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Durward-Akhurst SA, Marlowe JL, Schaefer RJ, Springer K, Grantham B, Carey WK, Bellone RR, Mickelson JR, McCue ME. Predicted genetic burden and frequency of phenotype-associated variants in the horse. Sci Rep 2024; 14:8396. [PMID: 38600096 PMCID: PMC11006912 DOI: 10.1038/s41598-024-57872-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2023] [Accepted: 03/22/2024] [Indexed: 04/12/2024] Open
Abstract
Disease-causing variants have been identified for less than 20% of suspected equine genetic diseases. Whole genome sequencing (WGS) allows rapid identification of rare disease causal variants. However, interpreting the clinical variant consequence is confounded by the number of predicted deleterious variants that healthy individuals carry (predicted genetic burden). Estimation of the predicted genetic burden and baseline frequencies of known deleterious or phenotype associated variants within and across the major horse breeds have not been performed. We used WGS of 605 horses across 48 breeds to identify 32,818,945 variants, demonstrate a high predicted genetic burden (median 730 variants/horse, interquartile range: 613-829), show breed differences in predicted genetic burden across 12 target breeds, and estimate the high frequencies of some previously reported disease variants. This large-scale variant catalog for a major and highly athletic domestic animal species will enhance its ability to serve as a model for human phenotypes and improves our ability to discover the bases for important equine phenotypes.
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Affiliation(s)
- S A Durward-Akhurst
- Department of Veterinary Clinical Sciences, University of Minnesota, C339 VMC, 1353 Boyd Avenue, St. Paul, MN, 55108, USA.
| | - J L Marlowe
- Department of Veterinary Clinical Sciences, University of Minnesota, C339 VMC, 1353 Boyd Avenue, St. Paul, MN, 55108, USA
| | - R J Schaefer
- Department of Veterinary Population Medicine, University of Minnesota, 225 VMC, 1365 Gortner Avenue, St. Paul, MN, 55108, USA
| | - K Springer
- Department of Veterinary Population Medicine, University of Minnesota, 225 VMC, 1365 Gortner Avenue, St. Paul, MN, 55108, USA
| | - B Grantham
- Interval Bio LLC, 408 Stierline Road, Mountain View, CA, 94043, USA
| | - W K Carey
- Interval Bio LLC, 408 Stierline Road, Mountain View, CA, 94043, USA
| | - R R Bellone
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California-Davis, Davis, CA, USA
- Population Health and Reproduction and Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California, Davis, CA, USA
| | - J R Mickelson
- Department of Veterinary and Biomedical Sciences, University of Minnesota, 295F Animal Science Veterinary Medicine Building, 1988 Fitch Avenue, St. Paul, MN, 55108, USA
| | - M E McCue
- Department of Veterinary Population Medicine, University of Minnesota, 225 VMC, 1365 Gortner Avenue, St. Paul, MN, 55108, USA
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2
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Al Abri M, Alfoudari A, Mohammad Z, Almathen F, Al-Marzooqi W, Al-Hajri S, Al-Amri M, Bahbahani H. Assessing genetic diversity and defining signatures of positive selection on the genome of dromedary camels from the southeast of the Arabian Peninsula. Front Vet Sci 2023; 10:1296610. [PMID: 38098998 PMCID: PMC10720651 DOI: 10.3389/fvets.2023.1296610] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2023] [Accepted: 11/17/2023] [Indexed: 12/17/2023] Open
Abstract
Dromedary camels (Camelus dromedarius) are members of the Camelini tribe within the Camelidae family. They are distributed throughout North Africa, the Arabian Peninsula and Southeast Asia. This domestic species is characterized by its superior adaptability to the harsh desert environment. In this study, whole autosomal data of 29 dromedary samples from the Southeast Arabian Peninsula in Oman; 10 from Muscat, 14 from Al-Batinah, and 5 from Al-Sharqiya, were investigated to assess their genetic relationship and to define candidate signatures of positive selection. A minimal genetic distinction that separates Muscat dromedaries from the other two populations was observed, with a degree of genetic admixture between them. Using the de-correlated composite of multiple signals (DCMS) approach, a total of 47 candidate regions within the autosomes of these dromedary populations were defined with signatures of positive selection. These candidate regions harbor a total of 154 genes that are mainly associated with functional categories related to immune response, lipid metabolism and energy expenditure, optical and auditory functions, and long-term memory. Different functional genomic variants were called on the candidate regions and respective genes that warrant further investigation to find possible association with the different favorable phenotypes in dromedaries. The output of this study paves the way for further research efforts aimed at defining markers for use in genomic breeding programs, with the goal of conserving the genetic diversity of the species and enhancing its productivity.
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Affiliation(s)
- Mohammad Al Abri
- Department of Animal and Veterinary Sciences, Sultan Qaboos University, Muscat, Oman
| | - Ahmad Alfoudari
- Department of Biological Sciences, Faculty of Science, Kuwait University, Safat, Kuwait
| | - Zainab Mohammad
- Department of Biological Sciences, Faculty of Science, Kuwait University, Safat, Kuwait
| | - Faisal Almathen
- Department of Veterinary Public Health and Animal Husbandry, College of Veterinary Medicine, King Faisal University, Al-Ahsa, Saudi Arabia
- Camel Research Center, King Faisal University, Al-Ahsa, Saudi Arabia
| | - Waleed Al-Marzooqi
- Department of Animal and Veterinary Sciences, Sultan Qaboos University, Muscat, Oman
| | - Salim Al-Hajri
- Laboratories and Research Administration, Directorate General of Veterinary Services, Royal Court Affairs, Muscat, Oman
| | - Mahmood Al-Amri
- Laboratories and Research Administration, Directorate General of Veterinary Services, Royal Court Affairs, Muscat, Oman
| | - Hussain Bahbahani
- Department of Biological Sciences, Faculty of Science, Kuwait University, Safat, Kuwait
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3
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Gmel AI, Brem G, Neuditschko M. New genomic insights into the conformation of Lipizzan horses. Sci Rep 2023; 13:8990. [PMID: 37268682 DOI: 10.1038/s41598-023-36272-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Accepted: 05/31/2023] [Indexed: 06/04/2023] Open
Abstract
Conformation traits are important selection criteria in equine breeding, as they describe the exterior aspects of the horse (height, joint angles, shape). However, the genetic architecture of conformation is not well understood, as data of these traits mainly consist of subjective evaluation scores. Here, we performed genome-wide association studies on two-dimensional shape data of Lipizzan horses. Based on this data, we identified significant quantitative trait loci (QTL) associated with cresty neck on equine chromosome (ECA)16 within the MAGI1 gene, and with type, hereby differentiating heavy from light horses on ECA5 within the POU2F1 gene. Both genes were previously described to affect growth, muscling and fatty deposits in sheep, cattle and pigs. Furthermore, we pin-pointed another suggestive QTL on ECA21, near the PTGER4 gene, associated with human ankylosing spondylitis, for shape differences in the back and pelvis (roach back vs sway back). Further differences in the shape of the back and abdomen were suggestively associated with the RYR1 gene, involved in core muscle weakness in humans. Therefore, we demonstrated that horse shape space data enhance the genomic investigations of horse conformation.
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Affiliation(s)
- A I Gmel
- Equine Department, Vetsuisse Faculty, University of Zurich, Winterthurerstrasse 260, 8057, Zurich, Switzerland
- Animal GenoPhenomics, Agroscope, Rte de La Tioleyre 4, 1725, Posieux, Switzerland
| | - G Brem
- Institute of Animal Breeding and Genetics, Veterinary University Vienna, Veterinärplatz 1, 1220, Vienna, Austria
| | - M Neuditschko
- Animal GenoPhenomics, Agroscope, Rte de La Tioleyre 4, 1725, Posieux, Switzerland.
- Institute of Animal Breeding and Genetics, Veterinary University Vienna, Veterinärplatz 1, 1220, Vienna, Austria.
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4
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Rosengren MK, Sigurðardóttir H, Eriksson S, Naboulsi R, Jouni A, Novoa-Bravo M, Albertsdóttir E, Kristjánsson Þ, Rhodin M, Viklund Å, Velie BD, Negro JJ, Solé M, Lindgren G. A QTL for conformation of back and croup influences lateral gait quality in Icelandic horses. BMC Genomics 2021; 22:267. [PMID: 33853519 PMCID: PMC8048352 DOI: 10.1186/s12864-021-07454-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2020] [Accepted: 02/19/2021] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND The back plays a vital role in horse locomotion, where the spine functions as a spring during the stride cycle. A complex interaction between the spine and the muscles of the back contribute to locomotion soundness, gait ability, and performance of riding and racehorses. Conformation is commonly used to select horses for breeding and performance in multiple horse breeds, where the back and croup conformation plays a significant role. The conformation of back and croup plays an important role on riding ability in Icelandic horses. However, the genes behind this trait are still unknown. Therefore, the aim of this study was to identify genomic regions associated with conformation of back and croup in Icelandic horses and to investigate their effects on riding ability. One hundred seventy-seven assessed Icelandic horses were included in the study. A genome-wide association analysis was performed using the 670 K+ Axiom Equine Genotyping Array, and the effects of different haplotypes in the top associated region were estimated for riding ability and additional conformation traits assessed during breeding field tests. RESULTS A suggestive quantitative trait loci (QTL) for the score of back and croup was detected on Equus caballus (ECA) 22 (p-value = 2.67 × 10- 7). Haplotype analysis revealed two opposite haplotypes, which resulted in higher and lower scores of the back and croup, respectively (p-value < 0.001). Horses with the favorable haplotype were more inclined to have a well-balanced backline with an uphill conformation and had, on average, higher scores for the lateral gaits tölt (p-value = 0.02) and pace (p-value = 0.004). This genomic region harbors three genes: C20orf85, ANKRD60 and LOC100056167. ANKRD60 is associated with body height in humans. C20orf85 and ANKRD60 are potentially linked to adolescent idiopathic scoliosis in humans. CONCLUSIONS Our results show that the detected QTL for conformation of back and croup is of importance for quality of lateral gaits in Icelandic horses. These findings could result in a genetic test to aid in the selection of breeding horses, thus they are of major interest for horse breeders. The results may also offer a gateway to comparative functional genomics by potentially linking both motor laterality and back inclination in horses with scoliosis in humans.
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Affiliation(s)
- Maria K Rosengren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.
| | - Heiðrún Sigurðardóttir
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- The Agricultural University of Iceland, Borgarnes, Iceland
| | - Susanne Eriksson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Rakan Naboulsi
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ahmad Jouni
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Miguel Novoa-Bravo
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Genética Animal de Colombia Ltda, Bogotá, Colombia
| | | | | | - Marie Rhodin
- Department of Anatomy, Physiology and Biochemistry, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Åsa Viklund
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Brandon D Velie
- School of Life & Environmental Sciences, University of Sydney, Sydney, Australia
| | - Juan J Negro
- Department of Evolutionary Ecology, Doñana Biological Station, CSIC, Seville, Spain
| | - Marina Solé
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Gabriella Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- Livestock Genetics, Department of Biosystems, KU Leuven, Leuven, Belgium
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5
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Al Abri MA, Brooks SA, Al-Saqri N, Alkharousi K, Johnson EH, Alqaisi O, Al-Rawahi A, Al Marzooqi W. Investigating the population structure and genetic diversity of Arabian horses in Oman using SNP markers. Anim Genet 2021; 52:304-310. [PMID: 33730759 DOI: 10.1111/age.13056] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/26/2021] [Indexed: 11/27/2022]
Abstract
Arabian horses were selected for metabolic efficiency, beauty, efficiency and endurance. Therefore, Bedouins have for centuries traced their prized horses' ancestries. With the establishment of the World Arabian Horse Organization (WAHO), registration of Arabian horses became centralized and countries worldwide registered them in its database. Most existing Arabian horses in Oman today were imported after the 1970s and are predominantly flat-racing Arabians. This work aimed at revealing the genetic background and diversity of Omani Arabian horses by comparing them with Arabian horses from a diverse genetic background. To that end, we genotyped 63 randomly sampled Arabian horses from Oman using the Illumina Equine SNP70. For comparison, SNP genotypes of 12 Saudi Arabian horses, 27 French, 77 Egyptian, 11 Polish and 36 US Arabians were included in the study. We additionally included 17 Thoroughbred horses and 21 horses representing large and small breeds as an outgroup. Our MDS analysis and phylogenetic analysis showed that the Arabian horses in Oman cluster primarily with French Arabian horses, with a few horses clustering within the Polish/US Arabians. The French Arabian horse cluster was the closest to the Thoroughbred horses. Amongst the Arabian horses, plink average genomic inbreeding levels were highest in the Egyptian Arabian (0.169) followed by the Saudi Arabian horses (0.137) and lowest in the Omani and French Arabian horses, -0.041 and -0.079 respectively. To our knowledge, this is the first report on the genetic background and diversity of Arabian horses in Oman. Our results demonstrated a definite subpopulation structure among Arabian horses and this information should advise future decision-making on Arabian horse breeding.
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Affiliation(s)
- M A Al Abri
- Department of Animal and Veterinary Sciences, College of Agriculture and Marine Sciences, Sultan Qaboos University, PO Box 34, Al Khod, Muscat, 123, Oman
| | - S A Brooks
- Department of Animal Sciences, University of Florida, Gainesville, FL, 32611, USA
| | - N Al-Saqri
- Department of Animal and Veterinary Sciences, College of Agriculture and Marine Sciences, Sultan Qaboos University, PO Box 34, Al Khod, Muscat, 123, Oman
| | - K Alkharousi
- Department of Animal and Veterinary Sciences, College of Agriculture and Marine Sciences, Sultan Qaboos University, PO Box 34, Al Khod, Muscat, 123, Oman
| | - E H Johnson
- Department of Animal and Veterinary Sciences, College of Agriculture and Marine Sciences, Sultan Qaboos University, PO Box 34, Al Khod, Muscat, 123, Oman
| | - O Alqaisi
- Department of Animal and Veterinary Sciences, College of Agriculture and Marine Sciences, Sultan Qaboos University, PO Box 34, Al Khod, Muscat, 123, Oman
| | - A Al-Rawahi
- The Royal Cavalry of Oman, PO Box 70, Al Seeb, Muscat, 111, Oman
| | - W Al Marzooqi
- Department of Animal and Veterinary Sciences, College of Agriculture and Marine Sciences, Sultan Qaboos University, PO Box 34, Al Khod, Muscat, 123, Oman
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6
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Abstract
Orthopedic diseases are a common cause for limited exercise capacity in the horse. They often underlie genetic risk factors, which can affect bone, articular cartilage, tendons, ligaments, and adnexal structures among others. The genetic effects can directly interfere with tissue development and skeletal growth or can trigger degenerative or inflammatory processes. Many of these diseases of the locomotor system like osteochondrosis are complex and can be affected by multifactorial influences. For this reason, it is important for those performing diagnostic procedures to have a comprehensive knowledge of orthopedic diseases, their prevalence within breeds, and genetic background.
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Affiliation(s)
- Julia Metzger
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Buenteweg 17p, Hannover 30559, Germany.
| | - Ottmar Distl
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, Buenteweg 17p, Hannover 30559, Germany
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7
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Bisbee D, Carpenter ML, Hoefs-Martin K, Brooks SA, Lafayette C. Identification of a novel missense variant in SLC45A2 associated with dilute snowdrop phenotype in Gypsy horses. Anim Genet 2020; 51:342-343. [PMID: 31961951 DOI: 10.1111/age.12913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/19/2019] [Indexed: 11/28/2022]
Affiliation(s)
| | | | | | - Samantha A Brooks
- Etalon Inc., Menlo Park, CA, 94025, USA.,Department of Animal Sciences, University of Florida, Gainesville, FL, 32607, USA
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8
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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] [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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9
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Raudsepp T, Finno CJ, Bellone RR, Petersen JL. Ten years of the horse reference genome: insights into equine biology, domestication and population dynamics in the post-genome era. Anim Genet 2019; 50:569-597. [PMID: 31568563 PMCID: PMC6825885 DOI: 10.1111/age.12857] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/09/2019] [Indexed: 12/14/2022]
Abstract
The horse reference genome from the Thoroughbred mare Twilight has been available for a decade and, together with advances in genomics technologies, has led to unparalleled developments in equine genomics. At the core of this progress is the continuing improvement of the quality, contiguity and completeness of the reference genome, and its functional annotation. Recent achievements include the release of the next version of the reference genome (EquCab3.0) and generation of a reference sequence for the Y chromosome. Horse satellite‐free centromeres provide unique models for mammalian centromere research. Despite extremely low genetic diversity of the Y chromosome, it has been possible to trace patrilines of breeds and pedigrees and show that Y variation was lost in the past approximately 2300 years owing to selective breeding. The high‐quality reference genome has led to the development of three different SNP arrays and WGSs of almost 2000 modern individual horses. The collection of WGS of hundreds of ancient horses is unique and not available for any other domestic species. These tools and resources have led to global population studies dissecting the natural history of the species and genetic makeup and ancestry of modern breeds. Most importantly, the available tools and resources, together with the discovery of functional elements, are dissecting molecular causes of a growing number of Mendelian and complex traits. The improved understanding of molecular underpinnings of various traits continues to benefit the health and performance of the horse whereas also serving as a model for complex disease across species.
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Affiliation(s)
- T Raudsepp
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Research, Texas A&M University, College Station, TX, 77843, USA
| | - C J Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA
| | - R R Bellone
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California-Davis, Davis, CA, 95616, USA.,School of Veterinary Medicine, Veterinary Genetics Laboratory, University of California-Davis, Davis, CA, 95616, USA
| | - J L Petersen
- Department of Animal Science, University of Nebraska, Lincoln, NE, 68583-0908, USA
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10
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Holl HM, Pflug KM, Yates KM, Hoefs‐Martin K, Shepard C, Cook DG, Lafayette C, Brooks SA. A candidate gene approach identifies variants in
SLC
45A2
that explain dilute phenotypes, pearl and sunshine, in compound heterozygote horses. Anim Genet 2019; 50:271-274. [DOI: 10.1111/age.12790] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/20/2019] [Indexed: 02/06/2023]
Affiliation(s)
- H. M. Holl
- Etalon Inc Menlo Park CA 94025 USA
- Department of Animal Sciences University of Florida Gainesville FL 32607 USA
| | - K. M. Pflug
- Department of Animal Sciences University of Florida Gainesville FL 32607 USA
| | - K. M. Yates
- Department of Animal Sciences University of Florida Gainesville FL 32607 USA
| | | | | | - D. G. Cook
- Etalon Inc Menlo Park CA 94025 USA
- Biology Department Morehead State University Morehead KY 40351 USA
| | | | - S. A. Brooks
- Etalon Inc Menlo Park CA 94025 USA
- Department of Animal Sciences University of Florida Gainesville FL 32607 USA
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11
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Posbergh CJ, Pollott GE, Southard TL, Divers TJ, Brooks SA. A Nonsynonymous Change in Adhesion G Protein–Coupled Receptor L3 Associated With Risk for Equine Degenerative Myeloencephalopathy in the Caspian Horse. J Equine Vet Sci 2018. [DOI: 10.1016/j.jevs.2018.08.010] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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12
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A Frameshift Mutation in KIT is Associated with White Spotting in the Arabian Camel. Genes (Basel) 2017; 8:genes8030102. [PMID: 28282952 PMCID: PMC5368706 DOI: 10.3390/genes8030102] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2017] [Accepted: 03/03/2017] [Indexed: 12/04/2022] Open
Abstract
While the typical Arabian camel is characterized by a single colored coat, there are rare populations with white spotting patterns. White spotting coat patterns are found in virtually all domesticated species, but are rare in wild species. Theories suggest that white spotting is linked to the domestication process, and is occasionally associated with health disorders. Though mutations have been found in a diverse array of species, fewer than 30 genes have been associated with spotting patterns, thus providing a key set of candidate genes for the Arabian camel. We obtained 26 spotted camels and 24 solid controls for candidate gene analysis. One spotted and eight solid camels were whole genome sequenced as part of a separate project. The spotted camel was heterozygous for a frameshift deletion in KIT (c.1842delG, named KITW1 for White spotting 1), whereas all other camels were wild-type (KIT+/KIT+). No additional mutations unique to the spotted camel were detected in the EDNRB, EDN3, SOX10, KITLG, PDGFRA, MITF, and PAX3 candidate white spotting genes. Sanger sequencing of the study population identified an additional five KITW1/KIT+ spotted camels. The frameshift results in a premature stop codon five amino acids downstream, thus terminating KIT at the tyrosine kinase domain. An additional 13 spotted camels tested KIT+/KIT+, but due to phenotypic differences when compared to the KITW1/KIT+ camels, they likely represent an independent mutation. Our study suggests that there are at least two causes of white spotting in the Arabian camel, the newly described KITW1 allele and an uncharacterized mutation.
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13
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Staiger EA, Tseng CT, Miller D, Cassano JM, Nasir L, Garrick D, Brooks SA, Antczak DF. Host genetic influence on papillomavirus-induced tumors in the horse. Int J Cancer 2016; 139:784-92. [PMID: 27037728 DOI: 10.1002/ijc.30120] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2015] [Revised: 01/27/2016] [Accepted: 02/16/2016] [Indexed: 01/26/2023]
Abstract
The common equine skin tumors known as sarcoids have been causally associated with infection by bovine papillomavirus (BPV). Additionally, there is evidence for host genetic susceptibility to sarcoids. We investigated the genetic basis of susceptibility to sarcoid tumors on a cohort of 82 affected horses and 270 controls genotyped on a genome-wide platform and two custom panels. A Genome Wide Association Study (GWAS) identified candidate regions on six chromosomes. Bayesian probability analysis of the same dataset verified only the regions on equine chromosomes (ECA) 20 and 22. Fine mapping using custom-produced SNP arrays for ECA20 and ECA22 regions identified two marker loci with high levels of significance: SNP BIEC2-530826 (map position 32,787,619) on ECA20 in an intron of the DQA1 gene in the Major Histocompatibility Complex (MHC) class II region (p = 4.6e-06), and SNP BIEC2-589604 (map position 25,951,536) on ECA22 in a 200 kb region containing four candidate genes: PROCR, EDEM2, EIF6 and MMP24 (p = 2.14e-06). The marker loci yielded odds ratios of 5.05 and 4.02 for ECA20 and ECA22, respectively. Associations between genetic MHC class II variants and papillomavirus-induced tumors have been reported for human papillomavirus and cottontail rabbit papillomavirus infections. This suggests a common mechanism for susceptibility to tumor progression that may involve subversion of the host immune response. This study also identified a genomic region other than MHC that influenced papillomavirus-induced tumor development in the studied population.
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Affiliation(s)
| | - Chia T Tseng
- Baker Institute for Animal Health, Cornell University, Ithaca, NY
| | - Donald Miller
- Baker Institute for Animal Health, Cornell University, Ithaca, NY
| | | | - Lubna Nasir
- MRC-University of Glasgow Centre for Virus Research, Institute of Infection, Immunity and Inflammation, College of Medical Veterinary and Life Sciences, University of Glasgow, Glasgow, UK
| | - Dorian Garrick
- Department of Animal Science, Iowa State University, Ames, IA
| | - Samantha A Brooks
- Department of Animal Science, University of Florida, Gainesville, FL
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14
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Staiger EA, Albright JD, Brooks SA. Genome‐wide association mapping of heritable temperament variation in the
T
ennessee
W
alking
H
orse. GENES BRAIN AND BEHAVIOR 2016; 15:514-26. [DOI: 10.1111/gbb.12290] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2015] [Revised: 03/03/2016] [Accepted: 03/11/2016] [Indexed: 12/26/2022]
Affiliation(s)
- E. A. Staiger
- Department of Animal Science Cornell University Ithaca NY
| | - J. D. Albright
- Department of Small Animal Clinical Sciences, College of Veterinary Medicine University of Tennessee Knoxville TN
| | - S. A. Brooks
- Department of Animal Science University of Florida Gainesville FL USA
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15
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Staiger EA, Abri MA, Silva CAS, Brooks SA. Loci impacting polymorphic gait in the Tennessee Walking Horse1. J Anim Sci 2016; 94:1377-86. [DOI: 10.2527/jas.2015-9936] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Affiliation(s)
- E. A. Staiger
- Department of Animal Science, Cornell University, Ithaca, NY 14853
| | - M. A. Abri
- Department of Animal and Veterinary Sciences, College of Agriculture and Marine Sciences, Sultan Qaboos University, PO box 34 Al Khod, Postal Code 123, Muscat, Oman
| | - C. A. S. Silva
- Department of Animal Science, Instituto Federal Sul-Rio-Grandense, Pelotas, Rio Grande do Sul 96060-290, Brazil
| | - S. A. Brooks
- Department of Animal Science, University of Florida, Gainesville 32611
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16
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Staiger EA, Al Abri MA, Pflug KM, Kalla SE, Ainsworth DM, Miller D, Raudsepp T, Sutter NB, Brooks SA. Skeletal variation in Tennessee Walking Horses maps to the LCORL/NCAPG gene region. Physiol Genomics 2016; 48:325-35. [PMID: 26931356 DOI: 10.1152/physiolgenomics.00100.2015] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 02/19/2016] [Indexed: 11/22/2022] Open
Abstract
Conformation has long been a driving force in horse selection and breed creation as a predictor for performance. The Tennessee Walking Horse (TWH) ranges in size from 1.5 to 1.7 m and is often used as a trail, show, and pleasure horse. To investigate the contribution of genetics to body conformation in the TWH, we collected DNA samples, body measurements, and gait/training information from 282 individuals. We analyzed the 32 body measures with a principal component analysis. Principal component (PC)1 captured 28.5% of the trait variance, while PC2 comprised just 9.5% and PC3 6.4% of trait variance. All 32 measures correlated positively with PC1, indicating that PC1 describes overall body size. We genotyped 109 horses using the EquineSNP70 bead chip and marker association assessed the data using PC1 scores as a phenotype. Mixed-model linear analysis (EMMAX) revealed a well-documented candidate locus on ECA3 (raw P = 3.86 × 10(-9)) near the LCORL gene. A custom genotyping panel enabled fine-mapping of the PC1 body-size trait to the 3'-end of the LCORL gene (P = 7.09 × 10(-10)). This position differs from other reports suggesting single nucleotide polymorphisms (SNPs) upstream of the LCORL coding sequence regulate expression of the gene and, therefore, body size in horses. Fluorescent in situ hybridization analysis defined the position of a highly homologous 5 kb retrogene copy of LCORL (assigned to unplaced contigs of the EquCab 2.0 assembly) at ECA9 q12-q13. This is the first study to identify putative causative SNPs within the LCORL transcript itself, which are associated with skeletal size variation in horses.
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Affiliation(s)
- E A Staiger
- Department of Animal Science, Cornell University, Ithaca, New York
| | - M A Al Abri
- Department of Animal and Veterinary Sciences, College of Agriculture and Marine Sciences, Sultan Qaboos University, Muscat, Oman
| | - K M Pflug
- Department of Animal Science, University of Florida, Gainesville, Florida
| | - S E Kalla
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - D M Ainsworth
- Department of Clinical Sciences, College of Veterinary Medicine, Cornell University, Ithaca, New York
| | - D Miller
- Baker Institute for Animal Health, Cornell University, Ithaca, New York
| | - T Raudsepp
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine and Biomedical Sciences, Texas A&M University, College Station, Texas; and
| | - N B Sutter
- Department of Biology, La Sierra University, Riverside, California
| | - S A Brooks
- Department of Animal Science, University of Florida, Gainesville, Florida;
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17
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Jacobs LN, Staiger EA, Albright JD, Brooks SA. The MC1R and ASIP Coat Color Loci May Impact Behavior in the Horse. J Hered 2016; 107:214-9. [PMID: 26884605 DOI: 10.1093/jhered/esw007] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/11/2015] [Accepted: 01/27/2016] [Indexed: 12/11/2022] Open
Abstract
Shared signaling pathways utilized by melanocytes and neurons result in pleiotropic traits of coat color and behavior in many mammalian species. For example, in humans polymorphisms at MC1R cause red hair, increased heat sensitivity, and lower pain tolerance. In deer mice, rats, and foxes, ASIP polymorphisms causing black coat color lead to more docile demeanors and reduced activity. Horse (Equus caballus) base coat color is primarily determined by polymorphisms at the Melanocortin-1 Receptor (MC1R) and Agouti Signaling Protein (ASIP) loci, creating a black, bay, or chestnut coat. Our goal was to investigate correlations between genetic loci for coat color and temperament traits in the horse. We genotyped a total of 215 North American Tennessee Walking Horses for the 2 most common alleles at the MC1R (E/e) and ASIP (A/a) loci using previously published PCR and RFLP methods. The horses had a mean age of 10.5 years and comprised 83 geldings, 25 stallions, and 107 mares. To assess behavior, we adapted a previously published survey for handlers to score horses from 1 to 9 on 20 questions related to specific aspects of temperament. We utilized principle component analysis to combine the individual survey scores into 4 factors of variation in temperament phenotype. A factor component detailing self-reliance correlated with genotypes at the ASIP locus; black mares (aa) were more independent than bay mares (A_) (P = 0.0063). These findings illuminate a promising and novel animal model for future study of neuroendocrine mechanisms in complex behavioral phenotypes.
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Affiliation(s)
- Lauren N Jacobs
- From the Department of Animal Science, Cornell University, Morrison Hall, Ithaca, NY 14853 (Jacobs and Staiger); Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Tennessee, 2407 River Drive, Knoxville, TN 37996 (Albright); Department of Animal Science, University of Florida, PO Box 110910, Gainesville, FL 32611 (Brooks)
| | - Elizabeth A Staiger
- From the Department of Animal Science, Cornell University, Morrison Hall, Ithaca, NY 14853 (Jacobs and Staiger); Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Tennessee, 2407 River Drive, Knoxville, TN 37996 (Albright); Department of Animal Science, University of Florida, PO Box 110910, Gainesville, FL 32611 (Brooks)
| | - Julia D Albright
- From the Department of Animal Science, Cornell University, Morrison Hall, Ithaca, NY 14853 (Jacobs and Staiger); Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Tennessee, 2407 River Drive, Knoxville, TN 37996 (Albright); Department of Animal Science, University of Florida, PO Box 110910, Gainesville, FL 32611 (Brooks)
| | - Samantha A Brooks
- From the Department of Animal Science, Cornell University, Morrison Hall, Ithaca, NY 14853 (Jacobs and Staiger); Department of Small Animal Clinical Sciences, College of Veterinary Medicine, University of Tennessee, 2407 River Drive, Knoxville, TN 37996 (Albright); Department of Animal Science, University of Florida, PO Box 110910, Gainesville, FL 32611 (Brooks).
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18
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Holl HM, Brooks SA, Archer S, Brown K, Malvick J, Penedo MCT, Bellone RR. Variant in theRFWD3gene associated withPATN1, a modifier of leopard complex spotting. Anim Genet 2015; 47:91-101. [DOI: 10.1111/age.12375] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/31/2015] [Indexed: 01/11/2023]
Affiliation(s)
- H. M. Holl
- Department of Animal Science; Cornell University; Ithaca NY 14853 USA
| | - S. A. Brooks
- Department of Animal Science; Cornell University; Ithaca NY 14853 USA
| | | | - K. Brown
- Department of Biology; University of Tampa; Tampa FL 33606 USA
| | - J. Malvick
- Veterinary Genetics Laboratory; School of Veterinary Medicine; University of California-Davis; Davis CA 95616 USA
| | - M. C. T. Penedo
- Veterinary Genetics Laboratory; School of Veterinary Medicine; University of California-Davis; Davis CA 95616 USA
| | - R. R. Bellone
- Department of Population Health and Reproduction; Veterinary Genetics Laboratory; School of Veterinary Medicine; University of California-Davis; Davis CA 95616 USA
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19
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McCue ME, Bannasch DL, Petersen JL, Gurr J, Bailey E, Binns MM, Distl O, Guérin G, Hasegawa T, Hill EW, Leeb T, Lindgren G, Penedo MCT, Røed KH, Ryder OA, Swinburne JE, Tozaki T, Valberg SJ, Vaudin M, Lindblad-Toh K, Wade CM, Mickelson JR. A high density SNP array for the domestic horse and extant Perissodactyla: utility for association mapping, genetic diversity, and phylogeny studies. PLoS Genet 2012; 8:e1002451. [PMID: 22253606 PMCID: PMC3257288 DOI: 10.1371/journal.pgen.1002451] [Citation(s) in RCA: 155] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2010] [Accepted: 11/21/2011] [Indexed: 11/18/2022] Open
Abstract
An equine SNP genotyping array was developed and evaluated on a panel of samples representing 14 domestic horse breeds and 18 evolutionarily related species. More than 54,000 polymorphic SNPs provided an average inter-SNP spacing of ∼43 kb. The mean minor allele frequency across domestic horse breeds was 0.23, and the number of polymorphic SNPs within breeds ranged from 43,287 to 52,085. Genome-wide linkage disequilibrium (LD) in most breeds declined rapidly over the first 50-100 kb and reached background levels within 1-2 Mb. The extent of LD and the level of inbreeding were highest in the Thoroughbred and lowest in the Mongolian and Quarter Horse. Multidimensional scaling (MDS) analyses demonstrated the tight grouping of individuals within most breeds, close proximity of related breeds, and less tight grouping in admixed breeds. The close relationship between the Przewalski's Horse and the domestic horse was demonstrated by pair-wise genetic distance and MDS. Genotyping of other Perissodactyla (zebras, asses, tapirs, and rhinoceros) was variably successful, with call rates and the number of polymorphic loci varying across taxa. Parsimony analysis placed the modern horse as sister taxa to Equus przewalski. The utility of the SNP array in genome-wide association was confirmed by mapping the known recessive chestnut coat color locus (MC1R) and defining a conserved haplotype of ∼750 kb across all breeds. These results demonstrate the high quality of this SNP genotyping resource, its usefulness in diverse genome analyses of the horse, and potential use in related species.
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Affiliation(s)
- Molly E McCue
- College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA.
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