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Ahmad HI, Ahmad MJ, Jabbir F, Ahmar S, Ahmad N, Elokil AA, Chen J. The Domestication Makeup: Evolution, Survival, and Challenges. Front Ecol Evol 2020. [DOI: 10.3389/fevo.2020.00103] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
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Niciura SCM, Cruvinel GG, Moraes CV, Bressani FA, Malagó Junior W, Benavides MV, de Chagas ACS. PCR-based genotyping of SNP markers in sheep. Mol Biol Rep 2018; 45:651-656. [PMID: 29869739 DOI: 10.1007/s11033-018-4206-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2018] [Accepted: 05/31/2018] [Indexed: 10/14/2022]
Abstract
Single nucleotide polymorphisms (SNPs) are the main type of variation in genome, enabling them to be associated with traits of economic importance in livestock. Genome-wide association studies (GWAS) have led to the discovery of SNPs associated with desirable traits in sheep. However, in these studies, SNPs are genotyped by high-throughput methods in genome scale, which are expensive and require sophisticated equipment and analysis methods. Therefore, the goal of this study was to develop a reliable, rapid, and inexpensive polymerase chain reaction (PCR)-based method to genotype a medium number of animals for a few candidate SNPs previously associated with desirable phenotypes in sheep by GWAS, using markers associated with gastrointestinal nematode resistance as a model. DNA extracted from white-blood cells of 150 sheep was submitted to PCR amplification followed by agarose gel electrophoresis and determination of banding pattern. Tetra-primer ARMS-PCR was successfully optimized after changes in annealing temperature; annealing and extension times; concentration of MgCl2 and DNA; ratios of inner, outer, forward and reverse primer; and addition of adjuvants, for genotyping the OAR2_14765360, OAR6_81718546, OAR11_62887032, and OAR12_69606944 SNPs in sheep. An extensive optimization of tetra-primer ARMS-PCR resulted in a suitable, simple, cost-effective PCR-based method of genotyping four SNP markers previously detected by chip arrays.
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Affiliation(s)
- Simone Cristina Méo Niciura
- Embrapa Pecuária Sudeste, Rodovia Washington Luiz, km 234, Fazenda Canchim, PO Box 339, São Carlos, SP, CEP 13560-970, Brazil.
| | | | - Caroline Valério Moraes
- Universidade Federal de São Carlos, Rodovia Washington Luiz, km 235, São Carlos, SP, CEP 13566-905, Brazil
| | - Flavia Aline Bressani
- Embrapa Pecuária Sudeste, Rodovia Washington Luiz, km 234, Fazenda Canchim, PO Box 339, São Carlos, SP, CEP 13560-970, Brazil
| | - Wilson Malagó Junior
- Embrapa Pecuária Sudeste, Rodovia Washington Luiz, km 234, Fazenda Canchim, PO Box 339, São Carlos, SP, CEP 13560-970, Brazil
| | - Magda Vieira Benavides
- Embrapa Pecuária Sul, Rodovia BR-153, Km 632,9, Vila Industrial, Bagé, RS, CEP 96401-970, Brazil
| | - Ana Carolina Souza de Chagas
- Embrapa Pecuária Sudeste, Rodovia Washington Luiz, km 234, Fazenda Canchim, PO Box 339, São Carlos, SP, CEP 13560-970, Brazil
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Genome-wide Target Enrichment-aided Chip Design: a 66 K SNP Chip for Cashmere Goat. Sci Rep 2017; 7:8621. [PMID: 28819310 PMCID: PMC5561203 DOI: 10.1038/s41598-017-09285-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2017] [Accepted: 07/14/2017] [Indexed: 01/24/2023] Open
Abstract
Compared with the commercially available single nucleotide polymorphism (SNP) chip based on the Bead Chip technology, the solution hybrid selection (SHS)-based target enrichment SNP chip is not only design-flexible, but also cost-effective for genotype sequencing. In this study, we propose to design an animal SNP chip using the SHS-based target enrichment strategy for the first time. As an update to the international collaboration on goat research, a 66 K SNP chip for cashmere goat was created from the whole-genome sequencing data of 73 individuals. Verification of this 66 K SNP chip with the whole-genome sequencing data of 436 cashmere goats showed that the SNP call rates was between 95.3% and 99.8%. The average sequencing depth for target SNPs were 40X. The capture regions were shown to be 200 bp that flank target SNPs. This chip was further tested in a genome-wide association analysis of cashmere fineness (fiber diameter). Several top hit loci were found marginally associated with signaling pathways involved in hair growth. These results demonstrate that the 66 K SNP chip is a useful tool in the genomic analyses of cashmere goats. The successful chip design shows that the SHS-based target enrichment strategy could be applied to SNP chip design in other species.
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Dymova MA, Zadorozhny AV, Mishukova OV, Khrapov EA, Druzhkova AS, Trifonov VA, Kichigin IG, Tishkin AA, Grushin SP, Filipenko ML. Mitochondrial DNA analysis of ancient sheep from Altai. Anim Genet 2017; 48:615-618. [DOI: 10.1111/age.12569] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/24/2017] [Indexed: 01/09/2023]
Affiliation(s)
- M. A. Dymova
- Laboratory of Paleogenomics; Novosibirsk State University; Novosibirsk 630090 Russian Federation
- Laboratory of Pharmacogenomics; Institute of Chemical Biology and Fundamental Medicine SB RAS; Novosibirsk 630090 Russian Federation
| | - A. V. Zadorozhny
- Laboratory of Pharmacogenomics; Institute of Chemical Biology and Fundamental Medicine SB RAS; Novosibirsk 630090 Russian Federation
| | - O. V. Mishukova
- Laboratory of Pharmacogenomics; Institute of Chemical Biology and Fundamental Medicine SB RAS; Novosibirsk 630090 Russian Federation
| | - E. A. Khrapov
- Laboratory of Pharmacogenomics; Institute of Chemical Biology and Fundamental Medicine SB RAS; Novosibirsk 630090 Russian Federation
| | - A. S. Druzhkova
- Institute of Molecular and Cell Biology SB RAS; Novosibirsk 630090 Russian Federation
| | - V. A. Trifonov
- Laboratory of Paleogenomics; Novosibirsk State University; Novosibirsk 630090 Russian Federation
- Institute of Molecular and Cell Biology SB RAS; Novosibirsk 630090 Russian Federation
| | - I. G. Kichigin
- Institute of Molecular and Cell Biology SB RAS; Novosibirsk 630090 Russian Federation
| | - A. A. Tishkin
- Laboratory of Paleogenomics; Novosibirsk State University; Novosibirsk 630090 Russian Federation
- Department of Archeology; Ethnography and Museology; Altai State University; Barnaul 656049 Russian Federation
| | - S. P. Grushin
- Laboratory of Paleogenomics; Novosibirsk State University; Novosibirsk 630090 Russian Federation
- Department of Archeology; Ethnography and Museology; Altai State University; Barnaul 656049 Russian Federation
| | - M. L. Filipenko
- Laboratory of Paleogenomics; Novosibirsk State University; Novosibirsk 630090 Russian Federation
- Laboratory of Pharmacogenomics; Institute of Chemical Biology and Fundamental Medicine SB RAS; Novosibirsk 630090 Russian Federation
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Roffler GH, Amish SJ, Smith S, Cosart T, Kardos M, Schwartz MK, Luikart G. SNP discovery in candidate adaptive genes using exon capture in a free-ranging alpine ungulate. Mol Ecol Resour 2016; 16:1147-64. [PMID: 27327375 DOI: 10.1111/1755-0998.12560] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2015] [Revised: 06/04/2016] [Accepted: 06/07/2016] [Indexed: 11/30/2022]
Abstract
Identification of genes underlying genomic signatures of natural selection is key to understanding adaptation to local conditions. We used targeted resequencing to identify SNP markers in 5321 candidate adaptive genes associated with known immunological, metabolic and growth functions in ovids and other ungulates. We selectively targeted 8161 exons in protein-coding and nearby 5' and 3' untranslated regions of chosen candidate genes. Targeted sequences were taken from bighorn sheep (Ovis canadensis) exon capture data and directly from the domestic sheep genome (Ovis aries v. 3; oviAri3). The bighorn sheep sequences used in the Dall's sheep (Ovis dalli dalli) exon capture aligned to 2350 genes on the oviAri3 genome with an average of 2 exons each. We developed a microfluidic qPCR-based SNP chip to genotype 476 Dall's sheep from locations across their range and test for patterns of selection. Using multiple corroborating approaches (lositan and bayescan), we detected 28 SNP loci potentially under selection. We additionally identified candidate loci significantly associated with latitude, longitude, precipitation and temperature, suggesting local environmental adaptation. The three methods demonstrated consistent support for natural selection on nine genes with immune and disease-regulating functions (e.g. Ovar-DRA, APC, BATF2, MAGEB18), cell regulation signalling pathways (e.g. KRIT1, PI3K, ORRC3), and respiratory health (CYSLTR1). Characterizing adaptive allele distributions from novel genetic techniques will facilitate investigation of the influence of environmental variation on local adaptation of a northern alpine ungulate throughout its range. This research demonstrated the utility of exon capture for gene-targeted SNP discovery and subsequent SNP chip genotyping using low-quality samples in a nonmodel species.
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Affiliation(s)
- Gretchen H Roffler
- Alaska Science Center, U.S. Geological Survey, 4210 University Drive, Anchorage, AK, 99508, USA.,Wildlife Biology Program, Department of Ecosystem Sciences and Conservation, College of Forestry and Conservation, University of Montana, Missoula, MT, 59812, USA
| | - Stephen J Amish
- Fish and Wildlife Genomics Group, Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | - Seth Smith
- Fish and Wildlife Genomics Group, Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | - Ted Cosart
- Fish and Wildlife Genomics Group, Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA
| | - Marty Kardos
- Fish and Wildlife Genomics Group, Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA.,Evolutionary Biology Centre, Uppsala University, SE-75236, Uppsala, Sweden
| | - Michael K Schwartz
- Evolutionary Biology Centre, Uppsala University, SE-75236, Uppsala, Sweden.,US Forest Service Rocky Mountain Research Station, National Genomics Center for Wildlife and Fish Conservation, 800 E. Beckwith Ave., Missoula, MT, 59801, USA
| | - Gordon Luikart
- Fish and Wildlife Genomics Group, Division of Biological Sciences, University of Montana, Missoula, MT, 59812, USA.,Flathead Lake Biological Station, University of Montana, Polson, MT, 59860, USA
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Abstract
Animal models are an important resource for studying human diseases. Genetically engineered mice are the most commonly used species and have made significant contributions to our understanding of basic biology, disease mechanisms, and drug development. However, they often fail to recreate important aspects of human diseases and thus can have limited utility as translational research tools. Developing disease models in species more similar to humans may provide a better setting in which to study disease pathogenesis and test new treatments. This unit provides an overview of the history of genetically engineered large animals and the techniques that have made their development possible. Factors to consider when planning a large animal model, including choice of species, type of modification and methodology, characterization, production methods, and regulatory compliance, are also covered. © 2016 by John Wiley & Sons, Inc.
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Pinnapureddy AR, Stayner C, McEwan J, Baddeley O, Forman J, Eccles MR. Large animal models of rare genetic disorders: sheep as phenotypically relevant models of human genetic disease. Orphanet J Rare Dis 2015; 10:107. [PMID: 26329332 PMCID: PMC4557632 DOI: 10.1186/s13023-015-0327-5] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/12/2015] [Accepted: 08/25/2015] [Indexed: 12/15/2022] Open
Abstract
Animals that accurately model human disease are invaluable in medical research, allowing a critical understanding of disease mechanisms, and the opportunity to evaluate the effect of therapeutic compounds in pre-clinical studies. Many types of animal models are used world-wide, with the most common being small laboratory animals, such as mice. However, rodents often do not faithfully replicate human disease, despite their predominant use in research. This discordancy is due in part to physiological differences, such as body size and longevity. In contrast, large animal models, including sheep, provide an alternative to mice for biomedical research due to their greater physiological parallels with humans. Completion of the full genome sequences of many species, and the advent of Next Generation Sequencing (NGS) technologies, means it is now feasible to screen large populations of domesticated animals for genetic variants that resemble human genetic diseases, and generate models that more accurately model rare human pathologies. In this review, we discuss the notion of using sheep as large animal models, and their advantages in modelling human genetic disease. We exemplify several existing naturally occurring ovine variants in genes that are orthologous to human disease genes, such as the Cln6 sheep model for Batten disease. These, and other sheep models, have contributed significantly to our understanding of the relevant human disease process, in addition to providing opportunities to trial new therapies in animals with similar body and organ size to humans. Therefore sheep are a significant species with respect to the modelling of rare genetic human disease, which we summarize in this review.
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Affiliation(s)
- Ashish R Pinnapureddy
- Department of Pathology, Dunedin School of Medicine, University of Otago, P.O. Box 913, Dunedin, 9054, New Zealand.
| | - Cherie Stayner
- Department of Pathology, Dunedin School of Medicine, University of Otago, P.O. Box 913, Dunedin, 9054, New Zealand.
| | - John McEwan
- AgResearch, Invermay Agricultural Centre, Mosgiel, New Zealand.
| | - Olivia Baddeley
- New Zealand Organisation for Rare Disorders, Wellington, New Zealand.
| | - John Forman
- New Zealand Organisation for Rare Disorders, Wellington, New Zealand.
| | - Michael R Eccles
- Department of Pathology, Dunedin School of Medicine, University of Otago, P.O. Box 913, Dunedin, 9054, New Zealand. .,Maurice Wilkins Centre for Molecular Biodiscovery, Level 2, 3A Symonds Street, Auckland, New Zealand.
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Greber D, Doherr M, Drögemüller C, Steiner A. Occurrence of congenital disorders in Swiss sheep. Acta Vet Scand 2013; 55:27. [PMID: 23521894 PMCID: PMC3616986 DOI: 10.1186/1751-0147-55-27] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2013] [Accepted: 03/12/2013] [Indexed: 11/19/2022] Open
Abstract
BACKGROUND The rates of congenital disorders in Swiss sheep were determined by a questionnaire which was sent to 3,183 members of the Swiss Sheep Breeders' Association. FINDINGS A total of 993 questionnaires were returned, giving a response rate of 31.2%. Of these, 862 questionnaires originated from farms keeping one of the predominant Swiss sheep breeds: Swiss White Alpine sheep, Brown-Headed Meat sheep, Swiss Black Brown Mountain sheep and Valais Blacknose sheep. During a 10-year-period, entropion was reported in 33.6% of the farms, brachygnathia inferior in 29.5%, abdominal/umbilical hernia in 15.9%, cryptorchidism in 10.5% and torticollis in 10.5%. The most significant difference between the four breeds (P<0.001) occurred for entropion in Swiss White Alpine sheep and Brown-Headed Meat sheep, brachygnathia inferior in Swiss Black Brown Mountain sheep, and scrotal/inguinal hernia in Valais Blacknose sheep. The Swiss White Alpine breed showed a significantly higher animal prevalence of entropion (6.2% in 2011 and 5.5% in 2012) than other breeds (P<0.001). CONCLUSIONS These findings indicate a breed-specific necessity for action, particularly regarding Swiss animal welfare legislation, especially entropion in Swiss White Alpine sheep is concerned. In general, careful selection of breeding stock is to be recommended.
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Affiliation(s)
- Deborah Greber
- Clinic for Ruminants, Vetsuisse Faculty, University of Bern, Bremgartenstrasse 109a, Bern 3001, Switzerland
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