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Shall the Wild Boar Pass? A Genetically Assessed Ecological Corridor in the Geneva Region. SUSTAINABILITY 2022. [DOI: 10.3390/su14127463] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Landscape fragmentation caused by road infrastructures represents a major threat to the genetic diversity of a region. The resulting genetic isolation between subpopulations may lead to consanguinity, and consequently to population collapse and extinction. However, the construction of wildlife crossings can help maintain connectivity. In the present paper, we evaluated the genetic spatial structuring of populations of wild boars (Sus scrofa) in three areas of the Geneva region connected by an ecological corridor. Those areas are cut off either by a highway that is crossed by a wildlife overpass or by an anthropized sector. Genetic profiling with 9 nuclear microsatellite markers yielded 61 single profiles, which allowed for clustering, parentage, and linkage disequilibrium analyses, uncovering the populations’ genetic structure. We also evaluated whether the genetic structure was affected by the sex of individuals. In our analyses, all individuals clustered into a single genetic group, suggesting that no structure limited significantly the gene flow in the region. However, a recent admixture indicated a potential increase in the gene flow between two of the subpopulations due to the wildlife overpass, while the other part of the ecological corridor was not or was only partially functional. Genetic distances between males were significantly higher than between females, although the role of sex remains unclear as to its influence on population genetics. Finally, in order to avoid a subregion becoming fully isolated, urbanization planning should consider this genetic evaluation and proceed with further monitoring, especially by focusing on species more sensitive to landscape fragmentation.
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Hernández FA, Carr AN, Milleson MP, Merrill HR, Avery ML, Parker BM, Pylant CL, Austin JD, Wisely SM. Dispersal and Land Cover Contribute to Pseudorabies Virus Exposure in Invasive Wild Pigs. ECOHEALTH 2020; 17:498-511. [PMID: 33447876 PMCID: PMC8192353 DOI: 10.1007/s10393-020-01508-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Revised: 10/17/2020] [Accepted: 10/19/2020] [Indexed: 06/12/2023]
Abstract
We investigated the landscape epidemiology of a globally distributed mammal, the wild pig (Sus scrofa), in Florida (U.S.), where it is considered an invasive species and reservoir to pathogens that impact the health of people, domestic animals, and wildlife. Specifically, we tested the hypothesis that two commonly cited factors in disease transmission, connectivity among populations and abundant resources, would increase the likelihood of exposure to both pseudorabies virus (PrV) and Brucella spp. (bacterial agent of brucellosis) in wild pigs across the Kissimmee Valley of Florida. Using DNA from 348 wild pigs and sera from 320 individuals at 24 sites, we employed population genetic techniques to infer individual dispersal, and an Akaike information criterion framework to compare candidate logistic regression models that incorporated both dispersal and land cover composition. Our findings suggested that recent dispersal conferred higher odds of exposure to PrV, but not Brucella spp., among wild pigs throughout the Kissimmee Valley region. Odds of exposure also increased in association with agriculture and open canopy pine, prairie, and scrub habitats, likely because of highly localized resources within those land cover types. Because the effect of open canopy on PrV exposure reversed when agricultural cover was available, we suggest that small-scale resource distribution may be more important than overall resource abundance. Our results underscore the importance of studying and managing disease dynamics through multiple processes and spatial scales, particularly for non-native pathogens that threaten wildlife conservation, economy, and public health.
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Affiliation(s)
- Felipe A Hernández
- School of Natural Resources and Environment, University of Florida, Gainesville, FL, 32611, USA
- Facultad de Ciencias Veterinarias, Instituto de Medicina Preventiva Veterinaria, Universidad Austral de Chile, Edificio Federico Saelzer, 5º Piso, Campus Isla Teja S/N, Valdivia, Chile
| | - Amanda N Carr
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL, 32611, USA
| | - Michael P Milleson
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, Gainesville, FL, 32641, USA
| | - Hunter R Merrill
- Department of Agricultural and Biological Engineering, University of Florida, Gainesville, FL, 32611, USA
| | - Michael L Avery
- United States Department of Agriculture, Animal and Plant Health Inspection Service, Wildlife Services, National Wildlife Research Center, Gainesville, FL, 32641, USA
| | - Brandon M Parker
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL, 32611, USA
| | - Cortney L Pylant
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL, 32611, USA
| | - James D Austin
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL, 32611, USA
| | - Samantha M Wisely
- Department of Wildlife Ecology and Conservation, University of Florida, Gainesville, FL, 32611, USA.
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Buzan E, Potušek S, Urzi F, Pokorny B, Šprem N. Genetic characterisation of wild ungulates: successful isolation and analysis of DNA from widely available bones can be cheap, fast and easy. Zookeys 2020; 965:141-156. [PMID: 32973384 PMCID: PMC7483325 DOI: 10.3897/zookeys.965.54862] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2020] [Accepted: 08/03/2020] [Indexed: 01/02/2023] Open
Abstract
Genetic characterisation of wild ungulates can be a useful tool in wildlife management and in obtaining a greater understanding of their biological and ecological roles in a wider spatiotemporal context. Different ways of optimising methodologies and reducing the costs of genetic analyses using widely available bone tissues collected within regular hunting allocations were examined. Successful isolation and analysis of DNA from widely available bones can be cheap, fast and easy. In particular, this study explored the possibility of using bones for extracting high quality nuclear DNA for microsatellite analysis. The utility of applying a modified demineralisation process using two commercially available DNA isolation kits, which differ significantly in price, was evaluated. The sample sets included bones and, for comparison, muscle tissues from four wild ungulate species: chamois (Rupicapra rupicapra), roe deer (Capreolus capreolus), wild boar (Sus scrofa), and Alpine ibex (Capra ibex). For the recent bones, these results confirmed that the DNA concentrations and microsatellite amplification were sufficiently high, even when using low-cost kits, after prior demineralisation. For old bones, prior demineralisation and use of a specially designed isolation kit led to a more successful extraction of DNA. Besides reducing kit-related costs, low-cost kits are much faster and therefore make genetic analysis more efficient.
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Affiliation(s)
- Elena Buzan
- University of Primorska, Faculty of Mathematics, Natural Sciences and Information Technologies, Glagoljaška 8, 6000, Koper, SloveniaUniversity of PrimorskaKoperSlovenia
- Environmental Protection College, Trg mladosti 7, 3320, Velenje, SloveniaEnvironmental Protection CollegeVelenjeSlovenia
| | - Sandra Potušek
- University of Primorska, Faculty of Mathematics, Natural Sciences and Information Technologies, Glagoljaška 8, 6000, Koper, SloveniaUniversity of PrimorskaKoperSlovenia
| | - Felicita Urzi
- University of Primorska, Faculty of Mathematics, Natural Sciences and Information Technologies, Glagoljaška 8, 6000, Koper, SloveniaUniversity of PrimorskaKoperSlovenia
| | - Boštjan Pokorny
- Environmental Protection College, Trg mladosti 7, 3320, Velenje, SloveniaEnvironmental Protection CollegeVelenjeSlovenia
- Slovenian Forestry Institute, Večna pot 2, 1000, Ljubljana, SloveniaUniversity of ZagrebZagrebSlovenia
| | - Nikica Šprem
- Department of Fisheries, Apiculture, Wildlife Management and Special Zoology, University of Zagreb, Faculty of Agriculture, Svetošimunska cesta 25, 10000, Zagreb, CroatiaUniversity of ZagrebZagrebCroatia
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Invasion ecology of wild pigs (Sus scrofa) in Florida, USA: the role of humans in the expansion and colonization of an invasive wild ungulate. Biol Invasions 2018. [DOI: 10.1007/s10530-018-1667-6] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023]
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5
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Conyers CM, Allnutt TR, Hird HJ, Kaye J, Chisholm J. Development of a microsatellite-based method for the differentiation of European wild boar (Sus scrofa scrofa) from domestic pig breeds (Sus scrofa domestica) in food. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2012; 60:3341-3347. [PMID: 22409233 DOI: 10.1021/jf205109b] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/31/2023]
Abstract
Twenty microsatellites (simple sequence repeats, SSR) were used to discriminate wild boar from domestic pig and to identify mixtures of the two. Reference groups of wild boar and pig samples were collected from the UK and Europe for genetic assignment tests. Bayesian Analysis of Populations software (BAPs) gave 100% correct assignment for blind wild boar and pig samples and correctly identified mixed samples. DNA was extracted from 12 commercial food samples (11 labeled as containing wild boar) including patés, salamis, and sausage, and good SSR profiles were obtained. Eleven samples were correctly assigned as pig, and two as mixed meats. One sample sold as wild boar meat was clearly assigned as pig. A further 10 blind samples of meat cuts were analyzed, eight wild boar and two pig, and all were correctly assigned.
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Affiliation(s)
- Christine M Conyers
- The Food and Environment Research Agency, Sand Hutton, York, United Kingdom.
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6
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Mitochondrial and nuclear DNA analyses reveal pronounced genetic structuring in Tunisian wild boar Sus scrofa. EUR J WILDLIFE RES 2010. [DOI: 10.1007/s10344-010-0452-3] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
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Reiner G, Kliemt D, Willems H, Berge T, Fischer R, Köhler F, Hepp S, Hertrampf B, Daugschies A, Geldermann H, Mackenstedt U, Zahner H. Mapping of quantitative trait loci affecting resistance/susceptibility to Sarcocystis miescheriana in swine. Genomics 2007; 89:638-46. [PMID: 17336038 DOI: 10.1016/j.ygeno.2007.01.011] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2006] [Revised: 01/15/2007] [Accepted: 01/24/2007] [Indexed: 10/23/2022]
Abstract
The outcome of infectious diseases in vertebrates is under genetic control at least to some extent. In swine, e.g., marked differences in resistance/susceptibility to Sarcocystis miescheriana have been shown between Chinese Meishan and European Pietrain pigs, and these differences are associated with high heritabilities. A first step toward the identification of genes and polymorphisms causal for these differences may be the mapping of quantitative trait loci (QTLs). Considering clinical, immunological, and parasitological traits in the above model system, this survey represents the first QTL study on parasite resistance in pigs. QTL mapping was performed in 139 F(2) pigs of a Meishan/Pietrain family infected with S. miescheriana. Fourteen genome-wide significant QTLs were mapped to several chromosomal areas. Among others, major QTLs were identified for bradyzoite numbers in skeletal muscles (F = 17.4; p < 0.001) and for S. miescheriana-specific plasma IgG(2) levels determined 42 days p.i. (F = 20.9; p < 0.001). The QTLs were mapped to different regions of chromosome 7, i.e., to the region of the major histocompatibility complex (bradyzoites) and to an immunoglobulin heavy chain cluster, respectively. These results provide evidence for a direct and causal role for gene variants within these gene clusters (cis-acting) in differences in resistance to S. miescheriana.
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Affiliation(s)
- Gerald Reiner
- Department of Veterinary Clinical Sciences, University of Giessen, D-35392 Giessen, Germany.
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Abstract
Real-time PCR analysis is a sensitive template DNA quantitation strategy that has recently gained considerable attention in the forensic community. However, the utility of real-time PCR methods extends beyond quantitation and allows for simultaneous evaluation of template DNA extraction quality. This study presents a computational method that allows analysts to identify problematic samples with statistical reliability by comparing the amplification efficiencies of unknown template DNA samples with clean standards. In this study, assays with varying concentrations of tannic acid are used to evaluate and adjust sample-specific amplification efficiency calculation methods in order to optimize their inhibitor detection capabilities. Kinetic outlier detection and prediction boundaries are calculated to identify amplification efficiency outliers. Sample-specific amplification efficiencies calculated over a four-cycle interval starting at the threshold cycle can be used to detect reliably the presence of 0.4 ng of tannic acid in a 25 microL PCR reaction. This approach provides analysts with a precise measure of inhibition severity when template samples are compromised. Early detection of problematic samples allows analysts the opportunity to consider inhibitor mitigation strategies prior to genotype or DNA sequence analysis, thereby facilitating sample processing in high-throughput forensic operations.
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Affiliation(s)
- Elias J Kontanis
- Department of Ecology and Evolutionary Biology, Cornell University, Ithaca NY 14853, USA.
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Yue G, Stratil A, Cepica S, Schroffel J, Schroffelova D, Fontanesi L, Cagnazzo M, Moser G, Bartenschlager H, Reiner G, Geldermann H. Linkage and QTL mapping for Sus scrofa chromosome 7. J Anim Breed Genet 2003. [DOI: 10.1046/j.0931-2668.2003.00424.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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10
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Yue G, Russo V, Davoli R, Sternstein I, Brunsch C, Schroffelova D, Stratil A, Moser G, Bartenschlager H, Reiner G, Geldermann H. Linkage and QTL mapping for Sus scrofa chromosome 13. J Anim Breed Genet 2003. [DOI: 10.1046/j.0931-2668.2003.00430.x] [Citation(s) in RCA: 18] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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King AH, Jiang Z, Gibson JP, Haley CS, Archibald AL. Mapping quantitative trait loci affecting female reproductive traits on porcine chromosome 8. Biol Reprod 2003; 68:2172-9. [PMID: 12606397 DOI: 10.1095/biolreprod.102.012955] [Citation(s) in RCA: 72] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
An understanding of the genetic control of porcine female reproductive performance would offer the opportunity to utilize natural variation and improve selective breeding programs through marker-assisted selection. The Chinese Meishan is one of the most prolific pig breeds known, farrowing three to five more viable piglets per litter than the European Large White breed. This difference in prolificacy is attributed to the Meishan's superior prenatal survival levels. The present study utilized a three-generation cross in which the founder grandparental animals were purebred Meishan and Large White pigs in a scan for quantitative trait loci (QTL) on porcine chromosome 8 (SSC8) associated with reproductive performance. Reproductive traits, including number of corpora lutea (ovulation rate), teat number, litter size, and prenatal survival, were recorded for as many as 220 F2 females. Putative QTL for the related traits of litter size and prenatal survival were identified at the distal end of the long arm of SSC8. A physiological candidate gene, SPP1, was found to lie within the 95% confidence interval of these QTL. A suggestive QTL for teat number was revealed on the short arm of SSC8. The present study demonstrates, to our knowledge, the first independent confirmation of QTL for fecundity on SSC8, and these QTL regions provide a crucial starting point in the search for the causal genetic variants.
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Affiliation(s)
- Annemarie H King
- Roslin Institute (Edinburgh), Roslin, Midlothian, EH25 9PS, United Kingdom.
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12
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Wada Y, Akita T, Awata T, Furukawa T, Sugai N, Inage Y, Ishii K, Ito Y, Kobayashi E, Kusumoto H, Matsumoto T, Mikawa S, Miyake M, Murase A, Shimanuki S, Sugiyama T, Uchida Y, Yanai S, Yasue H. Quantitative trait loci (QTL) analysis in a Meishan x Göttingen cross population. Anim Genet 2000; 31:376-84. [PMID: 11167524 DOI: 10.1046/j.1365-2052.2000.00696.x] [Citation(s) in RCA: 100] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
In order to locate the genetic regions in the swine genome that are responsible for economically important traits, a resource population has been constructed by mating two female Meishan pigs with a male Göttingen miniature pig. In subsequent generations, 265 F2 offspring were produced from two F1 males and 19 F1 females. The F2 offspring were scored for eight traits including growth rate, teat number, vertebra number and backfat thickness, and genotyped for 318 genetic markers spanning the swine genome. Least-square analysis revealed quantitative trait loci (QTL) effects for vertebra number on chromosomes 1 and 2; for teat number on chromosomes 1 and 7; for birth weight on chromosome 1; for average daily gain between 4 and 13 weeks of age on chromosomes 9 and 10; for backfat thickness on chromosome 7; and for backskin thickness on chromosome 3.
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Affiliation(s)
- Y Wada
- Department of Animal Breeding and Genetics, National Institute of Animal Industry, Tsukuba, Ibaraki, Japan
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13
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Yerle M, Lahbib-Mansais Y, Pinton P, Robic A, Goureau A, Milan D, Gellin J. The cytogenetic map of the domestic pig. Mamm Genome 1997; 8:592-607. [PMID: 9250869 DOI: 10.1007/s003359900512] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
Affiliation(s)
- M Yerle
- INRA, Laboratoire de Génétique Cellulaire, BP27, 31326 Castanet-Tolosan, France
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14
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Alexander LJ, Rohrer GA, Beattie CW. Cloning and characterization of 414 polymorphic porcine microsatellites. Anim Genet 1996; 27:137-48. [PMID: 8759113 DOI: 10.1111/j.1365-2052.1996.tb00941.x] [Citation(s) in RCA: 61] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
We report the sequences, sizes, and number of alleles of 414 new porcine microsatellites that were cloned in our laboratory and 21 microsatellites derived from GenBank DNA sequences. We also confirm the usefulness of porcine microsatellite primer pairs derived from short interdispersed elements.
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Affiliation(s)
- L J Alexander
- US Department of Agriculture, U.S. Meat Animal Research Center, Clay Center NE 68933-0166, USA
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15
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Rohrer GA, Alexander LJ, Hu Z, Smith TP, Keele JW, Beattie CW. A comprehensive map of the porcine genome. Genome Res 1996; 6:371-91. [PMID: 8743988 DOI: 10.1101/gr.6.5.371] [Citation(s) in RCA: 318] [Impact Index Per Article: 11.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023]
Abstract
We report the highest density genetic linkage map for a livestock species produced to date. Three published maps for Sus scrofa were merged by genotyping virtually every publicly available microsatellite across a single reference population to yield 1042 linked loci, 536 of which are novel assignments, spanning 2286.2 cM (average interval 2.23 cM) in 19 linkage groups (18 autosomal and X chromosomes, n = 19). Linkage groups were constructed de novo and mapped by locus content to avoid propagation of errors in older genotypes. The physical and genetic maps were integrated with 123 informative loci assigned previously by fluorescence in situ hybridization (FISH). Fourteen linkage groups span the entire length of each chromosome. Coverage of chromosomes 11, 12, 15, and 18 will be evaluated as more markers are physically assigned. Marker-deficient regions were identified only on 11q1.7-qter and 14 cen-q1.2. Recombination rates (cM/Mbp) varied between and within chromosomes. Short chromosomal arms recombined at higher rates than long arms, and recombination was more frequent in telomeric regions than in pericentric regions. The high-resolution comprehensive map has the marker density needed to identify quantitative trait loci (QTL), implement marker-assisted selection or introgression and YAC contig construction or chromosomal microdissection.
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Affiliation(s)
- G A Rohrer
- U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS), U.S. Meat Animal Research Center (MARC), Clay Center, Nebraska 68933-0166, USA
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16
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Sun HS, Kirkpatrick BW. Exploiting dinucleotide microsatellites conserved among mammalian species. Mamm Genome 1996; 7:128-32. [PMID: 8835529 DOI: 10.1007/s003359900032] [Citation(s) in RCA: 26] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023]
Abstract
Dinucleotide microsatellites are useful for gene mapping projects. Depending upon definition of conservation, published estimates of dinucleotide microsatellite conservation levels vary dramatically (30% to 100%). This study focused on well-characterized genes that contain microsatellites in the human genome. The objective was to examine the feasibility of developing microsatellite markers within genes on the basis of the assumption of microsatellite conservation across distantly related species. Eight genes (Gamma-actin, carcinoembryonic antigen, apolipoprotein A-II, cardiac beta myosin heavy chain, laminin B2 chain, MHC class I CD8 alpha chain, c-reactive protein, and retinoblastoma susceptibility protein) containing large dinucleotide repeat units (N > or = 15), complete genomic structure information, and homologous gene sequences in a second species were selected. Heterologous primers were designed from conserved exon sequences flanking a microsatellite motif. PCR products from bovine and porcine genomic DNA were tested for the presence of microsatellite sequences by Southern blot hybridization with biotin-labeled (CA)12 oligonucleotides. Fragments containing microsatellites were cloned and sequenced. Homology was verified by sequence comparisons between human and corresponding bovine or porcine fragments. Four of sixteen (25%) cross-amplified PCR products contained dinucleotide repetitive sequences with repeat unit lengths of 5 to 23. Two dinucleotide repetitive sequences showed microsatellite length polymorphism, and an additional sequence displayed single-strand conformational polymorphism. Results from this study suggest that exploitation of conserved microsatellite sequences is a useful approach for developing specific genetic markers for comparative mapping purposes.
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Affiliation(s)
- H S Sun
- Department of Meat and Animal Science, University of Wisconsin-Madison 53706, USA
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17
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Smith TP, Rohrer GA, Alexander LJ, Troyer DL, Kirby-Dobbels KR, Janzen MA, Cornwell DL, Louis CF, Schook LB, Beattie CW. Directed integration of the physical and genetic linkage maps of swine chromosome 7 reveals that the SLA spans the centromere. Genome Res 1995; 5:259-71. [PMID: 8593613 DOI: 10.1101/gr.5.3.259] [Citation(s) in RCA: 55] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
The first integrated physical and genetic linkage map encompassing the entire swine chromosome 7 (SSC7) reveals that the porcine MHC (SLA) spans the centromere. A SLA class II antigen gene lies on the q arm, whereas class I and III genes lie on the p arm, suggesting that the presence of a centromere within the SLA does not preclude a functional complex. The SLA appears smaller than other mammalian MHC, as the genetic distance across two class I, three class II, and three class III SLA gene markers is only 1.1 cM. There are significant variations in recombination rates as a function of position along the chromosome, and the SLA lies in the region with the lowest rate. Furthermore, the directed integration approach used in this study was more efficient than previous efforts that emphasized the screening of large insert libraries for random microsatellites.
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Affiliation(s)
- T P Smith
- U.S. Department of Agriculture (USDA), Roman L. Hruska U.S. Meat Animal Research Center (MARC), Clay Center, Nebraska 68933, USA.
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18
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Riquet J, Milan D, Woloszyn N, Schmitz A, Pitel F, Frelat G, Gellin J. A linkage map with microsatellites isolated from swine flow-sorted chromosome 11. Mamm Genome 1995; 6:623-8. [PMID: 8535070 DOI: 10.1007/bf00352369] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/31/2023]
Abstract
We have developed a simple and efficient method to construct partial libraries of swine Chromosome (Chr) 11, starting with only 300 flow-sorted copies. DNA is amplified by PARM-PCR with primer containing at the 5'-end the sequence AGCU-. After amplification, digestion of PCR products with uracil DNA glycosylase generates cohesive ends corresponding to the SstI site. The amplified fragments can then be ligated in vector linearized with the SstI enzyme. Using five different primers, we PARM-PCR amplified and cloned swine Chr 11 DNA. These chromosome-specific libraries have been used to develop 14 different (TG)n microsatellites. Ten of these markers were assigned to Chr 11 by PCR analysis of a panel of Pig-Rodent somatic hybrids and by linkage analysis of the 171 individuals of the PiGMaP reference families. A complete linkage map of 147 cM of this chromosome was then realized by integrating existing markers.
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Affiliation(s)
- J Riquet
- Laboratoire de Génétique Cellulaire, INRA BP27, Castanet Tolosan, France
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Archibald AL, Haley CS, Brown JF, Couperwhite S, McQueen HA, Nicholson D, Coppieters W, Van de Weghe A, Stratil A, Winterø AK. The PiGMaP consortium linkage map of the pig (Sus scrofa). Mamm Genome 1995; 6:157-75. [PMID: 7749223 DOI: 10.1007/bf00293008] [Citation(s) in RCA: 269] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/26/2023]
Abstract
A linkage map of the porcine genome has been developed by segregation analysis of 239 genetic markers. Eighty-one of these markers correspond to known genes. Linkage groups have been assigned to all 18 autosomes plus the X Chromosome (Chr). As 69 of the markers on the linkage map have also been mapped physically (by others), there is significant integration of linkage and physical map data. Six informative markers failed to show linkage to these maps. As in other species, the genetic map of the heterogametic sex (male) was significantly shorter (approximately 16.5 Morgans) than the genetic map of the homogametic sex (female) (approximately 21.5 Morgans). The sex-averaged genetic map of the pig was estimated to be approximately 18 Morgans in length. Mapping information for 61 Type I loci (genes) enhances the contribution of the pig gene map to comparative gene mapping. Because the linkage map incorporates both highly polymorphic Type II loci, predominantly microsatellites, and Type I loci, it will be useful both for large experiments to map quantitative trait loci and for the subsequent isolation of trait genes following a comparative and candidate gene approach.
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Affiliation(s)
- A L Archibald
- Roslin Institute (Edinburgh), Midlothian, United Kingdom
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