine DRB region coded by exon 2, and the SSCP technique demonstrated polymorphisms with sheep DNA. Family studies demonstrated the segregation of alleles, by amplification both of intronic microsatellites and of the exon 2 variable region. Close correspondence was found between the two regions for several alleles, suggesting that the intronic microsatellites were closely linked to DRB-variable region alleles. Three families of Merino sheep with different antibody responses to intestinal nematode parasites were examined. The sire group with the highest antibody levels possessed two microsatellite alleles of closely similar length (alleles 3 and 4) inherited from the sire and present in high frequency in the lambs. In contrast, the other two sires did not possess these two alleles and the alleles were in low frequency in their progeny. Further studies are required in unrelated sheep to confirm whether these two alleles are associated with resistance to nematode parasites.
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Affiliation(s)
- P M Outteridge
- Department of Farm Animal Medicine and Production, University of Queensland, Australia
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Abstract
The Swedish moose was analysed for genetic variability at major histocompatibility complex (MHC) class I and class II DQA, DQB and DRB loci using restriction fragment length polymorphism (RFLP) and single strand conformation polymorphism (SSCP) techniques. Both methods revealed limited amounts of polymorphism. Since the SSCP analysis concerned an expressed DRB gene it can be concluded that the level of functional MHC class II polymorphism, at least at the DRB locus, is low in Swedish moose. DNA fingerprinting was used to determine if the unusual pattern of low MHC variability could be explained by a low degree of genome-wide genetic diversity. Hybridizations with two minisatellite probes gave similarity indices somewhat higher than the average for other natural population, but the data suggest that the low MHC variability cannot be explained by a recent population bottleneck. However, since minisatellite sequences evolve more rapidly than MHC sequences, the low levels of MHC diversity may be attributed to a bottleneck of more ancient origin. The selection pressure for MHC variability in moose may also be reduced and we discuss the possibility that its solitary life style may reduce lateral transmission of pathogens in the population.
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Affiliation(s)
- H Ellegren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Biomedical Centre, Uppsala
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Abstract
Genetic diversity at the highly polymorphic BoLA-DRB3 locus was investigated by DNA sequence analyses of 18 African cattle from two breeds representing the two subspecies of cattle, Bos primigenius indicus and Bos primigenius taurus. The polymorphism was compared with that found in a sample of 32 European cattle from four breeds, all classified as B. p. taurus. Particularly extensive genetic diversity was found among African cattle, in which as many as 18 alleles were recognized in this small random sample of animals from two breeds. The observed similarity in allele frequency distribution between the two African populations, N'Dama and Zebu cattle, is consistent with the recent recognition of gene flow between B. p. indicus and B. p. taurus cattle in Africa. A total of 30 DRB3 alleles were documented and as many as 26 of these were classified as major allelic types showing at least five amino acid substitutions compared with other major types. The observation of extensive genetic diversity at MHC loci in cattle, as well as in other farm animals, provides a compelling argument against mating-type preferences as a primary cause in maintaining major histocompatibility complex diversity, since the reproduction of these animals has been controlled by humans for many generations.
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Affiliation(s)
- S Mikko
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, BMC, Box 597, S-751 24 Uppsala, Sweden
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Abstract
Major histocompatibility complex (MHC) genes encode cell surface proteins whose function is to bind and present intracellularly processed peptides to T lymphocytes of the immune system. Extensive MHC diversity has been documented in many species and is maintained by some form of balancing selection. We report here that both European and North American populations of moose (Alces alces) exhibit very low levels of genetic diversity at an expressed MHC class II DRB locus. The observed polymorphism was restricted to six amino acid substitutions, all in the peptide binding site, and four of these were shared between continents. The data imply that the moose have lost MHC diversity in a population bottleneck, prior to the divergence of the Old and New World subspecies. Sequence analysis of mtDNA showed that the two subspecies diverged at least 100,000 years ago. Thus, viable moose populations with very restricted MHC diversity have been maintained for a long period of time. Both positive selection for polymorphism and intraexonic recombination have contributed to the generation of MHC diversity after the putative bottleneck.
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Affiliation(s)
- S Mikko
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala
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Abstract
The occurrence and significance of recombination events in the generation of MHC class II diversity were discussed. Evidence that intragenic recombination has contributed to the generation of allelic diversity at a DRB locus in the moose was presented. Intergenic recombination (i.e. exchange of sequence information between nonallelic genes) is expected to be rare and only to play a minor role in the generation of class II diversity. Exchange of sequence information between the major isotypic forms of class II genes (DQ, DR and DP) is restricted to a segment encoding a major part of the a-helical region of polymorphic class II beta-chains. In this segment there is no or only weak locus divergence and the frequency of synonymous substitutions between nonallelic genes (DQB vs. DRB) within species is remarkably low, implying that exchange of sequence information has occurred repeatedly during the course of evolution.
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Affiliation(s)
- L Andersson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala Biomedical Center
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Affiliation(s)
- P Gwakisa
- Swedish University of Agricultural Sciences, Department of Animal Breeding and Genetics, Uppsala
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