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Davoudi P, Do DN, Colombo S, Rathgeber B, Sargolzaei M, Plastow G, Wang Z, Hu G, Valipour S, Miar Y. Genome-wide association studies for economically important traits in mink using copy number variation. Sci Rep 2024; 14:24. [PMID: 38167844 PMCID: PMC10762091 DOI: 10.1038/s41598-023-50497-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 12/20/2023] [Indexed: 01/05/2024] Open
Abstract
Copy number variations (CNVs) are structural variants consisting of duplications and deletions of DNA segments, which are known to play important roles in the genetics of complex traits in livestock species. However, CNV-based genome-wide association studies (GWAS) have remained unexplored in American mink. Therefore, the purpose of the current study was to investigate the association between CNVs and complex traits in American mink. A CNV-based GWAS was performed with the ParseCNV2 software program using deregressed estimated breeding values of 27 traits as pseudophenotypes, categorized into traits of growth and feed efficiency, reproduction, pelt quality, and Aleutian disease tests. The study identified a total of 10,137 CNVs (6968 duplications and 3169 deletions) using the Affymetrix Mink 70K single nucleotide polymorphism (SNP) array in 2986 American mink. The association analyses identified 250 CNV regions (CNVRs) associated with at least one of the studied traits. These CNVRs overlapped with a total of 320 potential candidate genes, and among them, several genes have been known to be related to the traits such as ARID1B, APPL1, TOX, and GPC5 (growth and feed efficiency traits); GRM1, RNASE10, WNT3, WNT3A, and WNT9B (reproduction traits); MYO10, and LIMS1 (pelt quality traits); and IFNGR2, APEX1, UBE3A, and STX11 (Aleutian disease tests). Overall, the results of the study provide potential candidate genes that may regulate economically important traits and therefore may be used as genetic markers in mink genomic breeding programs.
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Affiliation(s)
- Pourya Davoudi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Duy Ngoc Do
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Stefanie Colombo
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Bruce Rathgeber
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Mehdi Sargolzaei
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
- Select Sires Inc., Plain City, OH, USA
| | - Graham Plastow
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Zhiquan Wang
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Guoyu Hu
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Shafagh Valipour
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Younes Miar
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada.
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Davoudi P, Do DN, Rathgeber B, Colombo SM, Sargolzaei M, Plastow G, Wang Z, Karimi K, Hu G, Valipour S, Miar Y. Genome-wide detection of copy number variation in American mink using whole-genome sequencing. BMC Genomics 2022; 23:649. [PMID: 36096727 PMCID: PMC9468235 DOI: 10.1186/s12864-022-08874-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Accepted: 09/05/2022] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Copy number variations (CNVs) represent a major source of genetic diversity and contribute to the phenotypic variation of economically important traits in livestock species. In this study, we report the first genome-wide CNV analysis of American mink using whole-genome sequence data from 100 individuals. The analyses were performed by three complementary software programs including CNVpytor, DELLY and Manta. RESULTS A total of 164,733 CNVs (144,517 deletions and 20,216 duplications) were identified representing 5378 CNV regions (CNVR) after merging overlapping CNVs, covering 47.3 Mb (1.9%) of the mink autosomal genome. Gene Ontology and KEGG pathway enrichment analyses of 1391 genes that overlapped CNVR revealed potential role of CNVs in a wide range of biological, molecular and cellular functions, e.g., pathways related to growth (regulation of actin cytoskeleton, and cAMP signaling pathways), behavior (axon guidance, circadian entrainment, and glutamatergic synapse), lipid metabolism (phospholipid binding, sphingolipid metabolism and regulation of lipolysis in adipocytes), and immune response (Wnt signaling, Fc receptor signaling, and GTPase regulator activity pathways). Furthermore, several CNVR-harbored genes associated with fur characteristics and development (MYO5A, RAB27B, FGF12, SLC7A11, EXOC2), and immune system processes (SWAP70, FYN, ORAI1, TRPM2, and FOXO3). CONCLUSIONS This study presents the first genome-wide CNV map of American mink. We identified 5378 CNVR in the mink genome and investigated genes that overlapped with CNVR. The results suggest potential links with mink behaviour as well as their possible impact on fur quality and immune response. Overall, the results provide new resources for mink genome analysis, serving as a guideline for future investigations in which genomic structural variations are present.
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Affiliation(s)
- Pourya Davoudi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Duy Ngoc Do
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Bruce Rathgeber
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Stefanie M Colombo
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Mehdi Sargolzaei
- Department of Pathobiology, University of Guelph, Guelph, ON, Canada
- Select Sires Inc., Plain City, OH, USA
| | - Graham Plastow
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Zhiquan Wang
- Livestock Gentec, Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Karim Karimi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Guoyu Hu
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Shafagh Valipour
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Younes Miar
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada.
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Widmer S, Seefried FR, von Rohr P, Häfliger IM, Spengeler M, Drögemüller C. A major QTL at the LHCGR/FSHR locus for multiple birth in Holstein cattle. Genet Sel Evol 2021; 53:57. [PMID: 34217202 PMCID: PMC8255007 DOI: 10.1186/s12711-021-00650-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Accepted: 06/25/2021] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Twin and multiple births are rare in cattle and have a negative impact on the performance and health of cows and calves. Therefore, selection against multiple birth would be desirable in dairy cattle breeds such as Holstein. We applied different methods to decipher the genetic architecture of this trait using de-regressed breeding values for maternal multiple birth of ~ 2500 Holstein individuals to perform genome-wide association analyses using ~ 600 K imputed single nucleotide polymorphisms (SNPs). RESULTS In the population studied, we found no significant genetic trend over time of the estimated breeding values for multiple birth, which indicates that this trait has not been selected for in the past. In addition to several suggestive non-significant quantitative trait loci (QTL) on different chromosomes, we identified a major QTL on chromosome 11 for maternal multiple birth that explains ~ 16% of the total genetic variance. Using a haplotype-based approach, this QTL was fine-mapped to a 70-kb window on chromosome 11 between 31.00 and 31.07 Mb that harbors two functional candidate genes (LHCGR and FSHR). Analysis of whole-genome sequence data by linkage-disequilibrium estimation revealed a regulatory variant in the 5'-region of LHCGR as a possible candidate causal variant for the identified major QTL. Furthermore, the identified haplotype showed significant effects on stillbirth and days to first service. CONCLUSIONS QTL detection and subsequent identification of causal variants in livestock species remain challenging in spite of the availability of large-scale genotype and phenotype data. Here, we report for the first time a major QTL for multiple birth in Holstein cattle and provide evidence for a linked variant in the non-coding region of a functional candidate gene. This discovery, which is a first step towards the understanding of the genetic architecture of this polygenic trait, opens the path for future selection against this undesirable trait, and thus contributes to increased animal health and welfare.
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Affiliation(s)
- Sarah Widmer
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | | | | | - Irene M. Häfliger
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
| | | | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland
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Abstract
Neurologic disease in horses can be particularly challenging to diagnose and treat. These diseases can result in economic losses, emotional distress to owners, and injury to the horse or handlers. To date, there are 5 neurologic diseases caused by known genetic mutations and several more are suspected to be heritable: lethal white foal syndrome, lavender foal syndrome, cerebellar abiotrophy, occipitoatlantoaxial malformation, and Friesian hydrocephalus. Genetic testing allows owners, breeders, and veterinarians to make informed decisions when selecting dams and sires for breeding or deciding the treatment or prognosis of a neurologic animal.
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Affiliation(s)
- Lisa Edwards
- Department of Veterinary Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Room 4206 Vet Med 3A One Shields Avenue, Davis, CA 95616, USA
| | - Carrie J Finno
- Department of Veterinary Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Room 4206 Vet Med 3A One Shields Avenue, Davis, CA 95616, USA.
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Efendić M, Maćešić N, Samardžija M, Vojta A, Korabi N, Capak H, Sušnić MA, Žaja IŽ, Pećin M, Babić NP. Determination of Sublethal Mutation Causing Lavender Foal Syndrome in Arabian Horses From Croatia. J Equine Vet Sci 2018. [DOI: 10.1016/j.jevs.2017.11.014] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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Aleman M, Finno CJ, Weich K, Penedo MCT. Investigation of Known Genetic Mutations of Arabian Horses in Egyptian Arabian Foals with Juvenile Idiopathic Epilepsy. J Vet Intern Med 2017; 32:465-468. [PMID: 29171123 PMCID: PMC5787150 DOI: 10.1111/jvim.14873] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Revised: 09/22/2017] [Accepted: 10/12/2017] [Indexed: 12/18/2022] Open
Abstract
Background The carrier status of lavender foal syndrome (LFS), cerebellar abiotrophy (CA), severe combined immunodeficiency (SCID), and occipitoatlantoaxial malformation (OAAM1) in foals with juvenile idiopathic epilepsy (JIE) is unknown. Hypothesis/Objectives To determine the carrier status of LFS, CA, SCID, and OAAM1 in foals with JIE. Animals Ten foals with JIE. Materials and Methods Archived DNA samples were tested for known genetic mutations causing LFS, CA, SCID, and OAAM1. The inclusion criteria consisted of having been diagnosed with JIE by ruling out other causes of seizures in foals and supported by electroencephalographic examination. Results Ten Egyptian Arabian horses (5 females and 5 males) were phenotyped as foals with JIE by electroencephalography (EEG). All foals were negative for the genetic mutations that cause LFS, CA, SCID, and OAAM1 except for 1 foal that was a carrier of CA. Conclusions and Clinical Importance Juvenile idiopathic epilepsy of Egyptian Arabian foals and LFS appear to be phenotypically and genetically distinct disorders. There was no apparent association between JIE and LFS, CA, SCID, and OAAM1.
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Affiliation(s)
- M Aleman
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California Davis, Davis, CA
| | - C J Finno
- School of Veterinary Medicine, Population Health and Reproduction, University of California Davis, Davis, CA
| | - K Weich
- Department of Medicine and Epidemiology, School of Veterinary Medicine, University of California Davis, Davis, CA
| | - M C T Penedo
- School of Veterinary Medicine, Veterinary Genetics Laboratory, University of California Davis, Davis, CA
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Diseases of the Nervous System. Vet Med (Auckl) 2017. [PMCID: PMC7322266 DOI: 10.1016/b978-0-7020-5246-0.00014-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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Tarr CJ, Thompson PN, Guthrie AJ, Harper CK. The carrier prevalence of severe combined immunodeficiency, lavender foal syndrome and cerebellar abiotrophy in Arabian horses in South Africa. Equine Vet J 2013; 46:512-4. [DOI: 10.1111/evj.12177] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- C. J. Tarr
- Department of Production Animal Studies; Faculty of Veterinary Science; University of Pretoria; Onderstepoort South Africa
| | - P. N. Thompson
- Department of Production Animal Studies; Faculty of Veterinary Science; University of Pretoria; Onderstepoort South Africa
| | - A. J. Guthrie
- Equine Research Centre; Faculty of Veterinary Science; University of Pretoria; Onderstepoort South Africa
| | - C. K. Harper
- Veterinary Genetics Laboratory; Faculty of Veterinary Science; University of Pretoria; Onderstepoort South Africa
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Abstract
The aim of this study was to analyse data on 74,081 calvings, subsequent lactation performance and culling of 23,588 Black-and-White cows improved with Holstein-Friesians. The animals represented the active population in Pomerania and Kujavia, first calved in 2000 and 2001, and were culled before the end of 2008. Frequency of calvings, which averaged 1.5% for twin births and just 0.02% for triplet births, increased with age of cow and also with increasing milk yield in the preceding lactation. Performance results showed that mothers of twins were superior to mothers of single calves in terms of milk yield (1.3 kg milk/day milking). Despite the greater perinatal mortality of twins and triplets, multiple pregnancies gave rise to a greater number of calves compared to single pregnancies. However, multiple pregnancies were accompanied by adverse effects such as increased proportion of complications requiring human assistance, mechanical assistance and veterinary intervention (1.2 × more). Fertility of the cows deteriorated after multiple pregnancies, with particularly unfavourable indicators of fertility found for triplet births, decreased chance of survival to the next calving, and increased culling rates in cows, especially due to udder diseases, infertility, reproductive diseases, old age, metabolic and gastrointestinal diseases, and locomotor system diseases. It was found that the increasing milk yield was paralleled by the increasing proportion of multiple pregnancies. This has highlighted the need for early and reliable diagnosis and management of twin pregnancies, which is supposed to facilitate parturition and ensure survival of calves.
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Vinet A, Drouilhet L, Bodin L, Mulsant P, Fabre S, Phocas F. Genetic control of multiple births in low ovulating mammalian species. Mamm Genome 2012; 23:727-40. [PMID: 22872147 DOI: 10.1007/s00335-012-9412-4] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2012] [Accepted: 07/04/2012] [Indexed: 12/23/2022]
Abstract
In mammals, litter size is a highly variable trait. Some species such as humans or cattle are monotocous, with one or sometimes two newborns per birth, whereas others, the polytocous species such as mice or pigs, are highly prolific and often produce a dozen newborns at each farrowing. In monotocous species, however, two or three newborns per birth may sometime be unwanted. In more polytocous species such as sheep or pigs, litter size is studied in order to increase livestock prolificacy. By contrast, twinning rates in humans or cattle may increase birth difficulties and health problems in the newborns. In this context, the aim of our review was to provide a clearer understanding of the genetic and physiological factors that control multiple births in low-ovulating mammalian species, with particular focus on three species: sheep, cattle, and humans, where knowledge of the ovulation rate in one may enlighten findings in the others. This article therefore reviews the phenotypic and genetic variability observed with respect to ovulation and twinning rates. It then presents the QTL and major genes that have been identified in each species. Finally, we draw a picture of the diversity of the physiological mechanisms underlying multiple ovulation. Although several major genes have been discovered in sheep, QTL detection methods in humans or cattle have suggested that the determinism of litter size is complex and probably involves several genes in order to explain variations in the number of ovulations.
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Affiliation(s)
- Aurélie Vinet
- INRA, UMR1313 Génétique Animale et Biologie Intégrative, 78352, Jouy-en-Josas Cedex, France
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