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Gomes PT, Rosse IC, Moraes LÂG, Kalapothakis E, de Azevedo CS, Cardoso DC, Cristiano MP. Genetic diversity and relatedness in captive collared peccaries Dicotyles tajacu (Linnaeus, 1758) (Cetartiodactyla: Tayassuidae) estimated by microsatellite genotyping using high-throughput sequencing: Implications for their conservation and reintroduction. Zoo Biol 2023; 42:789-796. [PMID: 37466265 DOI: 10.1002/zoo.21796] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Revised: 05/04/2023] [Accepted: 07/07/2023] [Indexed: 07/20/2023]
Abstract
The global population of Dicotyles tajacu (Linnaeus, 1758) (Cetartiodactyla: Tayassuidae), commonly known as the collared peccary and distributed in the Neotropics, is currently in decline due to anthropogenic pressures. In this study, five microsatellite loci were used to genetically characterize a group of 20 captive-born collared peccaries intended for reintroduction. This study aimed to evaluate the genetic diversity and relatedness of captive individuals using microsatellite markers. The genetic data generated were used to evaluate the viability of the reintroduction and to propose measures for the management and conservation of this species. In this study, we found relatively high genetic diversity indices, indicating that the group was genetically diverse. Inbreeding coefficients with negative values were observed, indicating an excess of alleles in heterozygosis and an absence of inbreeding. One locus showed deviation from Hardy-Weinberg equilibrium, which may have been caused by the mixing of individuals from different origins. Relatedness analysis indicated that some individuals were highly related, with coefficients indicating they may be first-degree relatives. Our findings indicate that the studied group has enough genetic diversity to be released into nature, but the high individual relatedness found would require the adoption of strategies after the release of animals in the wild to ensure their persistence.
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Affiliation(s)
- Paula Teixeira Gomes
- Programa de Pós-Graduação em Ecologia de Biomas Tropicais, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto (UFOP), Ouro Preto, Minas Gerais, Brazil
| | - Izinara Cruz Rosse
- Departamento de Farmácia, Programa de Pós-Graduação em Biotecnologia, Universidade Federal de Ouro Preto (UFOP), Ouro Preto, Minas Gerais, Brazil
- Laboratório Multiusuário de Bioinformática da Universidade Federal de Ouro Preto (UFOP), Núcleo de Pesquisa em Ciências Biológicas (NUPEB), Ouro Preto, Minas Gerais, Brazil
| | - Lauro Ângelo Gonçalves Moraes
- Laboratório Multiusuário de Bioinformática da Universidade Federal de Ouro Preto (UFOP), Núcleo de Pesquisa em Ciências Biológicas (NUPEB), Ouro Preto, Minas Gerais, Brazil
| | - Evanguedes Kalapothakis
- Departamento de Genética, Evolução e Ecologia, Laboratório de Biotecnologia e Marcadores Moleculares, Instituto de Ciências Biológicas, Universidade Federal de Minas Gerais (UFMG), Belo Horizonte, Minas Gerais, Brazil
| | - Cristiano Schetini de Azevedo
- Programa de Pós-Graduação em Ecologia de Biomas Tropicais, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto (UFOP), Ouro Preto, Minas Gerais, Brazil
- Departamento de Biodiversidade Evolução e Meio Ambiente, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto (UFOP), Ouro Preto, Minas Gerais, Brazil
| | - Danon Clemes Cardoso
- Programa de Pós-Graduação em Ecologia de Biomas Tropicais, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto (UFOP), Ouro Preto, Minas Gerais, Brazil
- Departamento de Biodiversidade Evolução e Meio Ambiente, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto (UFOP), Ouro Preto, Minas Gerais, Brazil
| | - Maykon Passos Cristiano
- Programa de Pós-Graduação em Ecologia de Biomas Tropicais, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto (UFOP), Ouro Preto, Minas Gerais, Brazil
- Departamento de Biodiversidade Evolução e Meio Ambiente, Instituto de Ciências Exatas e Biológicas, Universidade Federal de Ouro Preto (UFOP), Ouro Preto, Minas Gerais, Brazil
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Hagemann J, Conejero C, Stillfried M, Mentaberre G, Castillo-Contreras R, Fickel J, López-Olvera JR. Genetic population structure defines wild boar as an urban exploiter species in Barcelona, Spain. THE SCIENCE OF THE TOTAL ENVIRONMENT 2022; 833:155126. [PMID: 35405223 DOI: 10.1016/j.scitotenv.2022.155126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Revised: 03/27/2022] [Accepted: 04/05/2022] [Indexed: 06/14/2023]
Abstract
Urban wildlife ecology is gaining relevance as metropolitan areas grow throughout the world, reducing natural habitats and creating new ecological niches. However, knowledge is still scarce about the colonisation processes of such urban niches, the establishment of new communities, populations and/or species, and the related changes in behaviour and life histories of urban wildlife. Wild boar (Sus scrofa) has successfully colonised urban niches throughout Europe. The aim of this study is to unveil the processes driving the establishment and maintenance of an urban wild boar population by analysing its genetic structure. A set of 19 microsatellite loci was used to test whether urban wild boars in Barcelona, Spain, are an isolated population or if gene flow prevents genetic differentiation between rural and urban wild boars. This knowledge will contribute to the understanding of the effects of synurbisation and the associated management measures on the genetic change of large mammals in urban ecosystems. Despite the unidirectional gene flow from rural to urban areas, the urban wild boars in Barcelona form an island population genotypically differentiated from the surrounding rural ones. The comparison with previous genetic studies of urban wild boar populations suggests that forest patches act as suitable islands for wild boar genetic differentiation. Previous results and the genetic structure of the urban wild boar population in Barcelona classify wild boar as an urban exploiter species. These wild boar peri-urban island populations are responsible for conflict with humans and thus should be managed by reducing the attractiveness of urban areas. The management of peri-urban wild boar populations should aim at reducing migration into urban areas and preventing phenotypic changes (either genetic or plastic) causing habituation of wild boars to humans and urban environments.
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Affiliation(s)
- Justus Hagemann
- Leibniz-Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, D-10315 Berlin, Germany; University of Potsdam, Evolutionary Adaptive Genomics, Institute for Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Carles Conejero
- Wildlife Ecology & Health group (WE&H) and Servei d'Ecopatologia de Fauna Salvatge (SEFaS), Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Barcelona, Spain
| | - Milena Stillfried
- Leibniz-Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, D-10315 Berlin, Germany
| | - Gregorio Mentaberre
- Wildlife Ecology & Health group (WE&H) and Servei d'Ecopatologia de Fauna Salvatge (SEFaS), Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Barcelona, Spain; Departament de Ciència Animal, Escola Tècnica Superior d'Enginyeria Agraria (ETSEA), Universitat de Lleida (UdL), 25098 Lleida, Spain
| | - Raquel Castillo-Contreras
- Wildlife Ecology & Health group (WE&H) and Servei d'Ecopatologia de Fauna Salvatge (SEFaS), Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Barcelona, Spain
| | - Jörns Fickel
- Leibniz-Institute for Zoo and Wildlife Research, Alfred-Kowalke-Str. 17, D-10315 Berlin, Germany; University of Potsdam, Molecular Ecology and Evolution, Institute for Biochemistry and Biology, Karl-Liebknecht-Str. 24-25, 14476 Potsdam, Germany
| | - Jorge Ramón López-Olvera
- Wildlife Ecology & Health group (WE&H) and Servei d'Ecopatologia de Fauna Salvatge (SEFaS), Departament de Medicina i Cirurgia Animals, Universitat Autònoma de Barcelona (UAB), 08193 Bellaterra, Barcelona, Spain.
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3
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Large microsatellite shifts in wild boar after the Fukushima accident. Glob Ecol Conserv 2022. [DOI: 10.1016/j.gecco.2022.e02059] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
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4
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Leonardo DE, Nogueira-Filho SLG, de Góes Maciel F, Biondo C, Mendl M, Nogueira SSDC. Third-party conflict interventions are kin biased in captive white-lipped peccaries (Mammalia, Tayassuidae). Behav Processes 2021; 193:104524. [PMID: 34592345 DOI: 10.1016/j.beproc.2021.104524] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2020] [Revised: 10/05/2020] [Accepted: 09/24/2021] [Indexed: 10/20/2022]
Abstract
Third-party interventions may regulate conflicts to reduce aggression and promote cohesion amongst group members, but are rarely documented in ungulates. The white-lipped peccary (Tayassu pecari) lives in mixed-sex herds of hundreds of individuals in Neotropical forests, which are likely to benefit from mechanisms that sustain social cohesiveness. We examined third-party conflict interventions between individuals in captive groups of white-lipped peccaries. During a period of 60 days, we recorded agonistic interactions and occurrences of third-party conflict interventions, and estimated the genetic relatedness between the individuals involved using multilocus microsatellite genotypes. Most third-party conflict interventions were by the dominant male of each group, resulting in conflict termination 100% of the time. Our results also revealed that white-lipped peccaries favour their closest relatives and that individuals showed lower levels of aggression towards kin than to non-kin, and interventions on behalf of kin were more frequent than on behalf of non-kin. Our findings support the idea that genetic relatedness is fundamental in both social structure and third-party conflict interventions in this species, allowing us to suggest that kin selection could have a key role in the evolution of social behaviour of white-lipped peccaries.
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Affiliation(s)
| | - Sérgio Luiz Gama Nogueira-Filho
- Laboratório de Etologia Aplicada, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil; National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN-TREE), Bahia, Brazil
| | - Fernanda de Góes Maciel
- Centro de Ciências Naturais e Humanas (CCNH), Universidade Federal do ABC (UFABC), São Bernardo do Campo, São Paulo, Brazil
| | - Cibele Biondo
- Centro de Ciências Naturais e Humanas (CCNH), Universidade Federal do ABC (UFABC), São Bernardo do Campo, São Paulo, Brazil
| | - Michael Mendl
- Bristol Veterinary School, University of Bristol, Langford House, Langford, UK
| | - Selene Siqueira da Cunha Nogueira
- Laboratório de Etologia Aplicada, Universidade Estadual de Santa Cruz, Ilhéus, Bahia, Brazil; National Institute of Science and Technology in Interdisciplinary and Transdisciplinary Studies in Ecology and Evolution (INCT IN-TREE), Bahia, Brazil.
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Anderson D, Negishi Y, Ishiniwa H, Okuda K, Hinton TG, Toma R, Nagata J, Tamate HB, Kaneko S. Introgression dynamics from invasive pigs into wild boar following the March 2011 natural and anthropogenic disasters at Fukushima. Proc Biol Sci 2021; 288:20210874. [PMID: 34187197 PMCID: PMC8242833 DOI: 10.1098/rspb.2021.0874] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Natural and anthropogenic disasters have the capability to cause sudden extrinsic environmental changes and long-lasting perturbations including invasive species, species expansion and influence evolution as selective pressures force adaption. Such disasters occurred on 11 March 2011, in Fukushima, Japan, when an earthquake, tsunami and meltdown of a nuclear power plant all drastically reformed anthropogenic land use. Using genetic data, we demonstrate how wild boar (Sus scrofa leucomystax) have persevered against these environmental changes, including an invasion of escaped domestic pigs (Sus scrofa domesticus). Concurrently, we show evidence of successful hybridization between pigs and native wild boar in this area; however in future offspring, the pig legacy has been diluted through time. We speculate that the range expansion dynamics inhibit long-term introgression and introgressed alleles will continue to decrease at each generation while only maternally inherited organelles will persist. Using the gene flow data among wild boar, we assume that offspring from hybrid lineages will continue dispersal north at low frequencies as climates warm. We conclude that future risks for wild boar in this area include intraspecies competition, revitalization of human-related disruptions and disease outbreaks.
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Affiliation(s)
- Donovan Anderson
- Symbiotic Systems Science and Technology, Fukushima University, Fukushima City, Fukushima, Japan
| | - Yuki Negishi
- Symbiotic Systems Science and Technology, Fukushima University, Fukushima City, Fukushima, Japan
| | - Hiroko Ishiniwa
- Institute of Environmental Radioactivity, Fukushima University, Fukushima City, Fukushima, Japan
| | - Kei Okuda
- Faculty of Human Environmental Studies, Hiroshima Shudo University, Hiroshima, Hiroshima, Japan
| | - Thomas G Hinton
- Centre for Environmental Radioactivity, Faculty of Environmental Sciences and Natural Resource Management, Norwegian University of Life Sciences, Ås, Norway
| | - Rio Toma
- Symbiotic Systems Science and Technology, Fukushima University, Fukushima City, Fukushima, Japan
| | - Junco Nagata
- Forestry and Forest Products Research Institute, Tsukuba, Ibaraki, Japan
| | | | - Shingo Kaneko
- Symbiotic Systems Science and Technology, Fukushima University, Fukushima City, Fukushima, Japan.,Institute of Environmental Radioactivity, Fukushima University, Fukushima City, Fukushima, Japan
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Hollifield MK, Lourenco D, Bermann M, Howard JT, Misztal I. Determining the stability of accuracy of genomic estimated breeding values in future generations in commercial pig populations. J Anim Sci 2021; 99:6176311. [PMID: 33733277 PMCID: PMC8051850 DOI: 10.1093/jas/skab085] [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] [Received: 11/30/2020] [Accepted: 03/15/2021] [Indexed: 01/08/2023] Open
Abstract
Genomic information has a limited dimensionality (number of independent chromosome segments [Me]) related to the effective population size. Under the additive model, the persistence of genomic accuracies over generations should be high when the nongenomic information (pedigree and phenotypes) is equivalent to Me animals with high accuracy. The objective of this study was to evaluate the decay in accuracy over time and to compare the magnitude of decay with varying quantities of data and with traits of low and moderate heritability. The dataset included 161,897 phenotypic records for a growth trait (GT) and 27,669 phenotypic records for a fitness trait (FT) related to prolificacy in a population with dimensionality around 5,000. The pedigree included 404,979 animals from 2008 to 2020, of which 55,118 were genotyped. Two single-trait models were used with all ancestral data and sliding subsets of 3-, 2-, and 1-generation intervals. Single-step genomic best linear unbiased prediction (ssGBLUP) was used to compute genomic estimated breeding values (GEBV). Estimated accuracies were calculated by the linear regression (LR) method. The validation population consisted of single generations succeeding the training population and continued forward for all generations available. The average accuracy for the first generation after training with all ancestral data was 0.69 and 0.46 for GT and FT, respectively. The average decay in accuracy from the first generation after training to generation 9 was −0.13 and −0.19 for GT and FT, respectively. The persistence of accuracy improves with more data. Old data have a limited impact on the predictions for young animals for a trait with a large amount of information but a bigger impact for a trait with less information.
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Affiliation(s)
| | - Daniela Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - Matias Bermann
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | | | - Ignacy Misztal
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
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7
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Genetic diversity and population structure of white-lipped peccaries (Tayassu pecari) in the Pantanal, Cerrado and Atlantic Forest from Brazil. Mamm Biol 2019. [DOI: 10.1016/j.mambio.2019.03.001] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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8
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Leite DA, Keuroghlian A, Rufo DA, Miyaki CY, Biondo C. Genetic evidence of promiscuity in a mammal without apparent sexual dimorphism, the white-lipped peccary (Tayassu pecari). Mamm Biol 2018. [DOI: 10.1016/j.mambio.2018.05.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Fève K, Foissac S, Pinton A, Mompart F, Esquerré D, Faraut T, Yerle M, Riquet J. Identification of a t(3;4)(p1.3;q1.5) translocation breakpoint in pigs using somatic cell hybrid mapping and high-resolution mate-pair sequencing. PLoS One 2017; 12:e0187617. [PMID: 29121641 PMCID: PMC5679599 DOI: 10.1371/journal.pone.0187617] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2017] [Accepted: 10/23/2017] [Indexed: 02/02/2023] Open
Abstract
Reciprocal translocations are the most frequently occurring constitutional structural rearrangements in mammalian genomes. In phenotypically normal pigs, an incidence of 1/200 is estimated for such rearrangements. Even if constitutional translocations do not necessarily induce defects and diseases, they are responsible for significant economic losses in domestic animals due to reproduction failures. Over the last 30 years, advances in molecular and cytogenetic technologies have led to major improvements in the resolution of the characterization of translocation events. Characterization of translocation breakpoints helps to decipher the mechanisms that lead to such rearrangements and the functions of the genes that are involved in the translocation. Here, we describe the fine characterization of a reciprocal translocation t(3;4) (p1.3;q1.5) detected in a pig line. The breakpoint was identified at the base-pair level using a positional cloning and chromosome walking strategy in somatic cell hybrids that were generated from an animal that carries this translocation. We show that this translocation occurs within the ADAMTSL4 gene and results in a loss of expression in homozygous carriers. In addition, by taking this translocation as a model, we used a whole-genome next-generation mate-pair sequencing approach on pooled individuals to evaluate this strategy for high-throughput screening of structural rearrangements.
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Affiliation(s)
- Katia Fève
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet-Tolosan, France
| | - Sylvain Foissac
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet-Tolosan, France
| | - Alain Pinton
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet-Tolosan, France
| | - Florence Mompart
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet-Tolosan, France
| | - Diane Esquerré
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet-Tolosan, France
| | - Thomas Faraut
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet-Tolosan, France
| | - Martine Yerle
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet-Tolosan, France
| | - Juliette Riquet
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Castanet-Tolosan, France
- * E-mail:
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10
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Kim JG, Nonneman D, Kim DW, Shin S, Rohrer GA. Polymorphism in the intron 20 of porcine O-linked N-acetylglucosamine transferase. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2017; 30:1086-1092. [PMID: 28669142 PMCID: PMC5494481 DOI: 10.5713/ajas.17.0143] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/01/2017] [Revised: 05/22/2017] [Accepted: 05/22/2017] [Indexed: 11/27/2022]
Abstract
Objective O-linked N-acetylglucosamine (O-GlcNAc) transferase (OGT) catalyzes the addition of O-GlcNAc and GlcNAcylation has extensive crosstalk with phosphorylation to regulate signaling and transcription. Pig OGT is located near the region of chromosome X that affects follicle stimulating hormone level and testes size. The objective of this study was to find the variations of OGT between European and Chinese pigs. Methods Pigs were tested initially for polymorphism in OGT among European and Chinese pigs by polymerase chain reaction and sequencing at the U.S. Meat Animal Research Center (USMARC). The polymorphism was also determined in an independent population of pigs including European and Chinese Meishan (ME) breeds at the National Institute of Animal Science (NIAS, RDA, Korea). Results The intron 20 of OGT from European and Chinese pigs was 514 and 233 bp, respectively, in the pigs tested initially. They included 1 White composite (WC) boar and 7 sows (2 Minzu×WC, 2 Duroc [DU]×WC, 2 ME×WC, 1 Fengzing×WC) at USMARC. The 281-bp difference was due to an inserted 276-bp element and GACTT in European pigs. When additional WC and ME boars, the grandparents that were used to generate the 1/2ME×1/2WC parents, and the 84 boars of 16 litters from mating of 1/2ME×1/2WC parents were analyzed, the breeds of origin of X chromosome quantitative trait locus (QTL) were confirmed. The polymorphism was determined in an independent population of pigs including DU, Landrace, Yorkshire, and ME breeds at NIAS. OGT was placed at position 67 cM on the chromosome X of the USMARC swine linkage map. Conclusion There was complete concordance with the insertion in European pigs at USMARC and NIAS. This polymorphism could be a useful marker to identify the breed of origin of X chromosome QTL in pigs produced by crossbreeding Chinese and European pigs.
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Affiliation(s)
- Jong Gug Kim
- Department of Animal Sciences, College of Agriculture and Life Science, and Institute of Molecular Biology and Genetics, Chonbuk National University, Jeonju 54896, Korea
| | - Dan Nonneman
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE 68933-0166, USA
| | - Doo-Wan Kim
- Swine Science Division, National Institute of Animal Science, RDA, Cheonan 31000, Korea
| | - Sangsu Shin
- Department of Animal Biotechnology, Kyungpook National University, Sangju 37224, Korea
| | - Gary A Rohrer
- U.S. Department of Agriculture, Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE 68933-0166, USA
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11
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Labuschagne C, Dalton DL, Grobler JP, Kotzé A. SNP discovery and characterisation in White Rhino (Ceratotherium simum) with application to parentage assignment. Genet Mol Biol 2017; 40:84-92. [PMID: 28170027 PMCID: PMC5409770 DOI: 10.1590/1678-4685-gmb-2016-0058] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Accepted: 05/17/2016] [Indexed: 11/24/2022] Open
Abstract
The white rhino is one of the great success stories of modern wildlife conservation,
growing from as few as 50-100 animals in the 1880s, to approximately 20,000 white
rhinoceros remaining today. However, illegal trade in conservational rhinoceros horns
is adding constant pressure on remaining populations. Captive management of
ex situ populations of endangered species using molecular methods
can contribute to improving the management of the species. Here we compare for the
first time the utility of 33 Single Nucleotide Polymorphisms (SNPs) and nine
microsatellites (MS) in isolation and in combination for assigning parentage in
captive White Rhinoceros. We found that a combined dataset of SNPs and
microsatellites was most informative with the highest confidence level. This study
thus provided us with a useful set of SNP and MS markers for parentage and
relatedness testing. Further assessment of the utility of these markers over multiple
(> three) generations and the incorporation of a larger variety of relationships
among individuals (e.g. half-siblings or cousins) is strongly suggested.
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Affiliation(s)
- Christiaan Labuschagne
- Department of Genetics, University of the Free State, Bloemfontein, Free State, South Africa.,Inqaba Biotechnical Industries (Pty) Ltd, Pretoria, Gauteng, South Africa
| | - Desiré L Dalton
- Department of Genetics, University of the Free State, Bloemfontein, Free State, South Africa.,National Zoological Gardens of South Africa, Pretoria, Gauteng, South Africa
| | - J Paul Grobler
- Department of Genetics, University of the Free State, Bloemfontein, Free State, South Africa
| | - Antoinette Kotzé
- Department of Genetics, University of the Free State, Bloemfontein, Free State, South Africa.,National Zoological Gardens of South Africa, Pretoria, Gauteng, South Africa
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12
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Rębała K, Rabtsava AA, Kotova SA, Kipen VN, Zhurina NV, Gandzha AI, Tsybovsky IS. STR Profiling for Discrimination between Wild and Domestic Swine Specimens and between Main Breeds of Domestic Pigs Reared in Belarus. PLoS One 2016; 11:e0166563. [PMID: 27851802 PMCID: PMC5112791 DOI: 10.1371/journal.pone.0166563] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2016] [Accepted: 10/30/2016] [Indexed: 12/04/2022] Open
Abstract
A panel comprising 16 short tandem repeats (STRs) and a gender-specific amelogenin marker was worked out and tested for robustness in discrimination between wild and domestic swine subspecies encountered in Europe, between regional populations of wild boars and between main breeds of domestic pigs reared in Belarus. The STR dataset comprised 310 wild boars, inhabiting all administrative regions of Belarus, and 313 domestic pigs, representing three local and three cosmopolitan lines. Additionally, a total of 835 wild boars were genotyped for the presence of melanocortin 1 receptor (MC1R) alleles specific for domestic pigs. Correctness of assignment of STR profiles to appropriate populations was measured by log-likelihood ratios (log-LRs). All samples were correctly identified as wild boars or domestic pigs with average log-LR of 42.4 (LR = 2.6×1018). On the other hand, as many as 50 out of 835 (6.0%) genotyped wild boars from Belarus possessed MC1R alleles specific to domestic pigs, demonstrating supremacy of our STR profiling system over traditional differentiation between wild boars and domestic pigs, based on single binary markers. Mean log-LRs for allocation of wild boars to their regions of origin and of domestic pigs to appropriate breeds were 2.3 (LR = 9.7) and 13.4 (LR = 6.6×105), respectively. Our results demonstrate the developed STR profiling system to be a highly efficient tool for differentiation between wild and domestic swine subspecies and between diverse breeds of domestic pigs as well as for verification of genetic identity of porcine specimens for the purpose of forensic investigations of wildlife crimes, assurance of veterinary public health, parentage control in animal husbandry, food safety management and traceability of livestock products.
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Affiliation(s)
- Krzysztof Rębała
- Department of Forensic Medicine, Medical University of Gdansk, Gdansk, Poland
- * E-mail:
| | - Alina A. Rabtsava
- Scientific and Practical Centre of the State Committee of Forensic Expertises, Minsk, Belarus
| | - Svetlana A. Kotova
- Scientific and Practical Centre of the State Committee of Forensic Expertises, Minsk, Belarus
| | - Viachaslau N. Kipen
- Scientific and Practical Centre of the State Committee of Forensic Expertises, Minsk, Belarus
| | - Natalja V. Zhurina
- Scientific and Practical Centre of the National Academy of Sciences on Animal Husbandry, Zhodino, Belarus
| | - Alla I. Gandzha
- Scientific and Practical Centre of the National Academy of Sciences on Animal Husbandry, Zhodino, Belarus
| | - Iosif S. Tsybovsky
- Scientific and Practical Centre of the State Committee of Forensic Expertises, Minsk, Belarus
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13
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Pocrnic I, Lourenco DAL, Masuda Y, Misztal I. Dimensionality of genomic information and performance of the Algorithm for Proven and Young for different livestock species. Genet Sel Evol 2016; 48:82. [PMID: 27799053 PMCID: PMC5088690 DOI: 10.1186/s12711-016-0261-6] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 10/25/2016] [Indexed: 12/19/2022] Open
Abstract
Background A genomic relationship matrix (GRM) can be inverted efficiently with the Algorithm for Proven and Young (APY) through recursion on a small number of core animals. The number of core animals is theoretically linked to effective population size (Ne). In a simulation study, the optimal number of core animals was equal to the number of largest eigenvalues of GRM that explained 98% of its variation. The purpose of this study was to find the optimal number of core animals and estimate Ne for different species. Methods Datasets included phenotypes, pedigrees, and genotypes for populations of Holstein, Jersey, and Angus cattle, pigs, and broiler chickens. The number of genotyped animals varied from 15,000 for broiler chickens to 77,000 for Holsteins, and the number of single-nucleotide polymorphisms used for genomic prediction varied from 37,000 to 61,000. Eigenvalue decomposition of the GRM for each population determined numbers of largest eigenvalues corresponding to 90, 95, 98, and 99% of variation. Results The number of eigenvalues corresponding to 90% (98%) of variation was 4527 (14,026) for Holstein, 3325 (11,500) for Jersey, 3654 (10,605) for Angus, 1239 (4103) for pig, and 1655 (4171) for broiler chicken. Each trait in each species was analyzed using the APY inverse of the GRM with randomly selected core animals, and their number was equal to the number of largest eigenvalues. Realized accuracies peaked with the number of core animals corresponding to 98% of variation for Holstein and Jersey and closer to 99% for other breed/species. Ne was estimated based on comparisons of eigenvalue decomposition in a simulation study. Assuming a genome length of 30 Morgan, Ne was equal to 149 for Holsteins, 101 for Jerseys, 113 for Angus, 32 for pigs, and 44 for broilers. Conclusions Eigenvalue profiles of GRM for common species are similar to those in simulation studies although they are affected by number of genotyped animals and genotyping quality. For all investigated species, the APY required less than 15,000 core animals. Realized accuracies were equal or greater with the APY inverse than with regular inversion. Eigenvalue analysis of GRM can provide a realistic estimate of Ne.
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Affiliation(s)
- Ivan Pocrnic
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, 30602, USA.
| | - Daniela A L Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, 30602, USA
| | - Yutaka Masuda
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, 30602, USA
| | - Ignacy Misztal
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, 30602, USA
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Yamazaki Y, Adachi F, Sawamura A. Multiple Origins and Admixture of Recently Expanding Japanese Wild Boar (Sus scrofa leucomystax) Populations in Toyama Prefecture of Japan. Zoolog Sci 2016; 33:38-43. [PMID: 26853867 DOI: 10.2108/zs150092] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Japanese wild boar (Sus scrofa leucomystax) populations have expanded drastically throughout the Japanese Archipelago in recent decades. To elucidate the dispersal patterns of Japanese wild boar in Toyama Prefecture in central Japan, we used a multi-locus microsatellite DNA analysis to determine its population structure and the degree of admixture. The deviation from Hardy-Weinberg equilibrium was detected in either total or separate regional wild boar samples from Toyama Prefecture. This result could be explained by the Wahlund effect resulting from the mixture of samples from different sources. Bayesian structure analysis, assignment test, and factorial correspondence analysis suggested that wild boars around Toyama Prefecture derive from at least two ancestral sources. The migration and possible mating of each individual may have occurred recently and continued in each geographically neighboring region. The present genetic results may be useful for prediction of future dispersal patterns of Japanese wild boar, as well as other animals in expansion.
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Affiliation(s)
- Yuji Yamazaki
- Graduate School of Science and Engineering for Research, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan
| | - Fuminari Adachi
- Graduate School of Science and Engineering for Research, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan
| | - Akira Sawamura
- Graduate School of Science and Engineering for Research, University of Toyama, 3190 Gofuku, Toyama 930-8555, Japan
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15
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Yaro M, Munyard KA, Stear MJ, Groth DM. Molecular identification of livestock breeds: a tool for modern conservation biology. Biol Rev Camb Philos Soc 2016; 92:993-1010. [DOI: 10.1111/brv.12265] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2015] [Revised: 02/14/2016] [Accepted: 02/18/2016] [Indexed: 12/22/2022]
Affiliation(s)
- Mohammed Yaro
- School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Faculty of Health Sciences; Curtin University; GPO Box U1987 Perth WA 6845 Australia
| | - Kylie A. Munyard
- School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Faculty of Health Sciences; Curtin University; GPO Box U1987 Perth WA 6845 Australia
| | - Michael J. Stear
- Institute of Biodiversity, Animal Health and Comparative Medicine; University of Glasgow; Bearsden Road Glasgow G61 1QH U.K
| | - David M. Groth
- School of Biomedical Sciences, CHIRI Biosciences Research Precinct, Faculty of Health Sciences; Curtin University; GPO Box U1987 Perth WA 6845 Australia
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16
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Stefanon B, Floris R, Braglia S, Davoli R, Fontanesi L, Dall’Olio S, Graziosi G, Susmel P, Russo V. A new approach in association study of single nucleotide polymorphism of genes for carcass and meat quality traits in commercial pigs. ITALIAN JOURNAL OF ANIMAL SCIENCE 2016. [DOI: 10.4081/ijas.2004.177] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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17
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Murase K, Horie R, Saito M, Koganezawa M, Sato T, Kaji K. Integrating Analyses of Population Genetics and Space-Time Information for Wildlife Management: An Empirical Study on Japanese Wild Boar Populations. MAMMAL STUDY 2015. [DOI: 10.3106/041.040.0202] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
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18
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Biondo C, Izar P, Miyaki CY, Bussab VSR. Social structure of collared peccaries (Pecari tajacu): does relatedness matter? Behav Processes 2014; 109 Pt A:70-8. [PMID: 25173619 DOI: 10.1016/j.beproc.2014.08.018] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/2014] [Revised: 08/19/2014] [Accepted: 08/20/2014] [Indexed: 11/26/2022]
Abstract
Relatedness is considered an important factor in shaping social structure as the association among kin might facilitate cooperation via inclusive fitness benefits. We addressed here the influence of relatedness on the social structure of a Neotropical ungulate, the collared peccary (Pecari tajacu). As peccaries are highly social and cooperative, live in stable cohesive herds and show certain degree of female philopatry and high mean relatedness within herds, we hypothesized that kin would be spatially closer and display more amicable and less agonistic interactions than non-kin. We recorded spatial association patterns and rates of interactions of two captive groups. Pairwise relatedness was calculated based on microsatellite data. As predicted, we found that kin were spatially closer than non-kin, which suggests that relatedness is a good predictor of spatial association in peccaries. However, relatedness did not predict the rates of social interactions. Although our results indirectly indicate some role of sex, age and familiarity, further studies are needed to clarify the factors that shape the rates of interactions in collared peccaries. This article is part of a Special Issue entitled: Neotropical Behaviour.
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Affiliation(s)
- Cibele Biondo
- Departamento de Psicologia Experimental, Instituto de Psicologia, Universidade de São Paulo, Av. Prof. Mello Moraes 1721, São Paulo, SP 05508-030, Brazil; Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, São Paulo, SP 05508-090, Brazil.
| | - Patrícia Izar
- Departamento de Psicologia Experimental, Instituto de Psicologia, Universidade de São Paulo, Av. Prof. Mello Moraes 1721, São Paulo, SP 05508-030, Brazil
| | - Cristina Y Miyaki
- Departamento de Genética e Biologia Evolutiva, Instituto de Biociências, Universidade de São Paulo, Rua do Matão 277, São Paulo, SP 05508-090, Brazil
| | - Vera S R Bussab
- Departamento de Psicologia Experimental, Instituto de Psicologia, Universidade de São Paulo, Av. Prof. Mello Moraes 1721, São Paulo, SP 05508-030, Brazil
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Kotzé A, Dalton DL, du Toit R, Anderson N, Moodley Y. Genetic structure of the black rhinoceros (Diceros bicornis) in south-eastern Africa. CONSERV GENET 2014. [DOI: 10.1007/s10592-014-0632-x] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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20
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Samardjieva KG, Marinova E. Microsatellites—A New Approach of Marker- Assisted Selection. BIOTECHNOL BIOTEC EQ 2014. [DOI: 10.1080/13102818.1995.10818855] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022] Open
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21
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Nicholas FW, Hobbs M. Mutation discovery for Mendelian traits in non-laboratory animals: a review of achievements up to 2012. Anim Genet 2013; 45:157-70. [PMID: 24372556 PMCID: PMC4225684 DOI: 10.1111/age.12103] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/08/2013] [Indexed: 01/21/2023]
Abstract
Within two years of the re-discovery of Mendelism, Bateson and Saunders had described six traits in non-laboratory animals (five in chickens and one in cattle) that show single-locus (Mendelian) inheritance. In the ensuing decades, much progress was made in documenting an ever-increasing number of such traits. In 1987 came the first discovery of a causal mutation for a Mendelian trait in non-laboratory animals: a non-sense mutation in the thyroglobulin gene (TG), causing familial goitre in cattle. In the years that followed, the rate of discovery of causal mutations increased, aided mightily by the creation of genome-wide microsatellite maps in the 1990s and even more mightily by genome assemblies and single-nucleotide polymorphism (SNP) chips in the 2000s. With sequencing costs decreasing rapidly, by 2012 causal mutations were being discovered in non-laboratory animals at a rate of more than one per week. By the end of 2012, the total number of Mendelian traits in non-laboratory animals with known causal mutations had reached 499, which was half the number of published single-locus (Mendelian) traits in those species. The distribution of types of mutations documented in non-laboratory animals is fairly similar to that in humans, with almost half being missense or non-sense mutations. The ratio of missense to non-sense mutations in non-laboratory animals to the end of 2012 was 193:78. The fraction of non-sense mutations (78/271 = 0.29) was not very different from the fraction of non-stop codons that are just one base substitution away from a stop codon (21/61 = 0.34).
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Affiliation(s)
- Frank W Nicholas
- Faculty of Veterinary Science, University of Sydney, Sydney, NSW, 2006, Australia
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22
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Engeman RM, Massei G, Sage M, Gentle MN. Monitoring wild pig populations: a review of methods. ENVIRONMENTAL SCIENCE AND POLLUTION RESEARCH INTERNATIONAL 2013; 20:8077-8091. [PMID: 23881593 DOI: 10.1007/s11356-013-2002-5] [Citation(s) in RCA: 35] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2013] [Accepted: 07/10/2013] [Indexed: 06/02/2023]
Abstract
Wild pigs (Sus scrofa) are widespread across many landscapes throughout the world and are considered to be an invasive pest to agriculture and the environment, or conversely a native or desired game species and resource for hunting. Wild pig population monitoring is often required for a variety of management or research objectives, and many methods and analyses for monitoring abundance are available. Here, we describe monitoring methods that have proven or potential applications to wild pig management. We describe the advantages and disadvantages of methods so that potential users can efficiently consider and identify the option(s) best suited to their combination of objectives, circumstances, and resources. This paper offers guidance to wildlife managers, researchers, and stakeholders considering population monitoring of wild pigs and will help ensure that they can fulfill their monitoring objectives while optimizing their use of resources.
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Affiliation(s)
- R M Engeman
- National Wildlife Research Center, 4101 LaPorte Ave, Fort Collins, CO, 80521-2154, USA,
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23
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Chen CH, Jiang BH, Huang SY, Yang TS, Lee KH, Tu CF, Wu SC. Genetic polymorphisms, growth performance, hematological parameters, serum enzymes, and reproductive characteristics in phenotypically normal Landrace boars produced by somatic cell nuclear transfer. Theriogenology 2013; 80:1088-96. [PMID: 24055399 DOI: 10.1016/j.theriogenology.2013.08.010] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2013] [Revised: 07/24/2013] [Accepted: 08/10/2013] [Indexed: 11/29/2022]
Abstract
Understanding the performances of cloned pigs and their offspring is critical to evaluate the practical applications of somatic cell nuclear transfer. In this study, genetic polymorphism, growth performance, hematological parameters, and reproduction characteristics of cloned Landrace boars were compared with those of controls. In addition, the growth performance of clone offspring was also evaluated. A total of 479 reconstructed embryos were transferred to five recipient pigs and resulted in the delivery of 14 piglets (overall cloning of 2.9%) from two litters. Analyses of microsatellite markers and polymorphisms of the specific genes confirmed that the 14 clones were genetically identical to the nuclear donor and maintained the desirable genotypes. Growth performance of five healthy, phenotypically normal cloned boars from one litter and eight of their male offspring did not differ from age, breed, and management-matched controls. Although some significant differences were observed between cloned and control boars in hematological and serum enzymes, most of these parameters were within the normal range. Cloned boars had less (P < 0.05) normal sperm in the ejaculated boars than in control boars (71.4% vs. 77.9%, respectively), but sperm production (ejaculate volume, sperm concentration, and total sperm) did not differ between these groups. In addition, use of frozen-thawed semen from cloned boars for insemination produced results that seemed comparable to a control. In conclusion, the present study reported that somatic cell nuclear transfer is effective in reproducing preferred genetic traits and has potential applications to conserve elite bloodlines in a routine pig breeding program.
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Affiliation(s)
- C H Chen
- Animal Technology Institute Taiwan, Miaoli, Taiwan, Republic of China
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24
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Kolodziej K, Nikolov I, Schulz HK, Theissinger K, Schulz R. Evaluation of fecal storage and DNA extraction methods in wild boar (Sus scrofa). Biochem Genet 2013; 51:406-12. [PMID: 23381667 DOI: 10.1007/s10528-013-9573-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2012] [Accepted: 09/06/2012] [Indexed: 10/27/2022]
Affiliation(s)
- Karolina Kolodziej
- Institute for Environmental Sciences, University of Koblenz-Landau, Fortstrasse 7, D-76829 Landau, Germany.
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25
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Choi BH, Lee JS, Lee SH, Kim SC, Kim SW, Kim KS, Lee JH, Seong HH, Kim TH. Porcine LMNA Is a Positional Candidate Gene Associated with Growth and Fat Deposition. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2012; 25:1649-59. [PMID: 25049529 PMCID: PMC4094157 DOI: 10.5713/ajas.2012.12288] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/25/2012] [Revised: 09/24/2012] [Accepted: 07/03/2012] [Indexed: 11/27/2022]
Abstract
Crosses between Korean and Landrace pigs have revealed a large quantitative trait loci (QTL) region for fat deposition in a region (89 cM) of porcine chromosome 4 (SSC4). To more finely map this QTL region and identify candidate genes for this trait, comparative mapping of pig and human chromosomes was performed in the present study. A region in the human genome that corresponds to the porcine QTL region was identified in HSA1q21. Furthermore, the LMNA gene, which is tightly associated with fat augmentation in humans, was localized to this region. Radiation hybrid (RH) mapping using a Sus scrofa RH panel localized LMNA to a region of 90.3 cM in the porcine genome, distinct from microsatellite marker S0214 (87.3 cM). Two-point analysis showed that LMNA was linked to S0214, SW1996, and S0073 on SSC4 with logarithm (base 10) of odds scores of 20.98, 17.78, and 16.73, respectively. To clone the porcine LMNA gene and to delineate the genomic structure and sequences, including the 3'untranslated region (UTR), rapid amplification of cDNA ends was performed. The coding sequence of porcine LMNA consisted of 1,719 bp, flanked by a 5'UTR and a 3'UTR. Two synonymous single nucleotide polymorphisms (SNPs) were identified in exons 3 and 7. Association tests showed that the SNP located in exon 3 (A193A) was significantly associated with weight at 30 wks (p<0.01) and crude fat content (p<0.05). This association suggests that SNPs located in LMNA could be used for marker-assisted selection in pigs.
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Affiliation(s)
- Bong Hwan Choi
- Department of Animal Science, Chungbuk National University, Cheongju 361-763, Korea
| | - Jung Sim Lee
- Department of Animal Science, Chungbuk National University, Cheongju 361-763, Korea
| | - Seung Hwan Lee
- Department of Animal Science, Chungbuk National University, Cheongju 361-763, Korea
| | - Seung Chang Kim
- Department of Animal Science, Chungbuk National University, Cheongju 361-763, Korea
| | - Sang Wook Kim
- Department of Animal Science, Chungbuk National University, Cheongju 361-763, Korea
| | - Kwan Suk Kim
- Department of Animal Science, Chungbuk National University, Cheongju 361-763, Korea
| | - Jun Heon Lee
- Division of Animal Science and Resources, College of Agriculture and Life Sciences Chungnam National University, Daejeon 305-764, Korea
| | - Hwan Hoo Seong
- Department of Animal Science, Chungbuk National University, Cheongju 361-763, Korea
| | - Tae Hun Kim
- Department of Animal Science, Chungbuk National University, Cheongju 361-763, Korea
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26
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Tortereau F, Servin B, Frantz L, Megens HJ, Milan D, Rohrer G, Wiedmann R, Beever J, Archibald AL, Schook LB, Groenen MAM. A high density recombination map of the pig reveals a correlation between sex-specific recombination and GC content. BMC Genomics 2012; 13:586. [PMID: 23152986 PMCID: PMC3499283 DOI: 10.1186/1471-2164-13-586] [Citation(s) in RCA: 121] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2012] [Accepted: 08/09/2012] [Indexed: 12/18/2022] Open
Abstract
Background The availability of a high-density SNP genotyping chip and a reference genome sequence of the pig (Sus scrofa) enabled the construction of a high-density linkage map. A high-density linkage map is an essential tool for further fine-mapping of quantitative trait loci (QTL) for a variety of traits in the pig and for a better understanding of mechanisms underlying genome evolution. Results Four different pig pedigrees were genotyped using the Illumina PorcineSNP60 BeadChip. Recombination maps for the autosomes were computed for each individual pedigree using a common set of markers. The resulting genetic maps comprised 38,599 SNPs, including 928 SNPs not positioned on a chromosome in the current assembly of the pig genome (build 10.2). The total genetic length varied according to the pedigree, from 1797 to 2149 cM. Female maps were longer than male maps, with a notable exception for SSC1 where male maps are characterized by a higher recombination rate than females in the region between 91–250 Mb. The recombination rates varied among chromosomes and along individual chromosomes, regions with high recombination rates tending to cluster close to the chromosome ends, irrespective of the position of the centromere. Correlations between main sequence features and recombination rates were investigated and significant correlations were obtained for all the studied motifs. Regions characterized by high recombination rates were enriched for specific GC-rich sequence motifs as compared to low recombinant regions. These correlations were higher in females than in males, and females were found to be more recombinant than males at regions where the GC content was greater than 0.4. Conclusions The analysis of the recombination rate along the pig genome highlighted that the regions exhibiting higher levels of recombination tend to cluster around the ends of the chromosomes irrespective of the location of the centromere. Major sex-differences in recombination were observed: females had a higher recombination rate within GC-rich regions and exhibited a stronger correlation between recombination rates and specific sequence features.
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Affiliation(s)
- Flavie Tortereau
- Wageningen University, Animal Breeding and Genomics Centre, 6700AH, Wageningen, The Netherlands
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Meadus WJ, Macinnis R. Testing for the RN(-) gene in retail pork chops. Meat Sci 2012; 54:231-7. [PMID: 22060693 DOI: 10.1016/s0309-1740(99)00084-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/23/1999] [Accepted: 06/25/1999] [Indexed: 10/18/2022]
Abstract
A random sample of pork chops were purchased from local retail outlets to determine if the frequency of the RN(-) phenotype could be roughly estimated by GP measurements in fresh raw pork products or by genotyping for the nearest DNA microsatellite markers. Glycolytic potential (GP) is the estimated sum of glycogen, the intermediate metabolites of glycogenolysis, and the end product, lactate. GP has been used to identify a genetic mutation known as the RN(-) or Hampshire gene. Currently, there is no genetic test for the RN(-) allele and flanking DNA microsatellite markers were not useful at predicting the RN(-) phenotype in the random samples. Excessively high GP was found in 25% of the samples which correlated with a significant (P>0.05) drop in pH (5.8 to 5.7), a paler (L* value; 54.1 to 57.5) more yellowish (b* value; 9.6 to 11.6) color, and an increased cooking loss (9 to 18%), typical of the RN(-) phenotype. A genetic test for skin colour in swine proved that the majority (79%) of high GP pork sampled were from phenotypically white pigs. Analysis of glucose levels in post-rigor samples may be useful in progeny testing for the RN gene until a true genetic marker can be identified.
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Affiliation(s)
- W J Meadus
- Lacombe Research Centre, Agriculture and Agri-Food Canada, Lacombe, AB, Canada T4L 1W1
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28
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Chen YC, Hsu JT, Chien CC, Leu YC, Chyr CYL, Lin DY, Lin EC, Chen CH, Wang PH. Investigation of Genetic Relationships Among Taiwan Black Pigs and Other Pig Breeds in Taiwan Based on Microsatellite Markers. Anim Biotechnol 2012; 23:278-90. [DOI: 10.1080/10495398.2012.700667] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Costa V, Pérez-González J, Santos P, Fernández-Llario P, Carranza J, Zsolnai A, Anton I, Buzgó J, Varga G, Monteiro N, Beja-Pereira A. Microsatellite markers for identification and parentage analysis in the European wild boar (Sus scrofa). BMC Res Notes 2012; 5:479. [PMID: 22943565 PMCID: PMC3475110 DOI: 10.1186/1756-0500-5-479] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2012] [Accepted: 08/22/2012] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The wild boar (Sus scrofa) is among the most widespread mammal species throughout the old world. Presently, studies concerning microsatellites in domestic pigs and wild boars have been carried out in order to investigate domestication, social behavior and general diversity patterns among either populations or breeds. The purpose of the current study is to develop a robust set of microsatellites markers for parentage analyses and individual identification. FINDINGS A set of 14 previously reported microsatellites markers have been optimized and tested in three populations from Hungary, Portugal and Spain, in a total of 167 samples. The results indicate high probabilities of exclusion (0.99999), low probability of identity (2.0E(-13) - 2.5E(-9)) and a parentage assignment of 100%. CONCLUSIONS Our results demonstrate that this set of markers is a useful and efficient tool for the individual identification and parentage assignment in wild boars.
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Affiliation(s)
- Vânia Costa
- Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto (CIBIO-UP), Rua Padre Armando Quintas 7, 4485-661 Vairão, Portugal
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30
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Velickovic N, Djan M, Obreht D, Vapa L. Population genetic structure of wild boars in the West Balkan region. RUSS J GENET+ 2012. [DOI: 10.1134/s1022795412080078] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Luo Y, Lin L, Bolund L, Jensen TG, Sørensen CB. Genetically modified pigs for biomedical research. J Inherit Metab Dis 2012; 35:695-713. [PMID: 22453682 DOI: 10.1007/s10545-012-9475-0] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/16/2011] [Revised: 02/09/2012] [Accepted: 03/02/2012] [Indexed: 01/17/2023]
Abstract
During the last two decades, pigs have been used to develop some of the most important large animal models for biomedical research. Advances in pig genome research, genetic modification (GM) of primary pig cells and pig cloning by nuclear transfer, have facilitated the generation of GM pigs for xenotransplantation and various human diseases. This review summarizes the key technologies used for generating GM pigs, including pronuclear microinjection, sperm-mediated gene transfer, somatic cell nuclear transfer by traditional cloning, and somatic cell nuclear transfer by handmade cloning. Broadly used genetic engineering tools for porcine cells are also discussed. We also summarize the GM pig models that have been generated for xenotransplantation and human disease processes, including neurodegenerative diseases, cardiovascular diseases, eye diseases, bone diseases, cancers and epidermal skin diseases, diabetes mellitus, cystic fibrosis, and inherited metabolic diseases. Thus, this review provides an overview of the progress in GM pig research over the last two decades and perspectives for future development.
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Affiliation(s)
- Yonglun Luo
- Department of Biomedicine, Aarhus University, Aarhus C, Denmark.
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Burgos-Paz W, Souza CA, Castelló A, Mercadé A, Okumura N, Sheremet'eva IN, Huang LS, Cho IC, Paiva SR, Ramos-Onsins S, Pérez-Enciso M. Worldwide genetic relationships of pigs as inferred from X chromosome SNPs. Anim Genet 2012; 44:130-8. [PMID: 22590984 DOI: 10.1111/j.1365-2052.2012.02374.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/22/2012] [Indexed: 02/04/2023]
Abstract
The phylogeography of the porcine X chromosome has not been studied despite the unique characteristics of this chromosome. Here, we genotyped 59 single nucleotide polymorphisms (SNPs) in 312 pigs from around the world, representing 39 domestic breeds and wild boars in 30 countries. Overall, widespread commercial breeds showed the highest heterozygosity values, followed by African and American populations. Structuring, as inferred from FST and analysis of molecular variance, was consistently larger in the non-pseudoautosomal (NPAR) than in the pseudoautosomal regions (PAR). Our results show that genetic relationships between populations can vary widely between the NPAR and the PAR, underscoring the fact that their genetic trajectories can be quite different. NPAR showed an increased commercial-like genetic component relative to the PAR, probably because human selection processes to obtain individuals with high productive parameters were mediated by introgressing boars rather than sows.
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Affiliation(s)
- W Burgos-Paz
- Center for Research in Agricultural Genomics, Universitat Autònoma de Barcelona, Bellaterra, Spain
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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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Mousel MR, Leymaster KA, Christenson RK, Nonneman DJ, Rohrer GA. Validation and fine mapping of a QTL for ovulation rate on swine chromosome 3. Anim Genet 2012; 43:220-4. [PMID: 22404359 DOI: 10.1111/j.1365-2052.2011.02235.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ovulation rate (OR) is an important component of litter size, but mutation(s) in gene(s) underlying OR QTL have yet to be identified in pigs. Markers within an OR QTL on SSC3 were genotyped in three white composite lines selected for ten generations for increased OR or uterine capacity (UC), with one line being an unselected control. Numbers of corpora lutea (CL) and UC (number of fully formed fetuses) were collected at approximately 105 days of gestation, as well as ovary weight (OW), uterine length (UL) and uterine weight (UW) measurements at 160 d of age in generation 12 and 13 females from all three lines. Six microsatellites and ten single nucleotide polymorphisms (SNPs; 0-42 cM) were genotyped in pigs from all lines of generations 11 through 13. The allele frequencies of 24269.1, SW2429, 7907.2 and 7637.2 were different (P < 0.01) in the OR line compared to the control line. A significant (P < 0.05) association of CL with 24269.1 (additive effect 0.65 ± 0.32) was detected, and additive genotypic effects approached significance for markers at 28 through 35 cM (16963.2, 27514.1 and SWR1637). Haplotyping of 7637.2 and 16963.2 (31 through 32 cM) identified a significant additive association of haplotype 1 with CL (-0.62 ± 0.30). These markers were also associated with OW (24296.1 and SWR1637), UL (16963.2, 27514.1 and haplotypes of 7637.2/16963.2) and UW (haplotypes of 7637.2/16963.2). This study verifies an OR QTL on SSC3. However, based on the data, it was concluded that there may be two genes, at 13 through 18 cM and 28 through 35 cM, controlling OR on SSC3p.
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Affiliation(s)
- M R Mousel
- U.S. Department of Agriculture-Agricultural Research Service, U.S. Meat Animal Research Center, Clay Center, NE 68933-0166, USA
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Parada R, Książkiewicz J, Kawka M, Jaszczak K. Studies on resources of genetic diversity in conservative flocks of geese using microsatellite DNA polymorphic markers. Mol Biol Rep 2011; 39:5291-7. [PMID: 22173720 PMCID: PMC3310985 DOI: 10.1007/s11033-011-1327-8] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2011] [Accepted: 12/03/2011] [Indexed: 11/23/2022]
Abstract
The studies conducted aimed at evaluating the genetic diversity within and between varieties of conservative flocks of geese, using the polymorphism of 14 microsatellite sequences. The experimental material included conservative flocks of geese the following indigenous breeds and varieties kept in Poland: Kielecka (Ki), Kartuska (Ka), Lubelska (Lu), Suvalska (Su), Rypinska (Ry), Sub-Carpathian (SC), Hunched Beak (HB) and Pomeranian (Po). Among the 14 microsatellite sequences a total of 97 microsatellite alleles were identified. The number of alleles at one locus ranged from 3 to 19. In the overall pool of 97 alleles, 26 (26.8%) were specific for individual breeds and varieties of geese. The values of the expected heterozygosity (He) for individual geese ranged from 0.38 (Sub-Carpathian) to 0.51 (HB). Similarly, the mean values for the observed heterozygosity (Ho) ranged from 0.45 (Po) to 0.55 (Ki and Su). The polymorphic information content reached the highest value of 0.80 at loci CKW21 (Ki) and TTUCG5 (Po and Su). The greatest genetic distance was observed between the HB and Ry (0.44) and between the HB and Po (0.39) varieties, while the smallest–between the Lu and Po as well as Lu and Ki (0.028) varieties. The phylogenetic tree, elaborated on the basis of the genetic distances, clearly confirms the specificity of the HB goose as compared to the remaining breeds and varieties.
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Affiliation(s)
- Rafał Parada
- Polish Academy of Sciences, Institute of Genetics and Animal Breeding, Jastrzebiec, 05-552, Wólka Kosowska, Poland.
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Kolodziej K, Theissinger K, Brün J, Schulz HK, Schulz R. Determination of the minimum number of microsatellite markers for individual genotyping in wild boar (Sus scrofa) using a test with close relatives. EUR J WILDLIFE RES 2011. [DOI: 10.1007/s10344-011-0588-9] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Čepica S, Óvilo C, Masopust M, Knoll A, Fernandez A, Lopez A, Rohrer GA, Nonneman D. Four genes located on a SSC2 meat quality QTL region are associated with different meat quality traits in Landrace × Chinese-European crossbred population. Anim Genet 2011; 43:333-6. [DOI: 10.1111/j.1365-2052.2011.02252.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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38
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Biondo C, Keuroghlian A, Gongora J, Miyaki CY. Population genetic structure and dispersal in white-lipped peccaries (Tayassu pecari) from the Brazilian Pantanal. J Mammal 2011. [DOI: 10.1644/10-mamm-a-174.1] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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39
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Cherel P, Glénisson J, Pires J. Tetranucleotide microsatellites contribute to a highly discriminating parentage test panel in pig. Anim Genet 2011; 42:659-61. [DOI: 10.1111/j.1365-2052.2011.02187.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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40
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Graphodatsky AS, Biltueva LS. Chromosome banding and gene conservation between humans and pigs. J Anim Breed Genet 2011. [DOI: 10.1111/j.1439-0388.1995.tb00551.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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41
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Rothschild MF, Liu HC, Tuggle CK, Yu TP, Wang L. Analysis of pig chromosome 7 genetic markers for growth and carcass performance traits. J Anim Breed Genet 2011. [DOI: 10.1111/j.1439-0388.1995.tb00576.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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42
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Burns BM, Gazzola C, Holroyd RG, Crisp J, McGowan MR. Male Reproductive Traits and Their Relationship to Reproductive Traits in Their Female Progeny: A Systematic Review. Reprod Domest Anim 2011; 46:534-53. [DOI: 10.1111/j.1439-0531.2011.01748.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
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43
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Geldermann H, Müller E, Beeckmann P, Knorr C, Yue G, Moser G. Mapping of quantitative-trait loci by means of marker genes in F2 generations of Wild boar, Pietrain and Meishan pigs. J Anim Breed Genet 2011. [DOI: 10.1111/j.1439-0388.1996.tb00629.x] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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44
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Evidence for additional functional genetic variation within the porcine IGF2 gene affecting body composition traits in an experimental Piétrain × Large White/Landrace cross. Animal 2011; 5:672-7. [DOI: 10.1017/s1751731110002466] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
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45
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Cooper JD, Waser PM, Gopurenko D, Hellgren EC, Gabor TM, DeWoody JA. Measuring sex-biased dispersal in social mammals: comparisons of nuclear and mitochondrial genes in collared peccaries. J Mammal 2010. [DOI: 10.1644/09-mamm-a-313.1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022] Open
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46
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Ma JG, Chang TC, Yasue H, Farmer AD, Crow JA, Eyer K, Hiraiwa H, Shimogiri T, Meyers SN, Beever JE, Schook LB, Retzel EF, Beattie CW, Liu WS. A high-resolution comparative map of porcine chromosome 4 (SSC4). Anim Genet 2010; 42:440-4. [PMID: 21749428 DOI: 10.1111/j.1365-2052.2010.02140.x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
We used the IMNpRH2(12,000-rad) RH and IMpRH(7,000-rad) panels to integrate 2019 transcriptome (RNA-seq)-generated contigs with markers from the porcine genetic and radiation hybrid (RH) maps and bacterial artificial chromosome finger-printed contigs, into 1) parallel framework maps (LOD ≥ 10) on both panels for swine chromosome (SSC) 4, and 2) a high-resolution comparative map of SSC4, thus and human chromosomes (HSA) 1 and 8. A total of 573 loci were anchored and ordered on SSC4 closing gaps identified in the porcine sequence assembly Sscrofa9. Alignment of the SSC4 RH with the genetic map identified five microsatellites incorrectly mapped around the centromeric region in the genetic map. Further alignment of the RH and comparative maps with the genome sequence identified four additional regions of discrepancy that are also suggestive of errors in assembly, three of which were resolved through conserved synteny with blocks on HSA1 and HSA8.
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Affiliation(s)
- J-G Ma
- Department of Biological Science and Engineering, Key Laboratory of Biomedical Information Engineering of Ministry of Education, School of Life Science and Technology, Xi'an Jiaotong University, China
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Masopust M, Vykoukalová Z, Knoll A, Bartenschlager H, Mileham A, Deeb N, Rohrer GA, Cepica S. Porcine insulin receptor substrate 4 (IRS4) gene: cloning, polymorphism and association study. Mol Biol Rep 2010; 38:2611-7. [PMID: 21104145 DOI: 10.1007/s11033-010-0402-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2010] [Accepted: 11/08/2010] [Indexed: 01/28/2023]
Abstract
Using PCR and inverse PCR techniques we obtained a 4,498 bp nucleotide sequence FN424076 encompassing the complete coding sequence of the porcine insulin receptor substrate 4 (IRS4) gene and its proximal promoter. The 1,269 amino acid porcine protein deduced from the nucleotide sequence shares 92% identity with the human IRS4 and possesses the same domains and the same number of tyrosine phosphorylation motifs as the human protein. We detected substitution FN424076:g.96C<G in the promoter region that segregates in Meishan and a synonymous substitution FN424076:g.1829T<C in the coding sequence with allele C present only in Meishan. Linkage mapping placed the IRS4 gene at position 82 cM on the current USDA-USMARC linkage map of porcine chromosome X. Association analyses were performed on 555 animals of 12th-15th generation of the Meishan × Large White cross and showed that both SNPs were highly significantly associated with backfat depth (P=0.0005) and that the SNP FN424076:g1829T<C was also associated with loin depth (P=0.017). The Meishan alleles increased back fat depth and decreased loin depth. IRS4 can be considered a positional candidate gene for at least some of the QTL located at the centromeric region of porcine chromosome X.
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Affiliation(s)
- Martin Masopust
- Institute of Animal Physiology and Genetics AS CR, v.v.i., Liběchov, Czech Republic
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Soma Y, Uemoto Y, Sato S, Shibata T, Kadowaki H, Kobayashi E, Suzuki K. Genome-wide mapping and identification of new quantitative trait loci affecting meat production, meat quality, and carcass traits within a Duroc purebred population. J Anim Sci 2010; 89:601-8. [PMID: 21097684 DOI: 10.2527/jas.2010-3119] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Most QTL detection studies in pigs have been carried out in experimental F(2) populations. However, segregation of a QTL must be confirmed within a purebred population for successful implementation of marker-assisted selection. Previously, QTL for meat quality and carcass traits were detected on SSC 7 in a Duroc purebred population. The objectives of the present study were to carry out a whole-genome QTL analysis (except for SSC 7) for meat production, meat quality, and carcass traits and to confirm the presence of segregating QTL in a Duroc purebred population. One thousand and four Duroc pigs were studied from base to seventh generation; the pigs comprised 1 closed population of a complex multigenerational pedigree such that all individuals were related. The pigs were evaluated for 6 growth traits, 7 body size traits, 8 carcass traits, 2 physiological traits, and 11 meat quality traits, and the number of pigs with phenotypes ranged from 421 to 953. A total of 119 markers were genotyped and then used for QTL analysis. We utilized a pedigree-based, multipoint variance components approach to test for linkage between QTL and the phenotypic values using a maximum likelihood method; the logarithm of odds score and QTL genotypic heritability were estimated. A total of 42 QTL with suggestive linkages and 3 QTL with significant linkages for 26 traits were detected. These included selection traits such as daily BW gain, backfat thickness, loin eye muscle area, and intramuscular fat content as well as correlated traits such as body size and meat quality traits. The present study disclosed QTL affecting growth, body size, and carcass, physiological, and meat quality traits in a Duroc purebred population.
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Affiliation(s)
- Y Soma
- Graduate School of Agricultural Science, Tohoku University, 1-1 Tsutsumidori-Amamiyamachi, Aoba-ku, Sendai, Miyagi 981-8555, Japan
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49
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Is sexual monomorphism a predictor of polygynandry? Evidence from a social mammal, the collared peccary. Behav Ecol Sociobiol 2010. [DOI: 10.1007/s00265-010-1081-2] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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50
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Abstract
AbstractFour litters produced by father-daughter matings (back crosses) resulting in 35 animals with a theoretical inbreeding coefficient of 25% were typed with 21 independent informative markers. The differences between the two founder animals were estimated, based on the marker information, and it was found that the founder boar had higher genetic potential for proportion of lean meat and lower genetic potential for groivth than the founder sow. The proportion of the genome of each offspring which was identical by descent was investigated. On the basis of these markers the realized inbreeding was found to vary between 7 and 47%. The linear decrease in weight at days 1, 26 and 136, average daily gain and proportion of lean meat regressed on the realized inbreeding were estimated to 0·6 kg, 2·4 kg, 18 kg, 95 g/day and 15 g/kg, respectively. For weight at day 88 a corresponding linear increase of 11 kg was observed. The joint effect of founder differences and realized inbreeding were as expected negative and statistically significant for all growth traits.
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