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Park J. Comprehensive genome-wide analysis of genetic loci and candidate genes associated with litter traits in purebred Berkshire pigs of Korea. Anim Biosci 2024; 37:1702-1711. [PMID: 39164087 PMCID: PMC11366516 DOI: 10.5713/ab.24.0046] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2024] [Revised: 04/15/2024] [Accepted: 05/20/2024] [Indexed: 08/22/2024] Open
Abstract
OBJECTIVE The objective of this study was to identify genomic regions and candidate genes associated with the total number of piglets born (TNB), number of piglets born alive (NBA), and total number of stillbirths (TNS) in Berkshire pigs. METHODS This study used a total of 11,228 records and 2,843 single-nucleotide polymorphism (SNP) data obtained from Illumina porcine 60 K and 80 K chips. The estimated genomic breeding values (GEBVs) and SNP effects were estimated using weighted single-step genomic BLUP (WssGBLUP). RESULTS The heritabilities of the TNB, NBA, and TNS were determined using single-step genomic best linear unbiased prediction (ssGBLUP). The heritability estimates were 0.13, 0.12, and 0.015 for TNB, NBA, and TNS, respectively. When comparing the accuracy of breeding value estimates, the results using pedigree-based BLUP (PBLUP) were 0.58, 0.60, and 0.31 for TNB, NBA, and TNS, respectively. In contrast, the accuracy increased to 0.67, 0.66, and 0.42 for TNB, NBA, and TNS, respectively, when using WssGBLUP, specifically in the last three iterations. The results of weighted single-step genome-wide association studies (WssGWAS) showed that the highest variance explained for each trait was predominantly located in the Sus scrofa chromosome 5 (SSC5) region. Specifically, the variance exceeded 4% for TNB, 3% for NBA, and 6% for TNS. Within the SSC5 region (12.26 to 12.76 Mb), which exhibited the highest variance for TNB, 20 SNPs were identified, and five candidate genes were identified: TIMP3, SYN3, FBXO7, BPIFC, and RTCB. CONCLUSION The identified SNP markers for TNB, NBA, and TNS were expected to provide valuable information for genetic improvement as an understanding of their expression and genetic architecture in Berkshire pigs. With the accumulation of more phenotype and SNP data in the future, it is anticipated that more effective SNP markers will be identified.
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Affiliation(s)
- Jun Park
- Department of Animal Biotechnology, Jeonbuk National University, Jeonju 54896,
Korea
- Dasan Pig Breeding Co., Namwon, 55716,
Korea
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2
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Dias De Castro LL, Oliveira Júnior GA, Perez BC, Carvalho ME, De Souza Ramos EA, Ferraz JBS, Molento MB. Genome-wide association study in thoroughbred horses naturally infected with cyathostomins. Anim Biotechnol 2023; 34:2467-2479. [PMID: 35856721 DOI: 10.1080/10495398.2022.2099880] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Cyathostomins are considered one of the most important parasites of horses. A group of horses within a herd can be responsible for eliminating the majority of parasite eggs. This phenotype might be explained by genetic factors. This study aimed to identify genomic regions associated with fecal egg count (FEC) and hematological parameters by performing a genomic-wide association study (GWAS) in Thoroughbred horses naturally infected with cyathostomins. Packed cell volume (PCV), differential leukocyte, and FEC were determined from 90 horses. All animals were genotyped using the Illumina Equine 70 K BeadChip panel containing 65,157 SNP markers. The five genomic windows that have explained the highest percentage of the additive genetic variance of a specific trait (top 5) were further explored to identify candidate genes. A total of 33, 21, 30, 21, and 19 genes were identified for FEC, PCV, eosinophils, neutrophils, and lymphocyte count, respectively. The top 5 marker regions explained 2.86, 2.56, 2.73, 2.33, and 2.37% of the additive genetic variation of FEC, PCV, eosinophils, neutrophils, and lymphocytes count, respectively. This is the first study correlating phenotypic horse health traits to GWAS analysis, which may be used for animal breeding activities, reducing losses due to parasite infections.
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Affiliation(s)
- Luciana L Dias De Castro
- Laboratory of Parasitology, Department of Veterinary Medicine, University of Caxias do Sul. R: Francisco Getúlio Vargas, Caxias do Sul, Brazil
| | - Gerson A Oliveira Júnior
- College of Animal Science and Food Science, University of São Paulo, Pirassununga, Brazil
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Canada
| | - Bruno Costa Perez
- College of Animal Science and Food Science, University of São Paulo, Pirassununga, Brazil
| | - Minos E Carvalho
- College of Animal Science and Food Science, University of São Paulo, Pirassununga, Brazil
| | - Edneia A De Souza Ramos
- Laboratory of Epigenetics, Department of Pathology, Federal University of Parana, Curitiba, Brazil
| | - José Bento S Ferraz
- College of Animal Science and Food Science, University of São Paulo, Pirassununga, Brazil
| | - Marcelo Beltrão Molento
- Laboratory of Veterinary Clinical Parasitology, Department of Veterinary Medicine, Federal University of Parana, Curitiba, Brazil
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3
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Cox A, Stewart AJ. Insect Bite Hypersensitivity in Horses: Causes, Diagnosis, Scoring and New Therapies. Animals (Basel) 2023; 13:2514. [PMID: 37570323 PMCID: PMC10416928 DOI: 10.3390/ani13152514] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Revised: 07/15/2023] [Accepted: 08/01/2023] [Indexed: 08/13/2023] Open
Abstract
Insect Bite Hypersensitivity (IBH, Queensland itch, sweet itch, equine summer eczema) is the most common pruritic disease of horses. It is most often caused by sensitivity to the saliva of Culicoides spp. of biting midges; however, it can also be caused by hypersensitivity to other insect species. The prevalence of IBH in horses is reported to be as high as 60% in some parts of the world. Due to the severe pruritus and effects of secondary self-trauma, IBH has animal welfare concerns, and there is currently no cure. Management of this condition is life-long, time consuming and costly. New grading systems to document disease severity are being validated, which will allow the comparison of clinical trial results of new and existing therapies. Management involves the minimisation of insect bites by use of stabling, fans, rugs and repellents. Symptomatic therapy involves the administration of systemic or topical corticosteroids, systemic antihistamines, and creams and sprays to promote skin healing and decrease inflammation. New immune-mediated therapeutics including vaccines, in addition to desensitisation procedures, show promise at controlling hypersensitivity reactions. This article will review aetiologic agents, pathophysiology, scoring systems and current and new therapies.
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Affiliation(s)
| | - Allison J. Stewart
- School of Veterinary Science, University of Queensland Gatton, 5391 Warrego Highway, Gatton, QLD 4343, Australia;
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4
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Vasoya D, Tzelos T, Benedictus L, Karagianni AE, Pirie S, Marr C, Oddsdóttir C, Fintl C, Connelley T. High-Resolution Genotyping of Expressed Equine MHC Reveals a Highly Complex MHC Structure. Genes (Basel) 2023; 14:1422. [PMID: 37510326 PMCID: PMC10379315 DOI: 10.3390/genes14071422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2023] [Revised: 06/29/2023] [Accepted: 07/04/2023] [Indexed: 07/30/2023] Open
Abstract
The Major Histocompatibility Complex (MHC) genes play a key role in a number of biological processes, most notably in immunological responses. The MHCI and MHCII genes incorporate a complex set of highly polymorphic and polygenic series of genes, which, due to the technical limitations of previously available technologies, have only been partially characterized in non-model but economically important species such as the horse. The advent of high-throughput sequencing platforms has provided new opportunities to develop methods to generate high-resolution sequencing data on a large scale and apply them to the analysis of complex gene sets such as the MHC. In this study, we developed and applied a MiSeq-based approach for the combined analysis of the expressed MHCI and MHCII repertoires in cohorts of Thoroughbred, Icelandic, and Norwegian Fjord Horses. The approach enabled us to generate comprehensive MHCI/II data for all of the individuals (n = 168) included in the study, identifying 152 and 117 novel MHCI and MHCII sequences, respectively. There was limited overlap in MHCI and MHCII haplotypes between the Thoroughbred and the Icelandic/Norwegian Fjord horses, showcasing the variation in MHC repertoire between genetically divergent breeds, and it can be inferred that there is much more MHC diversity in the global horse population. This study provided novel insights into the structure of the expressed equine MHC repertoire and highlighted unique features of the MHC in horses.
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Affiliation(s)
- Deepali Vasoya
- The Roslin Institute, The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Roslin EH25 9RG, UK
| | - Thomas Tzelos
- The Roslin Institute, The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Roslin EH25 9RG, UK
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik EH26 0PZ, UK
| | - Lindert Benedictus
- Faculty of Veterinary Medicine, Utrecht University, Yalelaan 1, 3584 CL Utrecht, The Netherlands
| | - Anna Eleonora Karagianni
- The Roslin Institute, The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Roslin EH25 9RG, UK
| | - Scott Pirie
- Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Roslin EH25 9RG, UK
| | - Celia Marr
- Rossdales Equine Hospital, Cotton End Road, Exning, Newmarket CD8 7NN, UK
| | - Charlotta Oddsdóttir
- The Institute for Experimental Pathology at Keldur, University of Iceland Keldnavegur 3, 112 Reykjavík, Iceland
| | - Constanze Fintl
- Department of Companion Animal Clinical Sciences, Faculty of Veterinary Medicine and Biosciences, Norwegian University of Life Sciences, P.O. Box 5003, 1432 Ås, Norway
| | - Timothy Connelley
- The Roslin Institute, The Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush Campus, Roslin EH25 9RG, UK
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Salek Ardestani S, Zandi MB, Vahedi SM, Janssens S. Population structure and genomic footprints of selection in five major Iranian horse breeds. Anim Genet 2022; 53:627-639. [PMID: 35919961 DOI: 10.1111/age.13243] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2022] [Revised: 06/08/2022] [Accepted: 07/04/2022] [Indexed: 11/28/2022]
Abstract
The genetic structure and characteristics of Iranian native breeds are yet to be comprehensibly investigated and studied. Therefore, we employed genomic information of 364 Iranian native horses representing the Asil (n = 109), Caspian (n = 40), Dareshuri (n = 44), Kurdish (n = 95), and Turkoman (n = 76) breeds to reveal the genetic structure and characteristics. For these and 19 other horse breeds, principal component analysis, Bayesian model-based, Neighbor-Net, and bootstrap-based TreeMix approaches were applied to investigate and compare their genetic structure. Additionally, three haplotype-based methods including haplotype homozygosity pooled, integrated haplotype score, and number of segregating sites by length were applied to trace genomic footprints of selection of Asil, Caspian, Dareshuri, Kurdish, and Turkoman groups. Then, the Mahalanobis distance based on the negative-log10 rank-based P-values was estimated based on the haplotype homozygosity pooled, integrated haplotype score, and number of segregating sites by length values. Asil, Caspian, Dareshuri, Kurdish, and Turkoman can be categorized into five different genetic clusters. Based on the top 1% of Mahalanobis distance based on the negative-log10 rank-based P-values of SNPs, we identified 24 SNPs formerly reported to be associated with different traits and >100 genes undergoing selection pressures in Asil, Caspian, Dareshuri, Kurdish, and Turkoman. The detected QTL undergoing selection pressures were associated with withers height, equine metabolic syndrome, overall body size, insect bite hypersensitivity, guttural pouch tympany, white markings, Rhodococcus equi infection, jumping test score, alternate gaits, and body weight traits. Our findings will aid to have a better perspective of the genetic characteristics and population structure of Asil, Caspian, Dareshuri, Kurdish, and Turkoman horses as Iranian native horse breeds.
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Affiliation(s)
| | | | - Seyed Milad Vahedi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, Nova Scotia, Canada
| | - Steven Janssens
- Department Biosystems, Center Animal Breeding and Genetics, KU Leuven, Leuven, Belgium
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6
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Nazari F, Seyedabadi HR, Noshary A, Emamjomeh-Kashan N, Banabazi MH. A genome-wide scan for signatures of selection in Kurdish horse breed. J Equine Vet Sci 2022; 113:103916. [PMID: 35218903 DOI: 10.1016/j.jevs.2022.103916] [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: 11/10/2021] [Revised: 02/20/2022] [Accepted: 02/21/2022] [Indexed: 11/17/2022]
Abstract
The genetic diversity and genomic regions being under putative natural selection in Kurdish horse population were studied. The samples from 72 horses were genotyped by using GGP Equine 70K SNP arrays. The Ne Slope (NeS) analyses revealed that a sharp decline in Ne has probably occurred around four generations ago, and high frequency of ROH with 2-4 Mbp in length suggested that the inbreeding has probably occurred around 20 generations ago. The effective population size (Ne) was 104 horses up to three generations ago and the average inbreeding (FROH) was 0.047(±0.045). Using de-correlated composite of multiple selection signals (DCMS) and runs of homozygosity (ROH) analyses the genomic regions being under putative selection were detected. By using DCMS, a total of 148 significant SNP (FDR < 0.05) were identified, 40% of which were located on ECA9, where the greatest peak was observed. This genomic region harbors several known QTL which are associated with withers height (body size). Also significant genomic regions (FDR<0.05), harboring QTL associated with insect bite hypersensitivity (IBH), hair density and coat texture, alternate gaits, guttural pouch tympany and temperament were identified. By using outputs of ROH analyses, two hotspot regions (i.e. 30% of individuals was considered as threshold), were identified on ECA7 (50.11-54.36 Mbp) and ECA11 (26.10-29.07 Mbp) harboring QTL associated with withers height, alternate gait and IBH. In summary, the genomic regions being under putative natural selection which harbors known QTL associated with body size and IBH, among others, were introduced. Nevertheless, additional functional and comparative studies are necessary to corroborate their effect on the observed genetic and phenotypic diversity of the Kurdish horses.
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Affiliation(s)
- Faezeh Nazari
- Department of Animal Science, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Hamid-Reza Seyedabadi
- Animal Science Research Institute of Iran (ASRI), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran.
| | - Alireza Noshary
- Department of Animal Science, Faculty of Agriculture, Karaj Branch, Islamic Azad University, Karaj, Iran
| | - Nasser Emamjomeh-Kashan
- Department of Animal Science, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Mohamad-Hosein Banabazi
- Animal Science Research Institute of Iran (ASRI), Agricultural Research, Education and Extension Organization (AREEO), Karaj, Iran; Department of animal breeding and genetics (HGEN), Centre for Veterinary Medicine and Animal Science (VHC), Swedish University of Agricultural Sciences (SLU), Uppsala 75007, Sweden
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7
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Trevisoli PA, Moreira GCM, Boschiero C, Cesar ASM, Petrini J, Margarido GRA, Ledur MC, Mourão GB, Garrick D, Coutinho LL. A Missense Mutation in the MYBPH Gene Is Associated With Abdominal Fat Traits in Meat-Type Chickens. Front Genet 2021; 12:698163. [PMID: 34456973 PMCID: PMC8386115 DOI: 10.3389/fgene.2021.698163] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2021] [Accepted: 07/09/2021] [Indexed: 12/14/2022] Open
Abstract
Chicken is an important source of protein for human nutrition and a model system for growth and developmental biology. Although the genetic architecture of quantitative traits in meat-type chickens has been the subject of ongoing investigation, the identification of mutations associated with carcass traits of economic interest remains challenging. Therefore, our aim was to identify predicted deleterious mutation, which potentially affects protein function, and test if they were associated with carcass traits in chickens. For that, we performed a genome-wide association analysis (GWAS) for breast, thigh and drumstick traits in meat-type chickens and detected 19 unique quantitative trait loci (QTL). We then used: (1) the identified windows; (2) QTL for abdominal fat detected in a previous study with the same population and (3) previously obtained whole genome sequence data, to identify 18 predicted deleterious single nucleotide polymorphisms (SNPs) in those QTL for further association with breast, thigh, drumstick and abdominal fat traits. Using the additive model, a predicted deleterious SNP c.482C > T (SIFT score of 0.4) was associated (p-value < 0.05) with abdominal fat weight and percentage. This SNP is in the second exon of the MYBPH gene, and its allele frequency deviates from Hardy–Weinberg equilibrium. In conclusion, our study provides evidence that the c.482C > T SNP in the MYBPH gene is a putative causal mutation for fat deposition in meat-type chickens.
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Affiliation(s)
- Priscila Anchieta Trevisoli
- Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, Brazil
| | - Gabriel Costa Monteiro Moreira
- Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, Brazil
| | - Clarissa Boschiero
- Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, Brazil
| | - Aline Silva Mello Cesar
- Agri-Food Industry, Food and Nutrition Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, Brazil
| | - Juliana Petrini
- Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, Brazil
| | | | | | - Gerson Barreto Mourão
- Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, Brazil
| | - Dorian Garrick
- School of Agriculture, Massey University, Wellington, New Zealand
| | - Luiz Lehmann Coutinho
- Animal Science Department, University of São Paulo (USP)/Luiz de Queiroz College of Agriculture (ESALQ), Piracicaba, Brazil
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8
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Vostry L, Vostra-Vydrova H, Citek J, Gorjanc G, Curik I. Association of inbreeding and regional equine leucocyte antigen homozygosity with the prevalence of insect bite hypersensitivity in Old Kladruber horse. Anim Genet 2021; 52:422-430. [PMID: 33970495 PMCID: PMC8360196 DOI: 10.1111/age.13075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/22/2021] [Indexed: 12/19/2022]
Abstract
Inbreeding depression is the reduction of performance caused by mating of close relatives. In livestock populations, inbreeding depression has been traditionally estimated by regression of phenotypes on pedigree inbreeding coefficients. This estimation can be improved by utilising genomic inbreeding coefficients. Here we estimate inbreeding depression for insect bite hypersensitivity (IBH) prevalence, the most common allergic horse disease worldwide, in Old Kladruber horse. In a deep pedigree with 3214 horses (187 genotyped), we used a generalised linear mixed model with IBH phenotype from 558 horses examined between 1996 and 2009 (1368 records). In addition to the classical pedigree information, we used the single-step approach that enabled joint use of pedigree and genomic information to estimate inbreeding depression overall genome and equine leucocyte antigen (ELA) class II region. Significant inbreeding depression was observed in all models fitting overall inbreeding coefficients (odds ratio between 1.018 and 1.074, P < 0.05) with the exception of Kalinowski's new inbreeding (P = 0.0516). The increase of ELA class II inbreeding was significantly associated with increased prevalence of IBH (odds ratio 1.018; P = 0.027). However, when fitted jointly with the overall inbreeding coefficient, the effect of ELA class II inbreeding was not significant (odds ratio 1.016; P = 0.062). Overall, the higher ELA class II and/or overall inbreeding (pedigree or genomic) was associated with increased prevalence of IBH in Old Kladruber horses. The single-step approach provides an efficient use of all the available pedigree, genomic, and phenotype information for estimation of overall and regional inbreeding effects.
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Affiliation(s)
- L Vostry
- Czech University of Life Sciences, Kamycka 129, Prague, 16500, Czech Republic
| | - H Vostra-Vydrova
- Czech University of Life Sciences, Kamycka 129, Prague, 16500, Czech Republic.,Institute of Animal Science, Pratelstvi 815, Prague, 10400, Czech Republic
| | - J Citek
- South Bohemia University, Branisovska 31a, Ceske Budejovice, 370 05, Czech Republic.,Veterinary Research Institute, Hudcova 296/70, Brno, 621 00, Czech Republic
| | - G Gorjanc
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Edinburgh, Midlothian, EH259RG, UK
| | - I Curik
- Faculty of Agriculture, University of Zagreb, Svetošimunska cesta 25, Zagreb, 10000, Croatia
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9
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Raschia M, Nani J, Carignano H, Amadio A, Maizon D, Poli M. Weighted single-step genome-wide association analyses for milk traits in Holstein and Holstein x Jersey crossbred dairy cattle. Livest Sci 2020. [DOI: 10.1016/j.livsci.2020.104294] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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10
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Mancin E, Ablondi M, Mantovani R, Pigozzi G, Sabbioni A, Sartori C. Genetic Variability in the Italian Heavy Draught Horse from Pedigree Data and Genomic Information. Animals (Basel) 2020; 10:E1310. [PMID: 32751586 PMCID: PMC7460293 DOI: 10.3390/ani10081310] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2020] [Revised: 07/17/2020] [Accepted: 07/28/2020] [Indexed: 12/26/2022] Open
Abstract
This study aimed to investigate the genetic diversity in the Italian Heavy Horse Breed from pedigree and genomic data. Pedigree information for 64,917 individuals were used to assess inbreeding level, effective population size (Ne), and effective numbers of founders and ancestors (fa/fe). Genotypic information from SNP markers were available for 267 individuals of both sexes, and it allowed estimating genomic inbreeding in two methods (observed versus expected homozygosity and from ROH) to study the breed genomic structure and possible selection signatures. Pedigree and genomic inbreeding were greatly correlated (0.65 on average). The inbreeding trend increased over time, apart from periods in which the base population enlarged, when Ne increased also. Recent bottlenecks did not occur in the genome, as fa/fe have shown. The observed homozygosity results were on average lower than expected, which was probably due to the use of French Breton stallions to support the breed genetic variability. High homozygous regions suggested that inbreeding increased in different periods. Two subpopulations were distinguished, which was probably due to the different inclusion of French animals by breeders. Few selection signatures were found at the population level, with possible associations to disease resistance. The almost low inbreeding rate suggested that despite the small breed size, conservation actions are not yet required.
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Affiliation(s)
- Enrico Mancin
- Department of Agronomy, Food, Natural resources, Animals and Environment—DAFNAE, University of Padova, Viale dell’Università 16, 35020 Legnaro (PD), Italy; (E.M.); (C.S.)
| | - Michela Ablondi
- Dipartimento di Scienze Medico-Veterinarie, University of Parma Via del Taglio 10, 43126 Parma, Italy; (M.A.); (A.S.)
| | - Roberto Mantovani
- Department of Agronomy, Food, Natural resources, Animals and Environment—DAFNAE, University of Padova, Viale dell’Università 16, 35020 Legnaro (PD), Italy; (E.M.); (C.S.)
| | - Giuseppe Pigozzi
- Italian Heavy Draught Horse Breeders Association (ANACAITPR), 37068 Vigasio (VR), Italy;
| | - Alberto Sabbioni
- Dipartimento di Scienze Medico-Veterinarie, University of Parma Via del Taglio 10, 43126 Parma, Italy; (M.A.); (A.S.)
| | - Cristina Sartori
- Department of Agronomy, Food, Natural resources, Animals and Environment—DAFNAE, University of Padova, Viale dell’Università 16, 35020 Legnaro (PD), Italy; (E.M.); (C.S.)
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11
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Lindgren G, Naboulsi R, Frey R, Solé M. Genetics of Skin Disease in Horses. Vet Clin North Am Equine Pract 2020; 36:323-339. [PMID: 32534850 DOI: 10.1016/j.cveq.2020.03.010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
Abstract
Equine skin diseases are common, causing increased costs and reduced welfare of affected horses.Genetic testing, if available, can complement early detection, disease diagnosis, and clinical treatment and offers horse breeders the possibility to rule out carrier status. The mechanisms of complex disease can be investigated by using the latest state-of-the-art genomic technologies. Genome-based strategies may also serve as an efficient and cost-effective strategy for the management of the disease severity levels, with particular interest in complex traits such as insect bite hypersensitivity, chronic progressive lymphedema, and melanoma.
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Affiliation(s)
- Gabriella Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Almas Allé 8, Uppsala 75007, Sweden; Livestock Genetics, Department of Biosystems, KU Leuven Leuven, KasteelparkArenberg 30, Leuven 3001, Belgium
| | - Rakan Naboulsi
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Almas Allé 8, Uppsala 75007, Sweden
| | - Rebecka Frey
- AniCura Norsholms Djursjukhus, Norsholm 61791, Sweden
| | - Marina Solé
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Almas Allé 8, Uppsala 75007, Sweden.
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12
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Genetic Diversity and Signatures of Selection in a Native Italian Horse Breed Based on SNP Data. Animals (Basel) 2020; 10:ani10061005. [PMID: 32521830 PMCID: PMC7341496 DOI: 10.3390/ani10061005] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 06/01/2020] [Accepted: 06/04/2020] [Indexed: 12/31/2022] Open
Abstract
Simple Summary The Bardigiano horse is a native Italian breed bred for living in rural areas, traditionally used in agriculture. The breed counts about 3000 horses, and it is nowadays mainly used for recreational purposes. The relatively small size and the closed status of the breed raise the issue of monitoring genetic diversity. We therefore characterized the breed’s genetic diversity based on molecular data. We showed a critical reduction of genetic variability mainly driven by past bottlenecks. We also highlighted homozygous genomic regions that might be the outcome of directional selection in recent years, in line with the conversion of Bardigiano horses from agricultural to riding purposes. Abstract Horses are nowadays mainly used for sport and leisure activities, and several local breeds, traditionally used in agriculture, have been exposed to a dramatic loss in population size and genetic diversity. The loss of genetic diversity negatively impacts individual fitness and reduces the potential long-term survivability of a breed. Recent advances in molecular biology and bioinformatics have allowed researchers to explore biodiversity one step further. This study aimed to evaluate the loss of genetic variability and identify genomic regions under selection pressure in the Bardigiano breed based on GGP Equine70k SNP data. The effective population size based on Linkage Disequilibrium (Ne) was equal to 39 horses, and it showed a decline over time. The average inbreeding based on runs of homozygosity (ROH) was equal to 0.17 (SD = 0.03). The majority of the ROH were relatively short (91% were ≤2 Mbp long), highlighting the occurrence of older inbreeding, rather than a more recent occurrence. A total of eight ROH islands, shared among more than 70% of the Bardigiano horses, were found. Four of them mapped to known quantitative trait loci related to morphological traits (e.g., body size and coat color) and disease susceptibility. This study provided the first genome-wide scan of genetic diversity and selection signatures in an Italian native horse breed.
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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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François L, Hoskens H, Velie BD, Stinckens A, Tinel S, Lamberigts C, Peeters L, Savelkoul HFJ, Tijhaar E, Lindgren G, Janssens S, Ducro BJ, Buys N, Schurink AA. Genomic Regions Associated with IgE Levels against Culicoides spp. Antigens in Three Horse Breeds. Genes (Basel) 2019; 10:genes10080597. [PMID: 31398914 PMCID: PMC6723964 DOI: 10.3390/genes10080597] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Revised: 07/25/2019] [Accepted: 08/06/2019] [Indexed: 11/16/2022] Open
Abstract
Insect bite hypersensitivity (IBH), which is a cutaneous allergic reaction to antigens from Culicoides spp., is the most prevalent skin disorder in horses. Misdiagnosis is possible, as IBH is usually diagnosed based on clinical signs. Our study is the first to employ IgE levels against several recombinant Culicoides spp. allergens as an objective, independent, and quantitative phenotype to improve the power to detect genetic variants that underlie IBH. Genotypes of 200 Shetland ponies, 127 Icelandic horses, and 223 Belgian Warmblood horses were analyzed while using a mixed model approach. No single-nucleotide polymorphism (SNP) passed the Bonferroni corrected significance threshold, but several regions were identified within and across breeds, which confirmed previously identified regions of interest and, in addition, identifying new regions of interest. Allergen-specific IgE levels are a continuous and objective phenotype that allow for more powerful analyses when compared to a case-control set-up, as more significant associations were obtained. However, the use of a higher density array seems necessary to fully employ the use of IgE levels as a phenotype. While these results still require validation in a large independent dataset, the use of allergen-specific IgE levels showed value as an objective and continuous phenotype that can deepen our understanding of the biology underlying IBH.
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Affiliation(s)
- Liesbeth François
- Livestock Genetics, Department of Biosystems, KU Leuven, B-3001 Leuven, Belgium
| | - Hanne Hoskens
- Department of Human Genetics, KU Leuven, B-3000 Leuven, Belgium
| | - Brandon D Velie
- School of Life & Environmental Sciences, B19-603 University of Sydney, Sydney, NSW 2006,Australia
| | - Anneleen Stinckens
- Livestock Genetics, Department of Biosystems, KU Leuven, B-3001 Leuven, Belgium
| | - Susanne Tinel
- Livestock Genetics, Department of Biosystems, KU Leuven, B-3001 Leuven, Belgium
| | - Chris Lamberigts
- Research Group Livestock Physiology, Department of Biosystems, KU Leuven, Leuven, B-3001 Leuven, Belgium
| | - Liesbet Peeters
- Biomedical Research Institute, Hasselt University, B-3590 Diepenbeek, Belgium
| | - Huub F J Savelkoul
- Cell Biology and Immunology Group, Wageningen University & Research, 6700 AH Wageningen, The Netherlands
| | - Edwin Tijhaar
- Cell Biology and Immunology Group, Wageningen University & Research, 6700 AH Wageningen, The Netherlands
| | - Gabriella Lindgren
- Livestock Genetics, Department of Biosystems, KU Leuven, B-3001 Leuven, Belgium
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, 75007 Uppsala, Sweden
| | - Steven Janssens
- Livestock Genetics, Department of Biosystems, KU Leuven, B-3001 Leuven, Belgium
| | - Bart J Ducro
- Animal Breeding and Genomics, Wageningen University & Research, 6700 AH Wageningen, The Netherlands
| | - Nadine Buys
- Livestock Genetics, Department of Biosystems, KU Leuven, B-3001 Leuven, Belgium
| | - And Anouk Schurink
- Animal Breeding and Genomics, Wageningen University & Research, 6700 AH Wageningen, The Netherlands.
- Centre for Genetic Resources, The Netherlands (CGN), Wageningen University & Research, 6700 AH Wageningen, The Netherlands.
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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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Hartley C. Eosinophilic keratitis in horses. IN PRACTICE 2018. [DOI: 10.1136/inp.k2134] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/04/2022]
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Affiliation(s)
- E. N. Adam
- Gluck Equine Research Center; University of Kentucky; Lexington USA
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18
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Metodiev S, Thekkoot D, Young J, Onteru S, Rothschild M, Dekkers J. A whole-genome association study for litter size and litter weight traits in pigs. Livest Sci 2018. [DOI: 10.1016/j.livsci.2018.03.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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19
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Prospecting genes associated with navel length, coat and scrotal circumference traits in Canchim cattle. Livest Sci 2018. [DOI: 10.1016/j.livsci.2018.02.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
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20
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Lomas HR, Robinson PA. A Pilot Qualitative Investigation of Stakeholders' Experiences and Opinions of Equine Insect Bite Hypersensitivity in England. Vet Sci 2018; 5:E3. [PMID: 29315275 PMCID: PMC5876561 DOI: 10.3390/vetsci5010003] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2017] [Revised: 01/04/2018] [Accepted: 01/06/2018] [Indexed: 02/06/2023] Open
Abstract
Equine insect bite hypersensitivity (IBH), commonly known as sweet itch or summer eczema, is a frustrating recurrent skin disease in the equine industry involving an immune reaction to the bites of Culicoides spp. midges. To investigate the impact of IBH in the field, an exploratory pilot study was conducted with equine stakeholders in one region of central England. Nine semi-structured, face-to-face interviews were conducted with horse owners and an equine veterinarian. The aim was to gain an understanding of experiences with IBH, and to gauge opinions on the value of the various management strategies horse owners use to control IBH. Awareness of IBH was generally high, particularly in those individuals who had previous experience with the condition. Those with previous experience of IBH commented on the significant effect on daily routines, and the associated cost implications. Most participants supported an integrated approach to hypersensitivity management, and this most commonly involved a combination of physical barriers and chemical repellents, but sometimes included feed supplementation. Overall, attitudes towards IBH suggested that the condition is a notable welfare and economic concern for stakeholders, but veterinary involvement tended to only be in more severe cases. Further research is required in the future to improve understanding, management and potential treatment of this condition.
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Affiliation(s)
- Hannah R Lomas
- Department of Animal Production, Welfare and Veterinary Sciences, Harper Adams University, Newport, Shropshire TF10 8NB, UK.
| | - Philip A Robinson
- Department of Animal Production, Welfare and Veterinary Sciences, Harper Adams University, Newport, Shropshire TF10 8NB, UK.
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Sadeghi R, Moradi-Shahrbabak M, Miraei Ashtiani SR, Miller DC, Antczak DF. MHC haplotype diversity in Persian Arabian horses determined using polymorphic microsatellites. Immunogenetics 2017; 70:305-315. [PMID: 29170799 DOI: 10.1007/s00251-017-1039-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Accepted: 10/19/2017] [Indexed: 01/15/2023]
Abstract
Previous research on the equine major histocompatibility complex (MHC) demonstrated strong correlations between haplotypes defined by polymorphic intra-MHC microsatellites and haplotypes defined using classical serology. Here, we estimated MHC diversity in a sample of 124 Arabian horses from an endangered strain native to Iran (Persian Asil Arabians), using a validated 10-marker microsatellite panel. In a group of 66 horses related as parent-offspring pairs or half-sibling groups, we defined 51 MHC haplotypes, 49 of which were new. In 47 of the remaining 58 unrelated horses, we could assign one previously identified MHC haplotype, and by default, we gave provisional haplotype status to the remaining constellation of microsatellite alleles. In these horses, we found 21 haplotypes that we had previously defined and 31 provisional haplotypes, two of which had been identified in an earlier study. This gave a total of 78 new MHC haplotypes. The final 11 horses were MHC heterozygotes that we could not phase using information from any of the previously validated or provisional haplotypes. However, we could determine that these horses carried a total of 22 different undefined haplotypes. In the overall population sample, we detected three homozygous horses and one maternally inherited recombinant from 21 informative segregations. Virtually all of the horses tested were MHC heterozygotes, and most unrelated horses (98%) were heterozygous for rare microsatellite-defined haplotypes found less than three times in the sampled horses. This is evidence for a very high level of MHC haplotype variation in the Persian Asil Arabian horse.
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Affiliation(s)
- R Sadeghi
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
- Department of Animal Science, University of Tehran, Karaj, 4111, Iran
| | | | | | - D C Miller
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Douglas F Antczak
- Baker Institute for Animal Health, College of Veterinary Medicine, Cornell University, Ithaca, NY, 14853, USA.
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Sollero BP, Junqueira VS, Gomes CCG, Caetano AR, Cardoso FF. Tag SNP selection for prediction of tick resistance in Brazilian Braford and Hereford cattle breeds using Bayesian methods. Genet Sel Evol 2017; 49:49. [PMID: 28619006 PMCID: PMC5471684 DOI: 10.1186/s12711-017-0325-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 05/31/2017] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Cattle resistance to ticks is known to be under genetic control with a complex biological mechanism within and among breeds. Our aim was to identify genomic segments and tag single nucleotide polymorphisms (SNPs) associated with tick-resistance in Hereford and Braford cattle. The predictive performance of a very low-density tag SNP panel was estimated and compared with results obtained with a 50 K SNP dataset. RESULTS BayesB (π = 0.99) was initially applied in a genome-wide association study (GWAS) for this complex trait by using deregressed estimated breeding values for tick counts and 41,045 SNP genotypes from 3455 animals raised in southern Brazil. To estimate the combined effect of a genomic region that is potentially associated with quantitative trait loci (QTL), 2519 non-overlapping 1-Mb windows that varied in SNP number were defined, with the top 48 windows including 914 SNPs and explaining more than 20% of the estimated genetic variance for tick resistance. Subsequently, the most informative SNPs were selected based on Bayesian parameters (model frequency and t-like statistics), linkage disequilibrium and minor allele frequency to propose a very low-density 58-SNP panel. Some of these tag SNPs mapped close to or within genes and pseudogenes that are functionally related to tick resistance. Prediction ability of this SNP panel was investigated by cross-validation using K-means and random clustering and a BayesA model to predict direct genomic values. Accuracies from these cross-validations were 0.27 ± 0.09 and 0.30 ± 0.09 for the K-means and random clustering groups, respectively, compared to respective values of 0.37 ± 0.08 and 0.43 ± 0.08 when using all 41,045 SNPs and BayesB with π = 0.99, or of 0.28 ± 0.07 and 0.40 ± 0.08 with π = 0.999. CONCLUSIONS Bayesian GWAS model parameters can be used to select tag SNPs for a very low-density panel, which will include SNPs that are potentially linked to functional genes. It can be useful for cost-effective genomic selection tools, when one or a few key complex traits are of interest.
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Affiliation(s)
- Bruna P. Sollero
- Embrapa Pecuária Sul, Caixa Postal 242 - BR 153 - Km 633, Bagé, Rio Grande do Sul 96.401-970 Brazil
| | - Vinícius S. Junqueira
- Departamento de Zootecnia, Universidade Federal de Viçosa, Avenida Peter Henry Rolfs, s/n - Campus Universitário, Viçosa, Minas Gerais 36.570-000 Brazil
| | - Cláudia C. G. Gomes
- Embrapa Pecuária Sul, Caixa Postal 242 - BR 153 - Km 633, Bagé, Rio Grande do Sul 96.401-970 Brazil
| | - Alexandre R. Caetano
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estacao Biologica Final Av. W/5 Norte, Brasilia-DF, C.P. 02372, Brasília, Distrito Federal 70770-917 Brazil
| | - Fernando F. Cardoso
- Embrapa Pecuária Sul, Caixa Postal 242 - BR 153 - Km 633, Bagé, Rio Grande do Sul 96.401-970 Brazil
- Universidade Federal de Pelotas, Capão do Leão, Rio Grande do Sul 96.000-010 Brazil
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Thekkoot DM, Young JM, Rothschild MF, Dekkers JCM. Genomewide association analysis of sow lactation performance traits in lines of Yorkshire pigs divergently selected for residual feed intake during grow-finish phase. J Anim Sci 2017; 94:2317-31. [PMID: 27285909 DOI: 10.2527/jas.2015-0258] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Lactation is an economically and biologically important phase in the life cycle of sows. Short generation intervals in nucleus herds and low heritability of traits associated with lactation along with challenges associated with collecting accurate lactation performance phenotypes emphasize the importance of using genomic tools to examine the underlying genetics of these traits. We report the first genomewide association study (GWAS) on traits associated with lactation and efficiency in 2 lines of Yorkshire pigs that were divergently selected for residual feed intake during grow-finish phase. A total of 862 farrowing records from 2 parities were analyzed using a Bayesian whole genome variable selection model (Bayes B) to locate 1-Mb regions that were most strongly associated with each trait. The GWAS was conducted separately for parity 1 and 2 records. Marker-based heritabilities ranged from 0.03 to 0.39 for parity 1 traits and from 0.06 to 0.40 for parity 2 traits. For all traits studied, around 90% of genetic variance came from a large number of genomic regions with small effects, whereas genomic regions with large effects were found to be different for the same trait measured in parity 1 and 2. The highest percentage of genetic variance explained by a 1-Mb window for each trait ranged from 0.4% for feed intake during lactation to 4.2% for back fat measured at farrowing in parity 1 sows and from 0.2% for lactation feed intake to 5.4% for protein mass loss during lactation in parity 2 sows. A total of thirteen 1-Mb nonoverlapping windows were found to explain more than 1.5% of genetic variance for either a single trait or across multiple traits. These 1-Mb windows were on chromosomes 2, 3, 6, 7, 8, 11, 14, 15, 17, and 18. The major positional candidate genes within 1 Mb upstream and downstream of these windows were , (SSC2), (SSC6) (SSC7), (SSC8), (SSC11), (SSC14), (SSC17). Further validation studies on larger populations are required to validate these findings and to improve our understanding of the biology and complex genetic architecture of traits associated with sow lactation performance.
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Citek J, Vostry L, Vostra-Vydrova H, Brzakova M, Prantlova V. Genetic parameters of insect bite hypersensitivity in the Old Grey Kladruber horse. J Anim Sci 2017; 95:53-58. [PMID: 28177358 DOI: 10.2527/jas.2016.0745] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
The objective of this study was to assess the genetic parameters of insect bite hypersensitivity (IBH) in the Old Grey Kladruber horse, an original Czech warmblood horse breed. Insect bite hypersensitivity is a recurrent allergic skin disease affecting horses worldwide. Its etiology is multifactorial. The defect is genetically controlled, and the starting impulse is a bite by midges of the spp. and less frequently spp. Knowledge about the associated genes is limited. Horses were kept by the National Stud in Kladruby (1,146 measurements) and by 10 private breeders (63 measurements). The horses were visually scored by the same inspector over a period of 13 yr from 1996 to 2009. A linear logistic model with a binary variable was used for subsequent statistical analysis. The fixed effects of the farm, year of evaluation, age of evaluation, and sex were significant, and the nonsignificant effect was the intensity of greying. The animals from the National Stud were more strongly affected by IBH than animals from private studs. The National Stud is located near the Labe River, at an altitude of 206 m; there are bottomland pastures in the vicinity, blind river arms, and numerous pools and marshes, and the climate is mild. These conditions are convenient for horse keeping but also for the propagation of . The stallions were less affected than the mares. The occurrence in years of age was influenced by selection; scoring began in the first year of age, and when the young animal was repeatedly positive, it was eliminated from breeding. The estimated h differed significantly from 0, and the direct h were 0.626 in the animal model with a maternal effect, 0.359 in the animal model without a maternal effect, and 0.363 in the animal model without correlation between direct and maternal effect. The maternal h was 0.305. The estimated repeatabilities were 0.636 with a maternal effect, 0.615 without a maternal effect, and 0.623 without correlation. The h of IBH was found to be medium to high, so there is a possibility to reduce the prevalence of IBH by selection.
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Viļuma A, Mikko S, Hahn D, Skow L, Andersson G, Bergström TF. Genomic structure of the horse major histocompatibility complex class II region resolved using PacBio long-read sequencing technology. Sci Rep 2017; 7:45518. [PMID: 28361880 PMCID: PMC5374520 DOI: 10.1038/srep45518] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 02/27/2017] [Indexed: 11/10/2022] Open
Abstract
The mammalian Major Histocompatibility Complex (MHC) region contains several gene families characterized by highly polymorphic loci with extensive nucleotide diversity, copy number variation of paralogous genes, and long repetitive sequences. This structural complexity has made it difficult to construct a reliable reference sequence of the horse MHC region. In this study, we used long-read single molecule, real-time (SMRT) sequencing technology from Pacific Biosciences (PacBio) to sequence eight Bacterial Artificial Chromosome (BAC) clones spanning the horse MHC class II region. The final assembly resulted in a 1,165,328 bp continuous gap free sequence with 35 manually curated genomic loci of which 23 were considered to be functional and 12 to be pseudogenes. In comparison to the MHC class II region in other mammals, the corresponding region in horse shows extraordinary copy number variation and different relative location and directionality of the Eqca-DRB, -DQA, -DQB and -DOB loci. This is the first long-read sequence assembly of the horse MHC class II region with rigorous manual gene annotation, and it will serve as an important resource for association studies of immune-mediated equine diseases and for evolutionary analysis of genetic diversity in this region.
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Affiliation(s)
- Agnese Viļuma
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences (SLU), Box 7023, 750 07 Uppsala, Sweden
| | - Sofia Mikko
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences (SLU), Box 7023, 750 07 Uppsala, Sweden
| | - Daniela Hahn
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences (SLU), Box 7023, 750 07 Uppsala, Sweden
| | - Loren Skow
- Department of Veterinary Integrative Biosciences, College of Veterinary Medicine, Texas A&M University, College Station, TX 77843, USA
| | - Göran Andersson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences (SLU), Box 7023, 750 07 Uppsala, Sweden
| | - Tomas F Bergström
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences (SLU), Box 7023, 750 07 Uppsala, Sweden
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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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27
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Velie BD, Shrestha M, Franҫois L, Schurink A, Tesfayonas YG, Stinckens A, Blott S, Ducro BJ, Mikko S, Thomas R, Swinburne JE, Sundqvist M, Eriksson S, Buys N, Lindgren G. Using an Inbred Horse Breed in a High Density Genome-Wide Scan for Genetic Risk Factors of Insect Bite Hypersensitivity (IBH). PLoS One 2016; 11:e0152966. [PMID: 27070818 PMCID: PMC4829256 DOI: 10.1371/journal.pone.0152966] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2015] [Accepted: 03/22/2016] [Indexed: 11/19/2022] Open
Abstract
While susceptibility to hypersensitive reactions is a common problem amongst humans and animals alike, the population structure of certain animal species and breeds provides a more advantageous route to better understanding the biology underpinning these conditions. The current study uses Exmoor ponies, a highly inbred breed of horse known to frequently suffer from insect bite hypersensitivity, to identify genomic regions associated with a type I and type IV hypersensitive reaction. A total of 110 cases and 170 controls were genotyped on the 670K Axiom Equine Genotyping Array. Quality control resulted in 452,457 SNPs and 268 individuals being tested for association. Genome-wide association analyses were performed using the GenABEL package in R and resulted in the identification of two regions of interest on Chromosome 8. The first region contained the most significant SNP identified, which was located in an intron of the DCC netrin 1 receptor gene. The second region identified contained multiple top SNPs and encompassed the PIGN, KIAA1468, TNFRSF11A, ZCCHC2, and PHLPP1 genes. Although additional studies will be needed to validate the importance of these regions in horses and the relevance of these regions in other species, the knowledge gained from the current study has the potential to be a step forward in unraveling the complex nature of hypersensitive reactions.
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Affiliation(s)
- Brandon D. Velie
- Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
- * E-mail:
| | - Merina Shrestha
- Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Liesbeth Franҫois
- Research Group Livestock Genetics, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Anouk Schurink
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, the Netherlands
| | - Yohannes G. Tesfayonas
- Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Anneleen Stinckens
- Research Group Livestock Genetics, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Sarah Blott
- School of Veterinary Medicine & Science, University of Nottingham, Leicestershire, United Kingdom
| | - Bart J. Ducro
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, the Netherlands
| | - Sofia Mikko
- Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Ruth Thomas
- Exmoor Pony Society, Cullompton, United Kingdom
| | - June E. Swinburne
- Animal DNA Diagnostics Ltd, Cambridgeshire, United Kingdom
- Animal Health Trust, Newmarket, United Kingdom
| | | | - Susanne Eriksson
- Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Nadine Buys
- Research Group Livestock Genetics, Department of Biosystems, KU Leuven, Leuven, Belgium
| | - Gabriella Lindgren
- Department of Animal Breeding & Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
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Schneider JF, Miles JR, Brown-Brandl TM, Nienaber JA, Rohrer GA, Vallet JL. Genomewide association analysis for average birth interval and stillbirth in swine. J Anim Sci 2016; 93:529-40. [PMID: 26020742 DOI: 10.2527/jas.2014-7899] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Reproductive efficiency has a great impact on the economic success of pork production. Stillborn pigs and average birth interval contribute to the number of pigs born alive in a litter. To better understand the underlying genetics of these traits, a genomewide association study was undertaken. Samples of DNA were collected and tested using the Illumina Porcine SNP60 BeadChip from 798 females farrowing over a 4-yr period (all first parity). Birth intervals and piglet birth status (stillborn or alive) were determined by videotaping each farrowing event. A total of 41,148 SNP were tested using the Bayes C option of GenSel (version 4.61) and 1-Mb windows. These 1-Mb windows explained proportions of 0.017, 0.002, 0.032, 0.029, and 0.030 of the total variation, respectively, for litter average birth interval after deletion of the last piglet born, last birth interval in the litter, number of stillborn piglets ignoring the last piglet born, number of stillborns in the last birth position, and percent stillborn ignoring the last piglet. Significant 1-Mb nonoverlapping SNP windows were identified by using a conservative approach requiring 1-Mb windows to have a genetic variance ≥1.0% of genomic variance and these were considered to be QTL. Quantitative trait loci were located for number of stillborn piglets ignoring the last piglet born (1 QTL), number of stillborns in the last birth position (1 QTL), and percent stillborn ignoring the last piglet (3 QTL). In addition, 2, 13, 3, and 6 suggestive 1-Mb nonoverlapping SNP windows were identified for litter average birth interval after deletion of the last piglet born, number of stillborn piglets ignoring the last piglet born, number of stillborns in the last birth position, and percent stillborn ignoring the last piglet, respectively. Possible candidate genes affecting both birth interval and stillbirth included () and (). Possible genes affecting only birth interval included (), and (), and those affecting only stillbirth included (), LOC100518697 (a nostrin-like gene), and (). The QTL and the suggestive 1-Mb nonoverlapping SNP windows may lead to genetic markers for marker assisted selection, marker assisted management, or genomic selection applications in commercial pig populations.
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29
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Sharma A, Lee JS, Dang CG, Sudrajad P, Kim HC, Yeon SH, Kang HS, Lee SH. Stories and Challenges of Genome Wide Association Studies in Livestock - A Review. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2015; 28:1371-9. [PMID: 26194229 PMCID: PMC4554843 DOI: 10.5713/ajas.14.0715] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 09/15/2014] [Revised: 12/09/2014] [Accepted: 01/30/2015] [Indexed: 11/27/2022]
Abstract
Undoubtedly livestock is one of the major contributors to the economy of any country. The economic value of livestock includes meat, dairy products, fiber, fertilizer etc. Understanding and identifying the associations of quantitative trait loci (QTL) with the economically important traits is believed to substantially benefit the livestock industry. The past two decades have seen a flurry of interest in mapping the QTL associated with traits of economic importance on the genome. With the availability of single nucleotide polymorphism chip of various densities it is possible to identify regions, QTL and genes on the genome that explain the association and its effect on the phenotype under consideration. Remarkable advancement has been seen in genome wide association studies (GWAS) since its inception till the present day. In this review we describe the progress and challenges of GWAS in various livestock species.
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Affiliation(s)
- Aditi Sharma
- Corresponding Authors: Aditi Sharma. Tel: +82-33-330-0600 (719), E-mail: / Seung-Hwan Lee. Tel: +82-033-330-0600 (717), E-mail:
| | | | | | | | | | | | | | - Seung-Hwan Lee
- Department of Animal Science and Biotechnology, Chung Nam National University, Daejeon 305-764,
Korea
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30
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Shrestha M, Eriksson S, Schurink A, Andersson LS, Sundquist M, Frey R, Broström H, Bergström T, Ducro B, Lindgren G. Genome-Wide Association Study of Insect Bite Hypersensitivity in Swedish-Born Icelandic Horses. J Hered 2015; 106:366-74. [PMID: 26026046 DOI: 10.1093/jhered/esv033] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2014] [Accepted: 05/08/2015] [Indexed: 12/18/2022] Open
Abstract
Insect bite hypersensitivity (IBH) is the most common allergic skin disease in horses and is caused by biting midges, mainly of the genus Culicoides. The disease predominantly comprises a type I hypersensitivity reaction, causing severe itching and discomfort that reduce the welfare and commercial value of the horse. It is a multifactorial disorder influenced by both genetic and environmental factors, with heritability ranging from 0.16 to 0.27 in various horse breeds. The worldwide prevalence in different horse breeds ranges from 3% to 60%; it is more than 50% in Icelandic horses exported to the European continent and approximately 8% in Swedish-born Icelandic horses. To minimize the influence of environmental effects, we analyzed Swedish-born Icelandic horses to identify genomic regions that regulate susceptibility to IBH. We performed a genome-wide association (GWA) study on 104 affected and 105 unaffected Icelandic horses genotyped using Illumina® EquineSNP50 Genotyping BeadChip. Quality control and population stratification analyses were performed with the GenABEL package in R (λ = 0.81). The association analysis was performed using the Bayesian variable selection method, Bayes C, implemented in GenSel software. The highest percentage of genetic variance was explained by the windows on X chromosomes (0.51% and 0.36% by 73 and 74 mb), 17 (0.34% by 77 mb), and 18 (0.34% by 26 mb). Overlapping regions with previous GWA studies were observed on chromosomes 7, 9, and 17. The windows identified in our study on chromosomes 7, 10, and 17 harbored immune system genes and are priorities for further investigation.
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Affiliation(s)
- Merina Shrestha
- From the Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden (Shrestha, Eriksson, Bergström, and Lindgren); Animal Breeding and Genomic Centre, Wageningen University, 6700 AH Wageningen, The Netherlands (Shrestha, Schurink, and Ducro); Capilet Genetics AB, SE-725 93 Västerås, Sweden (Andersson); Östra Greda Research Group, SE-387 91 Borgholm, Sweden (Sundquist); Norsholms Animal Hospital, SE-602 37 Norrköping, Sweden (Frey); and Department of Clinical Sciences, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden (Broström)
| | - Susanne Eriksson
- From the Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden (Shrestha, Eriksson, Bergström, and Lindgren); Animal Breeding and Genomic Centre, Wageningen University, 6700 AH Wageningen, The Netherlands (Shrestha, Schurink, and Ducro); Capilet Genetics AB, SE-725 93 Västerås, Sweden (Andersson); Östra Greda Research Group, SE-387 91 Borgholm, Sweden (Sundquist); Norsholms Animal Hospital, SE-602 37 Norrköping, Sweden (Frey); and Department of Clinical Sciences, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden (Broström)
| | - Anouk Schurink
- From the Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden (Shrestha, Eriksson, Bergström, and Lindgren); Animal Breeding and Genomic Centre, Wageningen University, 6700 AH Wageningen, The Netherlands (Shrestha, Schurink, and Ducro); Capilet Genetics AB, SE-725 93 Västerås, Sweden (Andersson); Östra Greda Research Group, SE-387 91 Borgholm, Sweden (Sundquist); Norsholms Animal Hospital, SE-602 37 Norrköping, Sweden (Frey); and Department of Clinical Sciences, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden (Broström)
| | - Lisa S Andersson
- From the Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden (Shrestha, Eriksson, Bergström, and Lindgren); Animal Breeding and Genomic Centre, Wageningen University, 6700 AH Wageningen, The Netherlands (Shrestha, Schurink, and Ducro); Capilet Genetics AB, SE-725 93 Västerås, Sweden (Andersson); Östra Greda Research Group, SE-387 91 Borgholm, Sweden (Sundquist); Norsholms Animal Hospital, SE-602 37 Norrköping, Sweden (Frey); and Department of Clinical Sciences, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden (Broström)
| | - Marie Sundquist
- From the Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden (Shrestha, Eriksson, Bergström, and Lindgren); Animal Breeding and Genomic Centre, Wageningen University, 6700 AH Wageningen, The Netherlands (Shrestha, Schurink, and Ducro); Capilet Genetics AB, SE-725 93 Västerås, Sweden (Andersson); Östra Greda Research Group, SE-387 91 Borgholm, Sweden (Sundquist); Norsholms Animal Hospital, SE-602 37 Norrköping, Sweden (Frey); and Department of Clinical Sciences, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden (Broström)
| | - Rebecka Frey
- From the Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden (Shrestha, Eriksson, Bergström, and Lindgren); Animal Breeding and Genomic Centre, Wageningen University, 6700 AH Wageningen, The Netherlands (Shrestha, Schurink, and Ducro); Capilet Genetics AB, SE-725 93 Västerås, Sweden (Andersson); Östra Greda Research Group, SE-387 91 Borgholm, Sweden (Sundquist); Norsholms Animal Hospital, SE-602 37 Norrköping, Sweden (Frey); and Department of Clinical Sciences, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden (Broström)
| | - Hans Broström
- From the Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden (Shrestha, Eriksson, Bergström, and Lindgren); Animal Breeding and Genomic Centre, Wageningen University, 6700 AH Wageningen, The Netherlands (Shrestha, Schurink, and Ducro); Capilet Genetics AB, SE-725 93 Västerås, Sweden (Andersson); Östra Greda Research Group, SE-387 91 Borgholm, Sweden (Sundquist); Norsholms Animal Hospital, SE-602 37 Norrköping, Sweden (Frey); and Department of Clinical Sciences, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden (Broström)
| | - Tomas Bergström
- From the Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden (Shrestha, Eriksson, Bergström, and Lindgren); Animal Breeding and Genomic Centre, Wageningen University, 6700 AH Wageningen, The Netherlands (Shrestha, Schurink, and Ducro); Capilet Genetics AB, SE-725 93 Västerås, Sweden (Andersson); Östra Greda Research Group, SE-387 91 Borgholm, Sweden (Sundquist); Norsholms Animal Hospital, SE-602 37 Norrköping, Sweden (Frey); and Department of Clinical Sciences, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden (Broström)
| | - Bart Ducro
- From the Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden (Shrestha, Eriksson, Bergström, and Lindgren); Animal Breeding and Genomic Centre, Wageningen University, 6700 AH Wageningen, The Netherlands (Shrestha, Schurink, and Ducro); Capilet Genetics AB, SE-725 93 Västerås, Sweden (Andersson); Östra Greda Research Group, SE-387 91 Borgholm, Sweden (Sundquist); Norsholms Animal Hospital, SE-602 37 Norrköping, Sweden (Frey); and Department of Clinical Sciences, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden (Broström)
| | - Gabriella Lindgren
- From the Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden (Shrestha, Eriksson, Bergström, and Lindgren); Animal Breeding and Genomic Centre, Wageningen University, 6700 AH Wageningen, The Netherlands (Shrestha, Schurink, and Ducro); Capilet Genetics AB, SE-725 93 Västerås, Sweden (Andersson); Östra Greda Research Group, SE-387 91 Borgholm, Sweden (Sundquist); Norsholms Animal Hospital, SE-602 37 Norrköping, Sweden (Frey); and Department of Clinical Sciences, Swedish University of Agricultural Sciences, SE-750 07 Uppsala, Sweden (Broström).
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31
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Brard S, Ricard A. Genome-wide association study for jumping performances in French sport horses. Anim Genet 2014; 46:78-81. [PMID: 25515185 DOI: 10.1111/age.12245] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/26/2014] [Indexed: 11/28/2022]
Abstract
A genome-wide association study was performed to identify single nucleotide polymorphisms (SNPs) associated with jumping performances of warmbloods in France. The 999 horses included in the study for jumping performances were sport horses [mostly Selle Français (68%), Anglo-Arabians (13%) and horses from the other European studbooks]. Horses were genotyped using the Illumina EquineSNP50 BeadChip. Of the 54,602 SNPs available on this chip, 44,424 were retained after quality testing. Phenotypes were obtained by deregressing official breeding values for jumping competitions to use all available information, that is, the performances of each horse as well as those of its relatives. Two models were used to test the effects of the genotypes on deregressed phenotypes: a single-marker mixed model and a haplotype-based mixed model (significant: P < 1E-05; suggestive: P < 1E-04). Both models included a polygenic effect to take into account familial structures. For jumping performances, one suggestive quantitative trait locus (QTL) located on chromosome 1 (BIEC2_31196 and BIEC2_31198) was detected with both models. This QTL explains 0.7% of the phenotypic variance. RYR2, a gene encoding a major calcium channel in cardiac muscle in humans and mice, is located 0.55 Mb from this potential QTL.
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Affiliation(s)
- S Brard
- INRA, GenPhySE (Génétique Physiologie et Systèmes d'Elevage), F-31326, Castanet-Tolosan, France; INP, ENSAT, GenPhySE (Génétique Physiologie et Systèmes d'Elevage), Université de Toulouse, F-31326, Castanet-Tolosan, France; INP, ENVT, GenPhySE (Génétique Physiologie et Systèmes d'Elevage), Université de Toulouse, F-31076, Toulouse, France
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32
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Finno CJ, Aleman M, Higgins RJ, Madigan JE, Bannasch DL. Risk of false positive genetic associations in complex traits with underlying population structure: a case study. Vet J 2014; 202:543-9. [PMID: 25278384 DOI: 10.1016/j.tvjl.2014.09.013] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/20/2014] [Revised: 09/08/2014] [Accepted: 09/13/2014] [Indexed: 10/24/2022]
Abstract
Genome-wide association (GWA) studies are widely used to investigate the genetic etiology of diseases in domestic animals. In the horse, GWA studies using 40-50,000 single nucleotide polymorphisms (SNPs) in sample sizes of 30-40 individuals, consisting of only 6-14 affected horses, have led to the discovery of genetic mutations for simple monogenic traits. Equine neuroaxonal dystrophy is a common inherited neurological disorder characterized by symmetric ataxia. A case-control GWA study was performed using genotypes from 42,819 SNP marker loci distributed across the genome in 99 clinically phenotyped Quarter horses (37 affected, 62 unaffected). A significant GWA was not achieved although a suggestive association was uncovered when only the most stringently phenotyped NAD-affected horses (n = 10) were included (chromosome 8:62130605 and 62134644 [log(1/P) = 5.56]). Candidate genes (PIK3C3, RIT2, and SYT4) within the associated region were excluded through sequencing, association testing of uncovered variants and quantitative RT-PCR. It was concluded that variants in PIK3C3, RIT2, and SYT4 are not responsible for equine neuroaxonal dystrophy. This study demonstrates the risk of false positive associations when performing GWA studies on complex traits and underlying population structure when using 40-50,000 SNP markers and small sample size.
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Affiliation(s)
- Carrie J Finno
- Department of Population Health and Reproduction, University of California, Davis, CA 95616, USA.
| | - Monica Aleman
- Department of Medicine and Epidemiology, University of California, Davis, CA 95616, USA
| | - Robert J Higgins
- Department of Pathology, Microbiology and Immunology, University of California, Davis, CA 95616, USA
| | - John E Madigan
- Department of Medicine and Epidemiology, University of California, Davis, CA 95616, USA
| | - Danika L Bannasch
- Department of Population Health and Reproduction, University of California, Davis, CA 95616, USA
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33
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Finno CJ, Bannasch DL. Applied equine genetics. Equine Vet J 2014; 46:538-44. [PMID: 24802051 DOI: 10.1111/evj.12294] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2013] [Accepted: 04/27/2014] [Indexed: 01/13/2023]
Abstract
Genome sequencing of the domestic horse and subsequent advancements in the field of equine genomics have led to an explosion in the development of tools for mapping traits and diseases and evaluating gene expression. The objective of this review is to discuss the current progress in the field of equine genomics, with specific emphasis on assembly and analysis of the reference sequence and subsequent sequencing of a Quarter Horse mare; the genomic tools currently available to researchers and their implications in genomic investigations in the horse; the genomics of Mendelian and non-Mendelian traits; the genomics of performance traits and considerations regarding genetic testing in the horse. The whole-genome sequencing of a Quarter Horse mare has provided additional variants within the equine genome that extend past single nucleotide polymorphisms to include insertions/deletions and copy number variants. Equine single nucleotide polymorphism arrays have allowed for the investigation of both simple and complex genetic traits while DNA microarrays have provided a tool for examining gene expression across various tissues and with certain disease conditions. Recently, next-generation sequencing has become more affordable and both whole-genome DNA sequencing and transcriptome-wide RNA sequencing are methodologies that are being applied to equine genomic research. Research in the field of equine genomics continues to expand rapidly as the cost of genotyping and sequencing decreases, resulting in a need for quality bioinformatics software and expertise to appropriately handle both the size and complexity of these data.
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Affiliation(s)
- C J Finno
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, USA
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34
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Kizilkaya K, Fernando RL, Garrick DJ. Reduction in accuracy of genomic prediction for ordered categorical data compared to continuous observations. Genet Sel Evol 2014. [PMID: 24912924 DOI: 10.1186/1297‐9686‐46‐37] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Accuracy of genomic prediction depends on number of records in the training population, heritability, effective population size, genetic architecture, and relatedness of training and validation populations. Many traits have ordered categories including reproductive performance and susceptibility or resistance to disease. Categorical scores are often recorded because they are easier to obtain than continuous observations. Bayesian linear regression has been extended to the threshold model for genomic prediction. The objective of this study was to quantify reductions in accuracy for ordinal categorical traits relative to continuous traits. METHODS Efficiency of genomic prediction was evaluated for heritabilities of 0.10, 0.25 or 0.50. Phenotypes were simulated for 2250 purebred animals using 50 QTL selected from actual 50k SNP (single nucleotide polymorphism) genotypes giving a proportion of causal to total loci of.0001. A Bayes C π threshold model simultaneously fitted all 50k markers except those that represented QTL. Estimated SNP effects were utilized to predict genomic breeding values in purebred (n = 239) or multibreed (n = 924) validation populations. Correlations between true and predicted genomic merit in validation populations were used to assess predictive ability. RESULTS Accuracies of genomic estimated breeding values ranged from 0.12 to 0.66 for purebred and from 0.04 to 0.53 for multibreed validation populations based on Bayes C π linear model analysis of the simulated underlying variable. Accuracies for ordinal categorical scores analyzed by the Bayes C π threshold model were 20% to 50% lower and ranged from 0.04 to 0.55 for purebred and from 0.01 to 0.44 for multibreed validation populations. Analysis of ordinal categorical scores using a linear model resulted in further reductions in accuracy. CONCLUSIONS Threshold traits result in markedly lower accuracy than a linear model on the underlying variable. To achieve an accuracy equal or greater than for continuous phenotypes with a training population of 1000 animals, a 2.25 fold increase in training population size was required for categorical scores fitted with the threshold model. The threshold model resulted in higher accuracies than the linear model and its advantage was greatest when training populations were smallest.
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Affiliation(s)
| | | | - Dorian J Garrick
- Department of Animal Science, Iowa State University, Ames IA 50011, USA.
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35
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Kizilkaya K, Fernando RL, Garrick DJ. Reduction in accuracy of genomic prediction for ordered categorical data compared to continuous observations. Genet Sel Evol 2014; 46:37. [PMID: 24912924 PMCID: PMC4094927 DOI: 10.1186/1297-9686-46-37] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2013] [Accepted: 04/17/2014] [Indexed: 12/04/2022] Open
Abstract
Background Accuracy of genomic prediction depends on number of records in the training
population, heritability, effective population size, genetic architecture,
and relatedness of training and validation populations. Many traits have
ordered categories including reproductive performance and susceptibility or
resistance to disease. Categorical scores are often recorded because they
are easier to obtain than continuous observations. Bayesian linear
regression has been extended to the threshold model for genomic prediction.
The objective of this study was to quantify reductions in accuracy for
ordinal categorical traits relative to continuous traits. Methods Efficiency of genomic prediction was evaluated for heritabilities of 0.10,
0.25 or 0.50. Phenotypes were simulated for 2250 purebred animals using 50
QTL selected from actual 50k SNP (single nucleotide polymorphism) genotypes
giving a proportion of causal to total loci of.0001. A Bayes C
π threshold model simultaneously fitted all 50k markers
except those that represented QTL. Estimated SNP effects were utilized to
predict genomic breeding values in purebred (n = 239) or multibreed (n =
924) validation populations. Correlations between true and predicted genomic
merit in validation populations were used to assess predictive ability. Results Accuracies of genomic estimated breeding values ranged from 0.12 to 0.66 for
purebred and from 0.04 to 0.53 for multibreed validation populations based
on Bayes C π linear model analysis of the simulated underlying
variable. Accuracies for ordinal categorical scores analyzed by the Bayes C
π threshold model were 20% to 50% lower and ranged from
0.04 to 0.55 for purebred and from 0.01 to 0.44 for multibreed validation
populations. Analysis of ordinal categorical scores using a linear model
resulted in further reductions in accuracy. Conclusions Threshold traits result in markedly lower accuracy than a linear model on the
underlying variable. To achieve an accuracy equal or greater than for
continuous phenotypes with a training population of 1000 animals, a 2.25
fold increase in training population size was required for categorical
scores fitted with the threshold model. The threshold model resulted in
higher accuracies than the linear model and its advantage was greatest when
training populations were smallest.
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Affiliation(s)
| | | | - Dorian J Garrick
- Department of Animal Science, Iowa State University, Ames IA 50011, USA.
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Wolc A, Arango J, Jankowski T, Dunn I, Settar P, Fulton JE, O'Sullivan NP, Preisinger R, Fernando RL, Garrick DJ, Dekkers JCM. Genome-wide association study for egg production and quality in layer chickens. J Anim Breed Genet 2014; 131:173-82. [PMID: 24628796 DOI: 10.1111/jbg.12086] [Citation(s) in RCA: 55] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2013] [Accepted: 02/14/2014] [Indexed: 12/21/2022]
Abstract
Discovery of genes with large effects on economically important traits has for many years been of interest to breeders. The development of SNP panels which cover the whole genome with high density and, more importantly, that can be genotyped on large numbers of individuals at relatively low cost, has opened new opportunities for genome-wide association studies (GWAS). The objective of this study was to find genomic regions associated with egg production and quality traits in layers using analysis methods developed for the purpose of whole genome prediction. Genotypes on over 4500 birds and phenotypes on over 13,000 hens from eight generations of a brown egg layer line were used. Birds were genotyped with a custom 42K Illumina SNP chip. Recorded traits included two egg production and 11 egg quality traits (puncture score, albumen height, yolk weight and shell colour) at early and late stages of production, as well as body weight and age at first egg. Egg weight was previously analysed by Wolc et al. (2012). The Bayesian whole genome prediction model--BayesB (Meuwissen et al. 2001) was used to locate 1 Mb regions that were most strongly associated with each trait. The posterior probability of a 1 Mb window contributing to genetic variation was used as the criterion for suggesting the presence of a quantitative trait locus (QTL) in that window. Depending upon the trait, from 1 to 7 significant (posterior probability >0.9) 1 Mb regions were found. The largest QTL, a region explaining 32% of genetic variance, was found on chr4 at 78 Mb for body weight but had pleiotropic effects on other traits. For the other traits, the largest effects were much smaller, explaining <7% of genetic variance, with regions on chromosomes 2, 12 and 17 explaining above 5% of genetic variance for albumen height, shell colour and egg production, respectively. In total, 45 of 1043 1 Mb windows were estimated to have a non-zero effect with posterior probability > 0.9 for one or more traits.
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Affiliation(s)
- A Wolc
- Department of Animal Science, Iowa State University, Ames, IA, USA; Hy-Line International, Dallas Center, IA, USA
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van der Meide NMA, Savelkoul HFJ, Meulenbroeks C, Ducro BJ, Tijhaar E. Evaluation of a diagnostic ELISA for insect bite hypersensitivity in horses using recombinant Obsoletus complex allergens. Vet J 2013; 200:31-7. [PMID: 24703873 DOI: 10.1016/j.tvjl.2013.12.004] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Revised: 11/28/2013] [Accepted: 12/04/2013] [Indexed: 10/25/2022]
Abstract
Culicoides spp. of the Obsoletus complex belong to the most important species of midge, involved in causing insect bite hypersensitivity (IBH) in horses in The Netherlands. The aim of the current study was to evaluate seven different Obsoletus complex-derived recombinant allergens (Cul o 1-Cul o 7) and to compare these with Obsoletus complex whole body extract (WBE) in an IgE ELISA, using sera of 194 clinically-confirmed cases of IBH and 175 unaffected horses. The highest test accuracy was obtained with WBE, followed by Cul o 2, 3 and 5. Two ELISAs with a combination of recombinant allergens, Combi-1 (Cul o 3, 5 and 7) and Combi-2 (Cul o 1, 2, 5 and 7) were additionally performed and both resulted in high test accuracies close to that obtained with WBE. Combi-1 resulted in the best sensitivity and specificity, both 89%. Both Combi-1 and Combi-2 performed less well with samples collected in winter, but over 70% of the IBH-affected horses could still be identified. In conclusion, a combination of three Obsoletus complex recombinant allergens (Cul o 3, 5 and 7) could potentially replace Obsoletus complex WBE in an IgE ELISA for diagnosis of IBH in horses.
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Affiliation(s)
- Nathalie M A van der Meide
- Cell Biology and Immunology Group, Wageningen University, De Elst 1, 6708 WD Wageningen, The Netherlands
| | - Huub F J Savelkoul
- Cell Biology and Immunology Group, Wageningen University, De Elst 1, 6708 WD Wageningen, The Netherlands
| | - Chantal Meulenbroeks
- Department of Infectious Diseases and Immunology, Faculty of Veterinary Medicine, Utrecht University, Utrecht, The Netherlands
| | - Bart J Ducro
- Animal Breeding and Genomics Centre, Wageningen University, Wageningen, The Netherlands
| | - Edwin Tijhaar
- Cell Biology and Immunology Group, Wageningen University, De Elst 1, 6708 WD Wageningen, The Netherlands.
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van den Berg I, Fritz S, Boichard D. QTL fine mapping with Bayes C(π): a simulation study. Genet Sel Evol 2013; 45:19. [PMID: 23782975 PMCID: PMC3700753 DOI: 10.1186/1297-9686-45-19] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2012] [Accepted: 06/07/2013] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Accurate QTL mapping is a prerequisite in the search for causative mutations. Bayesian genomic selection models that analyse many markers simultaneously should provide more accurate QTL detection results than single-marker models. Our objectives were to (a) evaluate by simulation the influence of heritability, number of QTL and number of records on the accuracy of QTL mapping with Bayes Cπ and Bayes C; (b) estimate the QTL status (homozygous vs. heterozygous) of the individuals analysed. This study focussed on the ten largest detected QTL, assuming they are candidates for further characterization. METHODS Our simulations were based on a true dairy cattle population genotyped for 38,277 phased markers. Some of these markers were considered biallelic QTL and used to generate corresponding phenotypes. Different numbers of records (4387 and 1500), heritability values (0.1, 0.4 and 0.7) and numbers of QTL (10, 100 and 1000) were studied. QTL detection was based on the posterior inclusion probability for individual markers, or on the sum of the posterior inclusion probabilities for consecutive markers, estimated using Bayes C or Bayes Cπ. The QTL status of the individuals was derived from the contrast between the sums of the SNP allelic effects of their chromosomal segments. RESULTS The proportion of markers with null effect (π) frequently did not reach convergence, leading to poor results for Bayes Cπ in QTL detection. Fixing π led to better results. Detection of the largest QTL was most accurate for medium to high heritability, for low to moderate numbers of QTL, and with a large number of records. The QTL status was accurately inferred when the distribution of the contrast between chromosomal segment effects was bimodal. CONCLUSIONS QTL detection is feasible with Bayes C. For QTL detection, it is recommended to use a large dataset and to focus on highly heritable traits and on the largest QTL. QTL statuses were inferred based on the distribution of the contrast between chromosomal segment effects.
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Affiliation(s)
- Irene van den Berg
- INRA, UMR1313 Génétique animale et biologie intégrative, Domaine de Vilvert, 78350 Jouy-en-Josas, France.
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