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Liu X, Chen W, Huang B, Wang X, Peng Y, Zhang X, Chai W, Khan MZ, Wang C. Advancements in copy number variation screening in herbivorous livestock genomes and their association with phenotypic traits. Front Vet Sci 2024; 10:1334434. [PMID: 38274664 PMCID: PMC10808162 DOI: 10.3389/fvets.2023.1334434] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Accepted: 12/27/2023] [Indexed: 01/27/2024] Open
Abstract
Copy number variations (CNVs) have garnered increasing attention within the realm of genetics due to their prevalence in human, animal, and plant genomes. These structural genetic variations have demonstrated associations with a broad spectrum of phenotypic diversity, economic traits, environmental adaptations, epidemics, and other essential aspects of both plants and animals. Furthermore, CNVs exhibit extensive sequence variability and encompass a wide array of genomes. The advancement and maturity of microarray and sequencing technologies have catalyzed a surge in research endeavors pertaining to CNVs. This is particularly prominent in the context of livestock breeding, where molecular markers have gained prominence as a valuable tool in comparison to traditional breeding methods. In light of these developments, a contemporary and comprehensive review of existing studies on CNVs becomes imperative. This review serves the purpose of providing a brief elucidation of the fundamental concepts underlying CNVs, their mutational mechanisms, and the diverse array of detection methods employed to identify these structural variations within genomes. Furthermore, it seeks to systematically analyze the recent advancements and findings within the field of CNV research, specifically within the genomes of herbivorous livestock species, including cattle, sheep, horses, and donkeys. The review also highlighted the role of CNVs in shaping various phenotypic traits including growth traits, reproductive traits, pigmentation and disease resistance etc., in herbivorous livestock. The main goal of this review is to furnish readers with an up-to-date compilation of knowledge regarding CNVs in herbivorous livestock genomes. By integrating the latest research findings and insights, it is anticipated that this review will not only offer pertinent information but also stimulate future investigations into the realm of CNVs in livestock. In doing so, it endeavors to contribute to the enhancement of breeding strategies, genomic selection, and the overall improvement of herbivorous livestock production and resistance to diseases.
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Affiliation(s)
| | | | | | | | | | | | | | - Muhammad Zahoor Khan
- Liaocheng Research Institute of Donkey High-Efficiency Breeding, Liaocheng University, Liaocheng, China
| | - Changfa Wang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding, Liaocheng University, Liaocheng, China
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Identification of Copy Number Variations in Four Horse Breed Populations in South Korea. Animals (Basel) 2022; 12:ani12243501. [PMID: 36552421 PMCID: PMC9774267 DOI: 10.3390/ani12243501] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 11/21/2022] [Accepted: 12/08/2022] [Indexed: 12/14/2022] Open
Abstract
In this study, genome-wide CNVs were identified using a total of 469 horses from four horse populations (Jeju horses, Thoroughbreds, Jeju riding horses, and Hanla horses). We detected a total of 843 CNVRs throughout all autosomes: 281, 30, 301, and 310 CNVRs for Jeju horses, Thoroughbreds, Jeju riding horses, and Hanla horses, respectively. Of the total CNVRs, copy number losses were found to be the most abundant (48.99%), while gains and mixed CNVRs accounted for 41.04% and 9.96% of the total CNVRs, respectively. The length of the CNVRs ranged from 0.39 kb to 2.8 Mb, while approximately 7.2% of the reference horse genome assembly was covered by the total CNVRs. By comparing the CNVRs among the populations, we found a significant portion of the CNVRs (30.13%) overlapped; the highest number of shared CNVRs was between Hanla horses and Jeju riding horses. When compared with the horse CNVRs of previous studies, 26.8% of CNVRs were found to be uniquely detected in this study. The CNVRs were not randomly distributed throughout the genome; in particular, the Equus caballus autosome (ECA) 7 comprised the largest proportion of its genome (16.3%), while ECA 24 comprised the smallest (0.7%). Furthermore, functional analysis was applied to CNVRs that overlapped with genes (genic-CNVRs); these overlapping areas may be potentially associated with the olfactory pathway and nervous system. A racing performance QTL was detected in a CNVR of Thoroughbreds, Jeju riding horses, and Hanla horses, and the CNVR value was mixed for three breeds.
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Copy Number Variation (CNV): A New Genomic Insight in Horses. Animals (Basel) 2022; 12:ani12111435. [PMID: 35681904 PMCID: PMC9179425 DOI: 10.3390/ani12111435] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2022] [Revised: 05/25/2022] [Accepted: 05/30/2022] [Indexed: 12/04/2022] Open
Abstract
Simple Summary This study aimed to contribute to our knowledge of CNVs, a type of genomic marker in equines, by producing, for the first time, a fine-scale characterization of the CNV regions (CNVRs) in the Pura Raza Española horse breed. We found not only the existence of a unique pattern of genomic regions enriched in CNVs in the PRE in comparison with the data available from other breeds but also the incidence of CNVs across the entire genome. Since these regions could affect the structure and dose of the genes involved, we also performed a gene ontology analysis which revealed that most of the genes overlapping in CNVRs were related to the olfactory pathways and immune response. Abstract Copy number variations (CNVs) are a new-fangled source of genetic variation that can explain changes in the phenotypes in complex traits and diseases. In recent years, their study has increased in many livestock populations. However, the study and characterization of CNVs in equines is still very limited. Our study aimed to investigate the distribution pattern of CNVs, characterize CNV regions (CNVRs), and identify the biological pathways affected by CNVRs in the Pura Raza Española (PRE) breed. To achieve this, we analyzed high-density SNP genotyping data (670,804 markers) from a large cohort of 654 PRE horses. In total, we identified 19,902 CNV segments and 1007 CNV regions in the whole population. The length of the CNVs ranged from 1.024 kb to 4.55 Mb, while the percentage of the genome covered by CNVs was 4.4%. Interestingly, duplications were more abundant than deletions and mixed CNVRs. In addition, the distribution of CNVs across the chromosomes was not uniform, with ECA12 being the chromosome with the largest percentage of its genome covered (19.2%), while the highest numbers of CNVs were found in ECA20, ECA12, and ECA1. Our results showed that 71.4% of CNVRs contained genes involved in olfactory transduction, olfactory receptor activity, and immune response. Finally, 39.1% of the CNVs detected in our study were unique when compared with CNVRs identified in previous studies. To the best of our knowledge, this is the first attempt to reveal and characterize the CNV landscape in PRE horses, and it contributes to our knowledge of CNVs in equines, thus facilitating the understanding of genetic and phenotypic variations in the species. However, further research is still needed to confirm if the CNVs observed in the PRE are also linked to variations in the specific phenotypical differences in the breed.
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Wang M, Liu Y, Bi X, Ma H, Zeng G, Guo J, Guo M, Ling Y, Zhao C. Genome-Wide Detection of Copy Number Variants in Chinese Indigenous Horse Breeds and Verification of CNV-Overlapped Genes Related to Heat Adaptation of the Jinjiang Horse. Genes (Basel) 2022; 13:genes13040603. [PMID: 35456409 PMCID: PMC9033042 DOI: 10.3390/genes13040603] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2022] [Revised: 03/23/2022] [Accepted: 03/25/2022] [Indexed: 02/05/2023] Open
Abstract
In the present study, genome-wide CNVs were detected in a total of 301 samples from 10 Chinese indigenous horse breeds using the Illumina Equine SNP70 Bead Array, and the candidate genes related to adaptability to high temperature and humidity in Jinjiang horses were identified and validated. We determined a total of 577 CNVs ranging in size from 1.06 Kb to 2023.07 Kb on the 31 pairs of autosomes. By aggregating the overlapping CNVs for each breed, a total of 495 CNVRs were detected in the 10 Chinese horse breeds. As many as 211 breed-specific CNVRs were determined, of which 64 were found in the Jinjiang horse population. By removing repetitive CNV regions between breeds, a total of 239 CNVRs were identified in the Chinese indigenous horse breeds including 102 losses, 133 gains and 4 of both events (losses and gains in the same region), in which 131 CNVRs were novel and only detected in the present study compared with previous studies. The total detected CNVR length was 41.74 Mb, accounting for 1.83% of the total length of equine autosomal chromosomes. The coverage of CNVRs on each chromosome varied from 0.47% to 15.68%, with the highest coverage on ECA 12, but the highest number of CNVRs was detected on ECA1 and ECA24. A total of 229 genes overlapping with CNVRs were detected in the Jinjiang horse population, which is an indigenous horse breed unique to the southeastern coast of China exhibiting adaptability to high temperature and humidity. The functional annotation of these genes showed significant relation to cellular heat acclimation and immunity. The expression levels of the candidate genes were validated by heat shock treatment of various durations on fibroblasts of horses. The results show that the expression levels of HSPA1A were significantly increased among the different heat shock durations. The expression level of NFKBIA and SOCS4 declined from the beginning of heat shock to 2 h after heat shock and then showed a gradual increase until it reached the highest value at 6 h and 10 h of heat shock, respectively. Breed-specific CNVRs of Chinese indigenous horse breeds were revealed in the present study, and the results facilitate mapping CNVs on the whole genome and also provide valuable insights into the molecular mechanisms of adaptation to high temperature and humidity in the Jinjiang horse.
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Affiliation(s)
- Min Wang
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (M.W.); (Y.L.); (X.B.); (Y.L.)
- Equine Center, China Agricultural University, Beijing 100193, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Beijing 100193, China
- National Engineering Laboratory for Animal Breeding, Beijing 100193, China
- Beijing Key Laboratory for Genetic Improvement of Livestock and Poultry, Beijing 100193, China
| | - Yu Liu
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (M.W.); (Y.L.); (X.B.); (Y.L.)
- Equine Center, China Agricultural University, Beijing 100193, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Beijing 100193, China
- National Engineering Laboratory for Animal Breeding, Beijing 100193, China
- Beijing Key Laboratory for Genetic Improvement of Livestock and Poultry, Beijing 100193, China
| | - Xiaokun Bi
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (M.W.); (Y.L.); (X.B.); (Y.L.)
- Equine Center, China Agricultural University, Beijing 100193, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Beijing 100193, China
- National Engineering Laboratory for Animal Breeding, Beijing 100193, China
- Beijing Key Laboratory for Genetic Improvement of Livestock and Poultry, Beijing 100193, China
| | - Hongying Ma
- Shaanxi Key Laboratory for Animal Conservation, Shaanxi Institute of Zoology, Xi’an 710032, China;
| | - Guorong Zeng
- Jinjiang Animal Husbandry and Veterinary Station, Quanzhou 362200, China; (G.Z.); (J.G.); (M.G.)
| | - Jintu Guo
- Jinjiang Animal Husbandry and Veterinary Station, Quanzhou 362200, China; (G.Z.); (J.G.); (M.G.)
| | - Minghao Guo
- Jinjiang Animal Husbandry and Veterinary Station, Quanzhou 362200, China; (G.Z.); (J.G.); (M.G.)
| | - Yao Ling
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (M.W.); (Y.L.); (X.B.); (Y.L.)
| | - Chunjiang Zhao
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China; (M.W.); (Y.L.); (X.B.); (Y.L.)
- Equine Center, China Agricultural University, Beijing 100193, China
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Beijing 100193, China
- National Engineering Laboratory for Animal Breeding, Beijing 100193, China
- Beijing Key Laboratory for Genetic Improvement of Livestock and Poultry, Beijing 100193, China
- Correspondence:
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The Immune Mechanisms of Severe Equine Asthma-Current Understanding and What Is Missing. Animals (Basel) 2022; 12:ani12060744. [PMID: 35327141 PMCID: PMC8944511 DOI: 10.3390/ani12060744] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2022] [Revised: 03/11/2022] [Accepted: 03/14/2022] [Indexed: 01/27/2023] Open
Abstract
Severe equine asthma is a chronic respiratory disease of adult horses, occurring when genetically susceptible individuals are exposed to environmental aeroallergens. This results in airway inflammation, mucus accumulation and bronchial constriction. Although several studies aimed at evaluating the genetic and immune pathways associated with the disease, the results reported are inconsistent. Furthermore, the complexity and heterogeneity of this disease bears great similarity to what is described for human asthma. Currently available studies identified two chromosome regions (ECA13 and ECA15) and several genes associated with the disease. The inflammatory response appears to be mediated by T helper cells (Th1, Th2, Th17) and neutrophilic inflammation significantly contributes to the persistence of airway inflammatory status. This review evaluates the reported findings pertaining to the genetical and immunological background of severe equine asthma and reflects on their implications in the pathophysiology of the disease whilst discussing further areas of research interest aiming at advancing treatment and prognosis of affected individuals.
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Šedová L, Buková I, Bažantová P, Petrezsélyová S, Prochazka J, Školníková E, Zudová D, Včelák J, Makovický P, Bendlová B, Šeda O, Sedlacek R. Semi-Lethal Primary Ciliary Dyskinesia in Rats Lacking the Nme7 Gene. Int J Mol Sci 2021; 22:ijms22083810. [PMID: 33916973 PMCID: PMC8067621 DOI: 10.3390/ijms22083810] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2021] [Revised: 04/01/2021] [Accepted: 04/06/2021] [Indexed: 12/19/2022] Open
Abstract
NME7 (non-metastatic cells 7, nucleoside diphosphate kinase 7) is a member of a gene family with a profound effect on health/disease status. NME7 is an established member of the ciliome and contributes to the regulation of the microtubule-organizing center. We aimed to create a rat model to further investigate the phenotypic consequences of Nme7 gene deletion. The CRISPR/Cas9 nuclease system was used for the generation of Sprague Dawley Nme7 knock-out rats targeting the exon 4 of the Nme7 gene. We found the homozygous Nme7 gene deletion to be semi-lethal, as the majority of SDNme7−/− pups died prior to weaning. The most prominent phenotypes in surviving SDNme7−/− animals were hydrocephalus, situs inversus totalis, postnatal growth retardation, and sterility of both sexes. Thinning of the neocortex was histologically evident at 13.5 day of gestation, dilation of all ventricles was detected at birth, and an external sign of hydrocephalus, i.e., doming of the skull, was usually apparent at 2 weeks of age. Heterozygous SDNme7+/− rats developed normally; we did not detect any symptoms of primary ciliary dyskinesia. The transcriptomic profile of liver and lungs corroborated the histological findings, revealing defects in cell function and viability. In summary, the knock-out of the rat Nme7 gene resulted in a range of conditions consistent with the presentation of primary ciliary dyskinesia, supporting the previously implicated role of the centrosomally located Nme7 gene in ciliogenesis and control of ciliary transport.
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Affiliation(s)
- Lucie Šedová
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., 252 50 Vestec, Czech Republic; (S.P.); (E.Š.); (R.S.)
- Institute of Biology and Medical Genetics, The First Faculty of Medicine, Charles University and the General University Hospital, 128 00 Prague, Czech Republic; (P.B.); (O.Š.)
- Correspondence:
| | - Ivana Buková
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., 252 50 Vestec, Czech Republic; (I.B.); (J.P.); (D.Z.)
| | - Pavla Bažantová
- Institute of Biology and Medical Genetics, The First Faculty of Medicine, Charles University and the General University Hospital, 128 00 Prague, Czech Republic; (P.B.); (O.Š.)
| | - Silvia Petrezsélyová
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., 252 50 Vestec, Czech Republic; (S.P.); (E.Š.); (R.S.)
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., 252 50 Vestec, Czech Republic; (I.B.); (J.P.); (D.Z.)
| | - Jan Prochazka
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., 252 50 Vestec, Czech Republic; (I.B.); (J.P.); (D.Z.)
| | - Elena Školníková
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., 252 50 Vestec, Czech Republic; (S.P.); (E.Š.); (R.S.)
- Institute of Biology and Medical Genetics, The First Faculty of Medicine, Charles University and the General University Hospital, 128 00 Prague, Czech Republic; (P.B.); (O.Š.)
| | - Dagmar Zudová
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., 252 50 Vestec, Czech Republic; (I.B.); (J.P.); (D.Z.)
| | - Josef Včelák
- Department of Molecular Endocrinology, Institute of Endocrinology, 116 94 Prague, Czech Republic; (J.V.); (B.B.)
| | - Pavol Makovický
- Department of Biology, Faculty of Education, J. Selye University, 945 01 Komarno, Slovakia;
| | - Běla Bendlová
- Department of Molecular Endocrinology, Institute of Endocrinology, 116 94 Prague, Czech Republic; (J.V.); (B.B.)
| | - Ondřej Šeda
- Institute of Biology and Medical Genetics, The First Faculty of Medicine, Charles University and the General University Hospital, 128 00 Prague, Czech Republic; (P.B.); (O.Š.)
| | - Radislav Sedlacek
- Laboratory of Transgenic Models of Diseases, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., 252 50 Vestec, Czech Republic; (S.P.); (E.Š.); (R.S.)
- Czech Centre for Phenogenomics, Institute of Molecular Genetics of the Czech Academy of Sciences, v.v.i., 252 50 Vestec, Czech Republic; (I.B.); (J.P.); (D.Z.)
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Couetil L, Cardwell JM, Leguillette R, Mazan M, Richard E, Bienzle D, Bullone M, Gerber V, Ivester K, Lavoie JP, Martin J, Moran G, Niedźwiedź A, Pusterla N, Swiderski C. Equine Asthma: Current Understanding and Future Directions. Front Vet Sci 2020; 7:450. [PMID: 32903600 PMCID: PMC7438831 DOI: 10.3389/fvets.2020.00450] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2019] [Accepted: 06/19/2020] [Indexed: 12/12/2022] Open
Abstract
The 2019 Havemeyer Workshop brought together researchers and clinicians to discuss the latest information on Equine Asthma and provide future research directions. Current clinical and molecular asthma phenotypes and endotypes in humans were discussed and compared to asthma phenotypes in horses. The role of infectious and non-infectious causes of equine asthma, genetic factors and proposed disease pathophysiology were reviewed. Diagnostic limitations were evident by the limited number of tests and biomarkers available to field practitioners. The participants emphasized the need for more accessible, standardized diagnostics that would help identify specific phenotypes and endotypes in order to create more targeted treatments or management strategies. One important outcome of the workshop was the creation of the Equine Asthma Group that will facilitate communication between veterinary practice and research communities through published and easily accessible guidelines and foster research collaboration.
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Affiliation(s)
- Laurent Couetil
- College of Veterinary Medicine, Purdue University, West Lafayette, IN, United States
| | - Jacqueline M Cardwell
- Department of Pathobiology and Population Sciences, Royal Veterinary College, London, United Kingdom
| | - Renaud Leguillette
- College of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Melissa Mazan
- Cummings School of Veterinary Medicine, Tufts University, Grafton, MA, United States
| | - Eric Richard
- LABÉO (Frank Duncombe), Normandie Université, UniCaen, Caen, France
| | - Dorothee Bienzle
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
| | - Michela Bullone
- Department of Veterinary Sciences, University of Turin, Grugliasco, Italy
| | - Vinzenz Gerber
- Vetsuisse Faculty, Institut Suisse de Médecine Équine (ISME), University of Bern and Agroscope, Bern, Switzerland
| | - Kathleen Ivester
- College of Veterinary Medicine, Purdue University, West Lafayette, IN, United States
| | - Jean-Pierre Lavoie
- Faculty of Veterinary Medicine, University of Montreal, Montreal, QC, Canada
| | - James Martin
- Meakins Christie Laboratories, McGill University Health Center Research Institute, Montreal, QC, Canada
| | - Gabriel Moran
- Department of Pharmacology, Faculty of Veterinary Sciences, Universidad Austral de Chile, Valdivia, Chile
| | - Artur Niedźwiedź
- Department of Internal Diseases With Clinic for Horses, Dogs and Cats, Wroclaw University of Environmental and Life Sciences, Wrocław, Poland
| | - Nicola Pusterla
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California, Davis, Davis, CA, United States
| | - Cyprianna Swiderski
- College of Veterinary Medicine, Mississippi State University, Starkville, MS, United States
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Abstract
Genetic factors influence the development of guttural pouch tympany, recurrent laryngeal neuropathy, severe equine asthma, exercise-induced pulmonary hemorrhage, and possibly also some malformations and infectious diseases of the respiratory tract. The current data suggest that most of these diseases are complex, resulting from the interaction between several genes and environmental factors. To date, no specific genes or causative mutations have been identified that would allow the development of practical genetic tests. In the future, genetic profiling panels, based on multiple genetic markers and environmental risk factors, may allow identification of individuals with an increased genetic risk.
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Affiliation(s)
- Vinzenz Gerber
- Department of Clinical Veterinary Medicine, Vetsuisse Faculty, Swiss Institute of Equine Medicine (ISME), University of Bern, and Agroscope, Laenggassstrasse 124, Berne 3012, Switzerland.
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9
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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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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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11
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Corbi-Botto CM, Morales-Durand H, Zappa ME, Sadaba SA, Peral-García P, Giovambattista G, Díaz S. Genomic structural diversity in Criollo Argentino horses: Analysis of copy number variations. Gene 2019; 695:26-31. [DOI: 10.1016/j.gene.2018.12.067] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/04/2018] [Accepted: 12/27/2018] [Indexed: 12/11/2022]
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12
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Schurink A, da Silva VH, Velie BD, Dibbits BW, Crooijmans RPMA, Franҫois L, Janssens S, Stinckens A, Blott S, Buys N, Lindgren G, Ducro BJ. Copy number variations in Friesian horses and genetic risk factors for insect bite hypersensitivity. BMC Genet 2018; 19:49. [PMID: 30060732 PMCID: PMC6065148 DOI: 10.1186/s12863-018-0657-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Accepted: 07/19/2018] [Indexed: 12/04/2022] Open
Abstract
Background Many common and relevant diseases affecting equine welfare have yet to be tested regarding structural variants such as copy number variations (CNVs). CNVs make up a substantial proportion of total genetic variability in populations of many species, resulting in more sequence differences between individuals than SNPs. Associations between CNVs and disease phenotypes have been established in several species, but equine CNV studies have been limited. Aim of this study was to identify CNVs and to perform a genome-wide association (GWA) study in Friesian horses to identify genomic loci associated with insect bite hypersensitivity (IBH), a common seasonal allergic dermatitis observed in many horse breeds worldwide. Results Genotypes were obtained using the Axiom® Equine Genotyping Array containing 670,796 SNPs. After quality control of genotypes, 15,041 CNVs and 5350 CNV regions (CNVRs) were identified in 222 Friesian horses. Coverage of the total genome by CNVRs was 11.2% with 49.2% of CNVRs containing genes. 58.0% of CNVRs were novel (i.e. so far only identified in Friesian horses). A SNP- and CNV-based GWA analysis was performed, where about half of the horses were affected by IBH. The SNP-based analysis showed a highly significant association between the MHC region on ECA20 and IBH in Friesian horses. Associations between the MHC region on ECA20 and IBH were also detected based on the CNV-based analysis. However, CNVs associated with IBH in Friesian horses were not often in close proximity to SNPs identified to be associated with IBH. Conclusions CNVs were identified in a large sample of the Friesian horse population, thereby contributing to our knowledge on CNVs in horses and facilitating our understanding of the equine genome and its phenotypic expression. A clear association was identified between the MHC region on ECA20 and IBH in Friesian horses based on both SNP- and CNV-based GWA studies. These results imply that MHC contributes to IBH sensitivity in Friesian horses. Although subsequent analyses are needed for verification, nucleotide differences, as well as more complex structural variations like CNVs, seem to contribute to IBH sensitivity. IBH should be considered as a common disease with a complex genomic architecture. Electronic supplementary material The online version of this article (10.1186/s12863-018-0657-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Anouk Schurink
- Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700, AH, Wageningen, the Netherlands.
| | - Vinicius H da Silva
- Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700, AH, Wageningen, the Netherlands.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, P.O. Box 7023, 75007, Uppsala, Sweden.,Department of Animal Ecology, Netherlands Institute of Ecology, NIOO-KNAW, 6708, PB, Wageningen, the Netherlands
| | - Brandon D Velie
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, P.O. Box 7023, 75007, Uppsala, Sweden
| | - Bert W Dibbits
- Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700, AH, Wageningen, the Netherlands
| | - Richard P M A Crooijmans
- Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700, AH, Wageningen, the Netherlands
| | - Liesbeth Franҫois
- KU Leuven, Department of Biosystems, Livestock Genetics, P.O. Box 2456, 3001, Heverlee, Belgium
| | - Steven Janssens
- KU Leuven, Department of Biosystems, Livestock Genetics, P.O. Box 2456, 3001, Heverlee, Belgium
| | - Anneleen Stinckens
- KU Leuven, Department of Biosystems, Livestock Genetics, P.O. Box 2456, 3001, Heverlee, Belgium
| | - Sarah Blott
- Reproductive Biology, Faculty of Medicine and Health Sciences, The University of Nottingham, Leicestershire, LE12 5RD, UK
| | - Nadine Buys
- KU Leuven, Department of Biosystems, Livestock Genetics, P.O. Box 2456, 3001, Heverlee, Belgium
| | - Gabriella Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, P.O. Box 7023, 75007, Uppsala, Sweden
| | - Bart J Ducro
- Animal Breeding and Genomics, Wageningen University & Research, P.O. Box 338, 6700, AH, Wageningen, the Netherlands
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Tessier L, Côté O, Clark ME, Viel L, Diaz-Méndez A, Anders S, Bienzle D. Impaired response of the bronchial epithelium to inflammation characterizes severe equine asthma. BMC Genomics 2017; 18:708. [PMID: 28886691 PMCID: PMC5591550 DOI: 10.1186/s12864-017-4107-6] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2017] [Accepted: 09/01/2017] [Indexed: 12/11/2022] Open
Abstract
BACKGROUND Severe equine asthma is a naturally occurring lung inflammatory disease of mature animals characterized by neutrophilic inflammation, bronchoconstriction, mucus hypersecretion and airway remodeling. Exacerbations are triggered by inhalation of dust and microbial components. Affected animals eventually are unable of aerobic performance. In this study transcriptomic differences between asthmatic and non-asthmatic animals in the response of the bronchial epithelium to an inhaled challenge were determined. RESULTS Paired endobronchial biopsies were obtained pre- and post-challenge from asthmatic and non-asthmatic animals. The transcriptome, determined by RNA-seq and analyzed with edgeR, contained 111 genes differentially expressed (DE) after challenge between horses with and without asthma, and 81 of these were upregulated. Genes involved in neutrophil migration and activation were in central location in interaction networks, and related gene ontology terms were significantly overrepresented. Relative abundance of specific gene products as determined by immunohistochemistry was correlated with differential gene expression. Gene sets involved in neutrophil chemotaxis, immune and inflammatory response, secretion, blood coagulation and apoptosis were overrepresented among up-regulated genes, while the rhythmic process gene set was overrepresented among down-regulated genes. MMP1, IL8, TLR4 and MMP9 appeared to be the most important proteins in connecting the STRING protein network of DE genes. CONCLUSIONS Several differentially expressed genes and networks in horses with asthma also contribute to human asthma, highlighting similarities between severe human adult and equine asthma. Neutrophil activation by the bronchial epithelium is suggested as the trigger of the inflammatory cascade in equine asthma, followed by epithelial injury and impaired repair and differentiation. Circadian rhythm dysregulation and the sonic Hedgehog pathway were identified as potential novel contributory factors in equine asthma.
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Affiliation(s)
- Laurence Tessier
- Department of Pathobiology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Olivier Côté
- Department of Pathobiology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.,Present address: BioAssay Works LLC, 10075 Tyler Place, Suite 18, Ijamsville, MD, 21754, USA
| | - Mary Ellen Clark
- Department of Pathobiology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Laurent Viel
- Department of Clinical Studies, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada
| | - Andrés Diaz-Méndez
- Department of Clinical Studies, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.,Present address: Centre for Equine Infectious Disease, The University of Melbourne, Melbourne, VIC, 3010, Australia
| | - Simon Anders
- Institute for Molecular Medicine, Finland (FIMM), University of Helsinki, Tukholmankatu 8, 00014, Helsinki, Finland
| | - Dorothee Bienzle
- Department of Pathobiology, University of Guelph, 50 Stone Road East, Guelph, ON, N1G 2W1, Canada.
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Pawlina-Tyszko K, Gurgul A, Szmatoła T, Ropka-Molik K, Semik-Gurgul E, Klukowska-Rötzler J, Koch C, Mählmann K, Bugno-Poniewierska M. Genomic landscape of copy number variation and copy neutral loss of heterozygosity events in equine sarcoids reveals increased instability of the sarcoid genome. Biochimie 2017; 140:122-132. [PMID: 28743673 DOI: 10.1016/j.biochi.2017.07.006] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 07/20/2017] [Indexed: 12/20/2022]
Abstract
Although they are the most common neoplasms in equids, sarcoids are not fully characterized at the molecular level. Therefore, the objective of this study was to characterize the landscape of structural rearrangements, such as copy number variation (CNV) and copy neutral loss of heterozygosity (cnLOH), in the genomes of sarcoid tumor cells. This information will not only broaden our understanding of the characteristics of this genome but will also improve the general knowledge of this tumor and the mechanisms involved in its generation. To this end, Equine SNP64K Illumina microarrays were applied along with bioinformatics tools dedicated for signal intensity analysis. The analysis revealed increased instability of the genome of sarcoid cells compared with unaltered skin tissue samples, which was manifested by the prevalence of CNV and cnLOH events. Many of the identified CNVs overlapped with the other research results, but the simultaneously observed variability in the number and sizes of detected aberrations indicated a need for further studies and the development of more reliable bioinformatics algorithms. The functional analysis of genes co-localized with the identified aberrations revealed that these genes are engaged in vital cellular processes. In addition, a number of these genes directly contribute to neoplastic transformation. Furthermore, large numbers of cnLOH events identified in the sarcoids suggested that they may play no less significant roles than CNVs in the carcinogenesis of this tumor. Thus, our results indicate the importance of cnLOH and CNV in equine sarcoid oncogenesis and present a direction of future research.
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Affiliation(s)
- Klaudia Pawlina-Tyszko
- Laboratory of Genomics, Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland.
| | - Artur Gurgul
- Laboratory of Genomics, Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland.
| | - Tomasz Szmatoła
- Laboratory of Genomics, Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland.
| | - Katarzyna Ropka-Molik
- Laboratory of Genomics, Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland.
| | - Ewelina Semik-Gurgul
- Laboratory of Genomics, Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland.
| | - Jolanta Klukowska-Rötzler
- Division of Pedriatric Hematology/Oncology, Department of Clinical Research, University of Bern, Murtenstrasse 35, 3008, Bern, Switzerland; Department of Emergency Medicine, University Hospital Bern, Inselspital, 3010, Bern, Switzerland.
| | - Christoph Koch
- Swiss Institute of Equine Medicine ISME, Faculty of Veterinary Medicine, University of Bern and Agroscope, Länggassstrasse 124c, Postfach 8466, CH-3001, Bern, Switzerland.
| | - Kathrin Mählmann
- Swiss Institute of Equine Medicine ISME, Faculty of Veterinary Medicine, University of Bern and Agroscope, Länggassstrasse 124c, Postfach 8466, CH-3001, Bern, Switzerland; Equine Clinic: Surgery and Radiology, Department of Veterinary Medicine, Free University of Berlin, Oertzenweg 19b, 14163, Berlin, Germany.
| | - Monika Bugno-Poniewierska
- Laboratory of Genomics, Department of Animal Genomics and Molecular Biology, National Research Institute of Animal Production, Krakowska 1, 32-083, Balice, Poland.
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