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Fulton JE, McCarron AM, Lund AR, Drobik-Czwarno W, Mullen A, Wolc A, Szadkowska J, Schmidt CJ, Taylor RL. The RHCE gene encodes the chicken blood system I. Genet Sel Evol 2024; 56:47. [PMID: 38898419 PMCID: PMC11188259 DOI: 10.1186/s12711-024-00911-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2023] [Accepted: 05/13/2024] [Indexed: 06/21/2024] Open
Abstract
BACKGROUND There are 13 known chicken blood systems, which were originally detected by agglutination of red blood cells by specific alloantisera. The genomic region or specific gene responsible has been identified for four of these systems (A, B, D and E). We determined the identity of the gene responsible for the chicken blood system I, using DNA from multiple birds with known chicken I blood system serology, 600K and 54K single nucleotide polymorphism (SNP) data, and lowpass sequence information. RESULTS The gene responsible for the chicken I blood system was identified as RHCE, which is also one of the genes responsible for the highly polymorphic human Rh blood group locus, for which maternal/fetal antigenic differences can result in fetal hemolytic anemia with fetal mortality. We identified 17 unique RHCE haplotypes in the chicken, with six haplotypes corresponding to known I system serological alleles. We also detected deletions in the RHCE gene that encompass more than 6000 bp and that are predicted to remove its last seven exons. CONCLUSIONS RHCE is the gene responsible for the chicken I blood system. This is the fifth chicken blood system for which the responsible gene and gene variants are known. With rapid DNA-based testing now available, the impact of I blood system variation on response against disease, general immune function, and animal production can be investigated in greater detail.
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Affiliation(s)
- Janet E Fulton
- Hy-Line International, Research and Development, PO Box 310, Dallas Center, IA, USA.
| | - Amy M McCarron
- Hy-Line International, Research and Development, PO Box 310, Dallas Center, IA, USA
| | - Ashlee R Lund
- Hy-Line International, Research and Development, PO Box 310, Dallas Center, IA, USA
| | - Wioleta Drobik-Czwarno
- Department of Animal Genetics and Conservation, Institute of Animal Science, Warsaw University of Life Sciences, Warsaw, Poland
| | - Abigail Mullen
- Hy-Line International, Research and Development, PO Box 310, Dallas Center, IA, USA
| | - Anna Wolc
- Hy-Line International, Research and Development, PO Box 310, Dallas Center, IA, USA
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | - Joanna Szadkowska
- Department of Animal Genetics and Conservation, Institute of Animal Science, Warsaw University of Life Sciences, Warsaw, Poland
| | - Carl J Schmidt
- Department of Animal and Food Science, University of Delaware, Newark, DE, USA
| | - Robert L Taylor
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV, USA
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Fulton JE, Drobik-Czwarno W, Lund AR, Schmidt CJ, Taylor RL. CD99 and the Chicken Alloantigen D Blood System. Genes (Basel) 2023; 14:402. [PMID: 36833329 PMCID: PMC9957549 DOI: 10.3390/genes14020402] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2022] [Revised: 12/09/2022] [Accepted: 01/28/2023] [Indexed: 02/05/2023] Open
Abstract
The chicken D blood system is one of 13 alloantigen systems found on chicken red blood cells. Classical recombinant studies located the D blood system on chicken chromosome 1, but the candidate gene was unknown. Multiple resources were utilized to identify the chicken D system candidate gene, including genome sequence information from both research and elite egg production lines for which D system alloantigen alleles were reported, and DNA from both pedigree and non-pedigree samples with known D alleles. Genome-wide association analyses using a 600 K or a 54 K SNP chip plus DNA from independent samples identified a strong peak on chicken chromosome 1 at 125-131 Mb (GRCg6a). Cell surface expression and the presence of exonic non-synonymous SNP were used to identify the candidate gene. The chicken CD99 gene showed the co-segregation of SNP-defined haplotypes and serologically defined D blood system alleles. The CD99 protein mediates multiple cellular processes including leukocyte migration, T-cell adhesion, and transmembrane protein transport, affecting peripheral immune responses. The corresponding human gene is found syntenic to the pseudoautosomal region 1 of human X and Y chromosomes. Phylogenetic analyses show that CD99 has a paralog, XG, that arose by duplication in the last common ancestor of the amniotes.
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Affiliation(s)
| | - Wiola Drobik-Czwarno
- Department of Animal Genetics and Conservation, Institute of Animal Science, Warsaw University of Life Sciences, 02-787 Warsaw, Poland
| | | | - Carl J. Schmidt
- Department of Animal and Food Science, University of Delaware, Newark, DE 19716, USA
| | - Robert L. Taylor
- Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV 26506, USA
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Fulton JE, Drobik-Czwarno W, Wolc A, McCarron AM, Lund AR, Schmidt CJ, Taylor RL. The Chicken A and E Blood Systems Arise from Genetic Variation in and around the Regulators of Complement Activation Region. THE JOURNAL OF IMMUNOLOGY 2022; 209:1128-1137. [DOI: 10.4049/jimmunol.2101010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/20/2021] [Accepted: 07/07/2022] [Indexed: 01/04/2023]
Abstract
Abstract
The tightly linked A and E blood alloantigen systems are 2 of 13 blood systems identified in chickens. Reported herein are studies showing that the genes encoding A and E alloantigens map within or near to the chicken regulator of complement activation (RCA) gene cluster, a region syntenic with the human RCA. Genome-wide association studies, sequence analysis, and sequence-derived single-nucleotide polymorphism information for known A and/or E system alleles show that the most likely candidate gene for the A blood system is C4BPM gene (complement component 4 binding protein, membrane). Cosegregation of single-nucleotide polymorphism–defined C4BPM haplotypes and blood system A alleles defined by alloantisera provide a link between chicken blood system A and C4BPM. The best match for the E blood system is the avian equivalent of FCAMR (Fc fragment of IgA and IgM receptor). C4BPM is located within the chicken RCA on chicken microchromosome 26 and is separated from FCAMR by 89 kbp. The genetic variation observed at C4BPM and FCAMR could affect the chicken complement system and differentially guide immune responses to infectious diseases.
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Affiliation(s)
- Janet E. Fulton
- *Research and Development, Hy-Line International, Dallas Center, IA
| | - Wiola Drobik-Czwarno
- †Department of Animal Genetics and Conservation, Institute of Animal Science, Warsaw University of Life Sciences, Warsaw, Poland
| | - Anna Wolc
- *Research and Development, Hy-Line International, Dallas Center, IA
- ‡Department of Animal Science, Iowa State University, Ames, IA
| | - Amy M. McCarron
- *Research and Development, Hy-Line International, Dallas Center, IA
| | - Ashlee R. Lund
- *Research and Development, Hy-Line International, Dallas Center, IA
| | - Carl J. Schmidt
- §Department of Animal and Food Science, University of Delaware, Newark, DE; and
| | - Robert L. Taylor
- ¶Division of Animal and Nutritional Sciences, West Virginia University, Morgantown, WV
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Romanov M, Sazanov A, Smirnov A. First century of chicken gene study and mapping – a look back and forward. WORLD POULTRY SCI J 2019. [DOI: 10.1079/wps20032] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Affiliation(s)
- M.N. Romanov
- Department of Microbiology and Molecular Genetics, 2209 Biomedical Physical Sciences, Michigan State University, East Lansing, MI 48824–4320, USA
| | - A.A. Sazanov
- All-Russian Institute of Animal Genetics and Breeding, Russian Academy of Agricultural Science, Moskovskoye shosse 55A, St Petersburg – Pushkin 189620, Russia
- Biological Research Institute, St Petersburg State University, Oranienbaumskoye shosse 2, St Petersburg – Stary Petergof 198504, Russia
| | - A.F. Smirnov
- All-Russian Institute of Animal Genetics and Breeding, Russian Academy of Agricultural Science, Moskovskoye shosse 55A, St Petersburg – Pushkin 189620, Russia
- Biological Research Institute, St Petersburg State University, Oranienbaumskoye shosse 2, St Petersburg – Stary Petergof 198504, Russia
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6
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Romanov MN, Betuel AM, Chemnick LG, Ryder OA, Kulibaba RO, Tereshchenko OV, Payne WS, Delekta PC, Dodgson JB, Tuttle EM, Gonser RA. Widely Applicable PCR Markers for Sex Identification in Birds. RUSS J GENET+ 2019. [DOI: 10.1134/s1022795419020121] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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Rodrigues P, Gutiérrez J, Seguel M, Verdugo C. Complete mitochondrial genome of the South American fur seal ( Arctocephalus australis). MITOCHONDRIAL DNA PART B-RESOURCES 2017; 2:871-872. [PMID: 33474016 PMCID: PMC7799521 DOI: 10.1080/23802359.2017.1407692] [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] [Indexed: 12/02/2022]
Abstract
The complete mitochondrial DNA sequence of the South America fur seal (Arctocephalus australis) was obtained by a shotgun sequencing approach. The mitogenome is 16,372 bp in length and includes the genes coding for the two rRNA species (12S and 16S), 13 protein-coding genes, 22 transfer RNA genes, and a control region. The base composition is 33.0% for A, 26.7% for C, 26.1 for T and 14.2% for G, with an overall GC content of 40.9%. The description of this mitogenome will be useful for further phylogeny and genetic studies on Pinnipeds.
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Affiliation(s)
- Pedro Rodrigues
- Instituto de Patología Animal, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
| | - Josefina Gutiérrez
- Instituto de Patología Animal, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile.,Programa de Investigación Aplicada en Fauna Silvestre, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
| | - Mauricio Seguel
- Department of Pathology, College of Veterinary Medicine, University of Georgia, Athens, GA, USA
| | - Claudio Verdugo
- Instituto de Patología Animal, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile.,Programa de Investigación Aplicada en Fauna Silvestre, Facultad de Ciencias Veterinarias, Universidad Austral de Chile, Valdivia, Chile
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Rodrigues P, Álvarez P, Verdugo C. Complete mitochondrial genome of the Neotropic cormorant (Phalacrocorax brasilianus). Mitochondrial DNA A DNA Mapp Seq Anal 2015; 28:401-402. [PMID: 26713786 DOI: 10.3109/19401736.2015.1127364] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
The complete sequence of the Neotropic cormorant (Phalacrocorax brasilianus) mitochondrial DNA was obtained by the shotgun sequencing approach. The mitogenome is 19 042 bp in length and includes 13 protein-coding genes, 2 ribosomal subunit genes, 22 transfer RNA genes, a control region and a duplicated region of 2418 bp. The base composition is 32.1% for C, 31.8% for A, 22.6% for T and 13.4% for G, with an overall GC content of 45.5%. This is the first mitogenome of the P. brasilianus described and will be a useful tool for further phylogenetic and population genetic studies.
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Affiliation(s)
- Pedro Rodrigues
- a Instituto De Patología Animal, Facultad De Ciencias Veterinarias, Universidad Austral De Chile , Valdivia , Chile
| | - Pedro Álvarez
- a Instituto De Patología Animal, Facultad De Ciencias Veterinarias, Universidad Austral De Chile , Valdivia , Chile
| | - Claudio Verdugo
- a Instituto De Patología Animal, Facultad De Ciencias Veterinarias, Universidad Austral De Chile , Valdivia , Chile.,b Programa De Investigación Aplicada En Fauna Silvestre, Facultad De Ciencias Veterinarias, Universidad Austral De Chile , Valdivia , Chile
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Sodhi SS, Jeong DK, Sharma N, Lee JH, Kim JH, Kim SH, Kim SW, Oh SJ. Marker Assisted Selection-Applications and Evaluation for Commercial Poultry Breeding. ACTA ACUST UNITED AC 2013. [DOI: 10.5536/kjps.2013.40.3.223] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
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Dawson DA, Ball AD, Spurgin LG, Martín-Gálvez D, Stewart IRK, Horsburgh GJ, Potter J, Molina-Morales M, Bicknell AWJ, Preston SAJ, Ekblom R, Slate J, Burke T. High-utility conserved avian microsatellite markers enable parentage and population studies across a wide range of species. BMC Genomics 2013; 14:176. [PMID: 23497230 PMCID: PMC3738869 DOI: 10.1186/1471-2164-14-176] [Citation(s) in RCA: 50] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2012] [Accepted: 02/19/2013] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND Microsatellites are widely used for many genetic studies. In contrast to single nucleotide polymorphism (SNP) and genotyping-by-sequencing methods, they are readily typed in samples of low DNA quality/concentration (e.g. museum/non-invasive samples), and enable the quick, cheap identification of species, hybrids, clones and ploidy. Microsatellites also have the highest cross-species utility of all types of markers used for genotyping, but, despite this, when isolated from a single species, only a relatively small proportion will be of utility. Marker development of any type requires skill and time. The availability of sufficient "off-the-shelf" markers that are suitable for genotyping a wide range of species would not only save resources but also uniquely enable new comparisons of diversity among taxa at the same set of loci. No other marker types are capable of enabling this. We therefore developed a set of avian microsatellite markers with enhanced cross-species utility. RESULTS We selected highly-conserved sequences with a high number of repeat units in both of two genetically distant species. Twenty-four primer sets were designed from homologous sequences that possessed at least eight repeat units in both the zebra finch (Taeniopygia guttata) and chicken (Gallus gallus). Each primer sequence was a complete match to zebra finch and, after accounting for degenerate bases, at least 86% similar to chicken. We assessed primer-set utility by genotyping individuals belonging to eight passerine and four non-passerine species. The majority of the new Conserved Avian Microsatellite (CAM) markers amplified in all 12 species tested (on average, 94% in passerines and 95% in non-passerines). This new marker set is of especially high utility in passerines, with a mean 68% of loci polymorphic per species, compared with 42% in non-passerine species. CONCLUSIONS When combined with previously described conserved loci, this new set of conserved markers will not only reduce the necessity and expense of microsatellite isolation for a wide range of genetic studies, including avian parentage and population analyses, but will also now enable comparisons of genetic diversity among different species (and populations) at the same set of loci, with no or reduced bias. Finally, the approach used here can be applied to other taxa in which appropriate genome sequences are available.
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Affiliation(s)
- Deborah A Dawson
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Alexander D Ball
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
- Current address: Department of Biology and Biochemistry, University of Bath, Bath, BA2 7AY, UK
| | - Lewis G Spurgin
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
- School of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK
| | - David Martín-Gálvez
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
- Current address: Estación Experimental de Zonas Áridas (CSIC), Almería, E-04120, Spain
| | - Ian R K Stewart
- Department of Biology, University of Delaware, Newark, DE, 19716, USA
| | - Gavin J Horsburgh
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Jonathan Potter
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Mercedes Molina-Morales
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
- Current address: Departamento de Zoología, Universidad de Granada, Granada, E-18071, Spain
| | - Anthony W J Bicknell
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
- Current address: Plymouth University, Marine Biology and Ecology Research Centre, Davy Building, Drake Circus, Plymouth, PL4 8AA, UK
| | - Stephanie A J Preston
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Robert Ekblom
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
- Current address: Department of Ecology and Genetics, Uppsala University, Norbyv. 18D, Uppsala, SE-75236, Sweden
| | - Jon Slate
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
| | - Terry Burke
- Department of Animal and Plant Sciences, University of Sheffield, Sheffield, S10 2TN, UK
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Douaud M, Feve K, Pituello F, Gourichon D, Boitard S, Leguern E, Coquerelle G, Vieaud A, Batini C, Naquet R, Vignal A, Tixier-Boichard M, Pitel F. Epilepsy caused by an abnormal alternative splicing with dosage effect of the SV2A gene in a chicken model. PLoS One 2011; 6:e26932. [PMID: 22046416 PMCID: PMC3203167 DOI: 10.1371/journal.pone.0026932] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2011] [Accepted: 10/06/2011] [Indexed: 11/18/2022] Open
Abstract
Photosensitive reflex epilepsy is caused by the combination of an individual's enhanced sensitivity with relevant light stimuli, such as stroboscopic lights or video games. This is the most common reflex epilepsy in humans; it is characterized by the photoparoxysmal response, which is an abnormal electroencephalographic reaction, and seizures triggered by intermittent light stimulation. Here, by using genetic mapping, sequencing and functional analyses, we report that a mutation in the acceptor site of the second intron of SV2A (the gene encoding synaptic vesicle glycoprotein 2A) is causing photosensitive reflex epilepsy in a unique vertebrate model, the Fepi chicken strain, a spontaneous model where the neurological disorder is inherited as an autosomal recessive mutation. This mutation causes an aberrant splicing event and significantly reduces the level of SV2A mRNA in homozygous carriers. Levetiracetam, a second generation antiepileptic drug, is known to bind SV2A, and SV2A knock-out mice develop seizures soon after birth and usually die within three weeks. The Fepi chicken survives to adulthood and responds to levetiracetam, suggesting that the low-level expression of SV2A in these animals is sufficient to allow survival, but does not protect against seizures. Thus, the Fepi chicken model shows that the role of the SV2A pathway in the brain is conserved between birds and mammals, in spite of a large phylogenetic distance. The Fepi model appears particularly useful for further studies of physiopathology of reflex epilepsy, in comparison with induced models of epilepsy in rodents. Consequently, SV2A is a very attractive candidate gene for analysis in the context of both mono- and polygenic generalized epilepsies in humans.
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Affiliation(s)
- Marine Douaud
- INRA-ENVT, Laboratoire de Génétique Cellulaire, Castanet-Tolosan, France
| | - Katia Feve
- INRA-ENVT, Laboratoire de Génétique Cellulaire, Castanet-Tolosan, France
| | - Fabienne Pituello
- CNRS-Université Toulouse III, Centre de Biologie du Développement, Toulouse, France
| | - David Gourichon
- INRA PEAT, Pôle d'Expérimentation Avicole de Tours, Nouzilly, France
| | - Simon Boitard
- INRA-ENVT, Laboratoire de Génétique Cellulaire, Castanet-Tolosan, France
| | - Eric Leguern
- INSERM, Neurogénétique Moléculaire et Cellulaire, Paris, France
| | - Gérard Coquerelle
- INRA, Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France
| | - Agathe Vieaud
- INRA, Génétique Animale et Biologie Intégrative, Jouy-en-Josas, France
| | - Cesira Batini
- CNRS, Laboratoire de Génétique Moléculaire de la Neurotransmission et des Processus Neurodégénératifs, Paris, France
| | - Robert Naquet
- CNRS, Institut de Neurobiologie Alfred Fessard, Gif-sur-Yvette, France
| | - Alain Vignal
- INRA-ENVT, Laboratoire de Génétique Cellulaire, Castanet-Tolosan, France
| | | | - Frédérique Pitel
- INRA-ENVT, Laboratoire de Génétique Cellulaire, Castanet-Tolosan, France
- * E-mail:
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Robb EA, Gitter CL, Cheng HH, Delany ME. Chromosomal mapping and candidate gene discovery of chicken developmental mutants and genome-wide variation analysis of MHC congenics. ACTA ACUST UNITED AC 2011; 102:141-56. [PMID: 21273214 DOI: 10.1093/jhered/esq122] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
The chicken has been widely used in experimental research given its importance to agriculture and its utility as a model for vertebrate biology and biomedical pursuits for over 100 years. Herein we used advanced technologies to investigate the genomic characteristics of specialized chicken congenic genetic resources developed on a highly inbred background. An Illumina 3K chicken single nucleotide polymorphism (SNP) array was utilized to study variation within and among major histocompatibility complex (MHC)-congenic lines as well as investigate line-specific genomic diversity, inbreeding coefficients, and MHC B haplotype-specific GGA 16 SNP profiles. We also investigated developmental mutant-congenic lines to map a number of single-gene mutations using both the Illumina 3K array and a recently developed Illumina 60K chicken SNP array. In addition to identifying the chromosomes and specific subregions, the mapping results affirmed prior analyses indicating recessive or dominant and autosomal or sex chromosome modes of inheritance. Priority candidate genes are described for each mutation based on association with similar phenotypes in other vertebrates. These single-gene mutations provide a means of studying amniote development and in particular serve as invaluable biomedical models for similar malformations found in human.
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Affiliation(s)
- Elizabeth A Robb
- Department of Animal Science, University of California, Davis, CA 95616, USA
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Solinhac R, Leroux S, Galkina S, Chazara O, Feve K, Vignoles F, Morisson M, Derjusheva S, Bed'hom B, Vignal A, Fillon V, Pitel F. Integrative mapping analysis of chicken microchromosome 16 organization. BMC Genomics 2010; 11:616. [PMID: 21050458 PMCID: PMC3091757 DOI: 10.1186/1471-2164-11-616] [Citation(s) in RCA: 37] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2010] [Accepted: 11/04/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The chicken karyotype is composed of 39 chromosome pairs, of which 9 still remain totally absent from the current genome sequence assembly, despite international efforts towards complete coverage. Some others are only very partially sequenced, amongst which microchromosome 16 (GGA16), particularly under-represented, with only 433 kb assembled for a full estimated size of 9 to 11 Mb. Besides the obvious need of full genome coverage with genetic markers for QTL (Quantitative Trait Loci) mapping and major genes identification studies, there is a major interest in the detailed study of this chromosome because it carries the two genetically independent MHC complexes B and Y. In addition, GGA16 carries the ribosomal RNA (rRNA) genes cluster, also known as the NOR (nucleolus organizer region). The purpose of the present study is to construct and present high resolution integrated maps of GGA16 to refine its organization and improve its coverage with genetic markers. RESULTS We developed 79 STS (Sequence Tagged Site) markers to build a physical RH (radiation hybrid) map and 34 genetic markers to extend the genetic map of GGA16. We screened a BAC (Bacterial Artificial Chromosome) library with markers for the MHC-B, MHC-Y and rRNA complexes. Selected clones were used to perform high resolution FISH (Fluorescent In Situ Hybridization) mapping on giant meiotic lampbrush chromosomes, allowing meiotic mapping in addition to the confirmation of the order of the three clusters along the chromosome. A region with high recombination rates and containing PO41 repeated elements separates the two MHC complexes. CONCLUSIONS The three complementary mapping strategies used refine greatly our knowledge of chicken microchromosome 16 organisation. The characterisation of the recombination hotspots separating the two MHC complexes demonstrates the presence of PO41 repetitive sequences both in tandem and inverted orientation. However, this region still needs to be studied in more detail.
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Affiliation(s)
- Romain Solinhac
- UMR INRA/ENVT Laboratoire de Génétique Cellulaire, INRA, Castanet-Tolosan, 31326, France
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Khatib H, Genislav E, Soller M. Chicken microsatellites at the HUJERELA and HUJ106 loci. Anim Genet 2009. [DOI: 10.1111/j.1365-2052.1994.tb00454.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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Hest BJV, Sheldon BL, Molloy PL, Frankham R. Heat shock protein gene HSP108 and a replication histone gene cluster are linked in the chicken. Anim Genet 2009. [DOI: 10.1111/j.1365-2052.1994.tb00437.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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16
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Khatib H, Genislav E, Soller M. Chicken microsatellites at the HUJERELA and HUJ106 loci. Anim Genet 2009. [DOI: 10.1111/j.1365-2052.1994.tb00062.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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17
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Hest BJ, Molloy PL, Frankham R, Sheldon BL. Heat shock protein gene HSP108 and a replication histone gene cluster are linked in the chicken. Anim Genet 2009. [DOI: 10.1111/j.1365-2052.1994.tb00089.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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18
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Levin I, Cheng HH, Baxter-Jones C, Hillel J. Turkey microsatellite DNA loci amplified by chicken-specific primers. Anim Genet 2009. [DOI: 10.1111/j.1365-2052.1995.tb02642.x] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
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Groenen MAM, Wahlberg P, Foglio M, Cheng HH, Megens HJ, Crooijmans RPMA, Besnier F, Lathrop M, Muir WM, Wong GKS, Gut I, Andersson L. A high-density SNP-based linkage map of the chicken genome reveals sequence features correlated with recombination rate. Genes Dev 2009; 19:510-9. [PMID: 19088305 PMCID: PMC2661806 DOI: 10.1101/gr.086538.108] [Citation(s) in RCA: 200] [Impact Index Per Article: 13.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2008] [Accepted: 12/04/2008] [Indexed: 11/25/2022]
Abstract
The resolution of the chicken consensus linkage map has been dramatically improved in this study by genotyping 12,945 single nucleotide polymorphisms (SNPs) on three existing mapping populations in chicken: the Wageningen (WU), East Lansing (EL), and Uppsala (UPP) mapping populations. As many as 8599 SNPs could be included, bringing the total number of markers in the current consensus linkage map to 9268. The total length of the sex average map is 3228 cM, considerably smaller than previous estimates using the WU and EL populations, reflecting the higher quality of the new map. The current map consists of 34 linkage groups and covers at least 29 of the 38 autosomes. Sex-specific analysis and comparisons of the maps based on the three individual populations showed prominent heterogeneity in recombination rates between populations, but no significant heterogeneity between sexes. The recombination rates in the F(1) Red Jungle fowl/White Leghorn males and females were significantly lower compared with those in the WU broiler population, consistent with a higher recombination rate in purebred domestic animals under strong artificial selection. The recombination rate varied considerably among chromosomes as well as along individual chromosomes. An analysis of the sequence composition at recombination hot and cold spots revealed a strong positive correlation between GC-rich sequences and high recombination rates. The GC-rich cohesin binding sites in particular stood out from other GC-rich sequences with a 3.4-fold higher density at recombination hot spots versus cold spots, suggesting a functional relationship between recombination frequency and cohesin binding.
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Affiliation(s)
- Martien A M Groenen
- Animal Breeding and Genomics Centre, Wageningen University, 6700 AH Wageningen, The Netherlands.
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20
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Hu X, Gao Y, Feng C, Liu Q, Wang X, Du Z, Wang Q, Li N. Advanced technologies for genomic analysis in farm animals and its application for QTL mapping. Genetica 2008; 136:371-86. [DOI: 10.1007/s10709-008-9338-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2008] [Accepted: 11/19/2008] [Indexed: 12/25/2022]
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21
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Noakes MA, Campbell MT, Van Hest BJ. The chicken CLOCK
gene maps to chromosome 4. Anim Genet 2008. [DOI: 10.1111/j.1365-2052.2000.00666.pp.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
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22
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Addition of the microchromosome GGA25 to the chicken genome sequence assembly through radiation hybrid and genetic mapping. BMC Genomics 2008; 9:129. [PMID: 18366813 PMCID: PMC2275740 DOI: 10.1186/1471-2164-9-129] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2007] [Accepted: 03/17/2008] [Indexed: 12/01/2022] Open
Abstract
Background The publication of the first draft chicken sequence assembly became available in 2004 and was updated in 2006. However, this does not constitute a definitive and complete sequence of the chicken genome, since the microchromosomes are notably under-represented. In an effort to develop maps for the microchromosomes absent from the chicken genome assembly, we developed radiation hybrid (RH) and genetic maps with markers isolated from sequence currently assigned to "chromosome Unknown" (chrUn). The chrUn is composed of sequence contigs not assigned to named chromosomes. To identify and map sequence belonging to the microchromosomes we used a comparative mapping strategy, and we focused on the small linkage group E26C13. Results In total, 139 markers were analysed with the chickRH6 panel, of which 120 were effectively assigned to the E26C13 linkage group, the remainder mapping elsewhere in the genome. The final RH map is composed of 22 framework markers extending over a 245.6 cR distance. A corresponding genetic map was developed, whose length is 103 cM in the East Lansing reference population. The E26C13 group was assigned to GGA25 (Gallus gallus chromosome 25) by FISH (fluorescence in situ hybridisation) mapping. Conclusion The high-resolution RH framework map obtained here covers the entire chicken chromosome 25 and reveals the existence of a high number of intrachromosomal rearrangements when compared to the human genome. The strategy used here for the characterization of GGA25 could be used to improve knowledge on the other uncharacterized small, yet gene-rich microchromosomes.
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23
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Temperley ND, Berlin S, Paton IR, Griffin DK, Burt DW. Evolution of the chicken Toll-like receptor gene family: a story of gene gain and gene loss. BMC Genomics 2008; 9:62. [PMID: 18241342 PMCID: PMC2275738 DOI: 10.1186/1471-2164-9-62] [Citation(s) in RCA: 231] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2007] [Accepted: 02/01/2008] [Indexed: 12/23/2022] Open
Abstract
Background Toll-like receptors (TLRs) perform a vital role in disease resistance through their recognition of pathogen associated molecular patterns (PAMPs). Recent advances in genomics allow comparison of TLR genes within and between many species. This study takes advantage of the recently sequenced chicken genome to determine the complete chicken TLR repertoire and place it in context of vertebrate genomic evolution. Results The chicken TLR repertoire consists of ten genes. Phylogenetic analyses show that six of these genes have orthologs in mammals and fish, while one is only shared by fish and three appear to be unique to birds. Furthermore the phylogeny shows that TLR1-like genes arose independently in fish, birds and mammals from an ancestral gene also shared by TLR6 and TLR10. All other TLRs were already present prior to the divergence of major vertebrate lineages 550 Mya (million years ago) and have since been lost in certain lineages. Phylogenetic analysis shows the absence of TLRs 8 and 9 in chicken to be the result of gene loss. The notable exception to the tendency of gene loss in TLR evolution is found in chicken TLRs 1 and 2, each of which underwent gene duplication about 147 and 65 Mya, respectively. Conclusion Comparative phylogenetic analysis of vertebrate TLR genes provides insight into their patterns and processes of gene evolution, with examples of both gene gain and gene loss. In addition, these comparisons clarify the nomenclature of TLR genes in vertebrates.
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Affiliation(s)
- Nicholas D Temperley
- Department of Genomics and Genetics, Roslin Institute (Edinburgh), Roslin, Midlothian EH25 9PS, UK.
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24
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Reed KM, Chaves LD, Mendoza KM. An integrated and comparative genetic map of the turkey genome. Cytogenet Genome Res 2007; 119:113-26. [PMID: 18160790 DOI: 10.1159/000109627] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2007] [Accepted: 05/15/2007] [Indexed: 12/30/2022] Open
Abstract
An integrated genetic linkage map was developed for the turkey (Meleagris gallopavo) that combines the genetic markers from the three previous mapping efforts. The UMN integrated map includes 613 loci arranged into 41 linkage groups. An additional 105 markers are tentatively placed within linkage groups based on two-point LOD scores and 19 markers remain unlinked. A total of 210 previously unmapped markers has been added to the UMN turkey genetic map. Markers from each of the 20 linkage groups identified in the Roslin map and the 22 linkage groups of the Nte map are incorporated into the new integrated map. Overall map distance contained within the 41 linkage groups is 3,365 cM (sex-averaged) with the largest linkage group (94 loci) measuring 533.1 cM. Average marker interval for the map was 7.86 cM. Sequences of markers included in the new map were compared to the chicken genome sequence by 'BLASTN'. Significant similarity scores were obtained for 95.6% of the turkey sequences encompassing an estimated 91% of the chicken genome. A physical map of the chicken genome based on positions of the turkey sequences was built and 36 of the 41 turkey linkage groups were aligned with the physical map, five linkage groups remain unassigned. Given the close similarities between the turkey and chicken genomes, the chicken genome sequence could serve as a scaffold for a genome sequencing effort in the turkey.
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Affiliation(s)
- K M Reed
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN, USA.
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25
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Abstract
The sequencing of the chicken genome has generated a wealth of good news for poultry science. It allows the chicken to be a major player in 21st century biology by providing an entrée into an arsenal of new technologies that can be used to explore virtually any chicken phenotype of interest. The initial technological onslaught has been described in this symposium. The wealth of data available now or soon to be available cannot be explained by simplistic models and will force us to treat the inherent complexity of the chicken in ways that are more realistic but at the same time more difficult to comprehend. Initial single nucleotide polymorphism analyses suggest that broilers retain a remarkable amount of the genetic diversity of predomesticated Jungle Fowl, whereas commercial layer genomes display less diversity and broader linkage disequilibrium. Thus, intensive commercial selection has not fixed a genome rich in wide selective sweeps, at least within the broiler population. Rather, a complex assortment of combinations of ancient allelic diversity survives. Low levels of linkage disequilibrium will make association analysis in broilers more difficult. The wider disequilibrium observed in layers should facilitate the mapping of quantitative trait loci, and at the same time make it more difficult to identify the causative nucleotide change(s). In addition, many quantitative traits may be specific to the genetic background in which they arose and not readily transferable to, or detectable in, other line backgrounds. Despite the obstacles it presents, the genetic complexity of the chicken may also be viewed as good news because it insures that long-term genetic progress will continue via breeding using quantitative genetics, and it surely will keep poultry scientists busy for decades to come. It is now time to move from an emphasis on obtaining "THE" chicken genome sequence to obtaining multiple sequences, especially of foundation stocks, and a broader understanding of the full genetic and phenotypic diversity of the domesticated chicken.
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Affiliation(s)
- J B Dodgson
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing 48824, USA.
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26
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Pardo BG, Fernández C, Hermida M, Vázquez-López A, Pérez M, Presa P, Calaza M, Alvarez-Dios JA, Comesaña AS, Raposo-Guillán J, Bouza C, Martínez P. Development and characterization of 248 novel microsatellite markers in turbot (Scophthalmus maximus). Genome 2007; 50:329-32. [PMID: 17502907 DOI: 10.1139/g06-154] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The turbot is a flatfish species of great relevance to marine aquaculture in Europe. Only a limited number of microsatellites have been isolated to date in this species. To increase the number of potentially useful mapping markers, we screened simple sequence repeat (SSR) - enriched genomic libraries obtained from several di-, tri-, and tetranucleotide tandem repeat motifs. A total of 248 new polymorphic microsatellites were successfully optimized. The efficiency of the protocol applied (6.4%) was higher than that in other studies of fish that used the same method. Dinucleotide and perfect microsatellites were predominant in this species; the (AC)n motif was the most frequent class of repeat. Polymorphism and structural properties at these loci, together with 30 variable loci previously reported in turbot, were evaluated in 6 wild individuals. The number of alleles per locus ranged from 2 to 10, with an average of 4.046. The microsatellite markers characterized in this study will contribute to the development of the turbot genetic map, which can be used for quantitative trait locus (QTL) identification, marker-assisted selection programs, and other applications to improve its culture.
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Affiliation(s)
- B G Pardo
- Departamento de Genética, Facultad de Veterinaria, Universidad de Santiago de Compostela, Spain
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27
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Abstract
The chicken has a proud history, both in genetic research and as a source of food. Here we attempt to provide an overview of past contributions of the chicken in both arenas and to link those contributions to the near future from a genetic perspective. Companion articles will discuss current poultry genetics research in greater detail. The chicken was the first animal species in which Mendelian inheritance was demonstrated. A century later, the chicken was the first among farm animals to have its genome sequenced. Between these firsts, the chicken remained a key organism used in genetic research. Breeding programs, based on sound genetic principles, facilitated the global emergence of the chicken meat and egg industries. Concomitantly, the chicken served as a model whose experimental populations and mutant stocks were used in basic and applied studies with broad application to other species, including humans. In this paper, we review some of these contributions, trace the path from the origin of molecular genetics to the sequence of the chicken genome, and discuss the merits of the chicken as a model organism for furthering our understanding of biology.
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Affiliation(s)
- P B Siegel
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg 24061, USA.
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28
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Zhou H, Deeb N, Evock-Clover CM, Ashwell CM, Lamont SJ. Genome-Wide Linkage Analysis to Identify Chromosomal Regions Affecting Phenotypic Traits in the Chicken. I. Growth and Average Daily Gain. Poult Sci 2006; 85:1700-11. [PMID: 17012159 DOI: 10.1093/ps/85.10.1700] [Citation(s) in RCA: 43] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
A genome scan was used to detect chromosomal regions and QTL that control quantitative traits of economic importance in chickens. Two unique F(2) crosses generated from a commercial broiler male line and 2 genetically distinct inbred lines (Leghorn and Fayoumi) were used to identify QTL affecting BW and daily average gain traits in chickens. Body weight at 2, 4, 6, and 8 wk was measured in the 2 F(2) crosses. Birds were genotyped for 269 microsatellite markers across the entire genome. Linkage distance among microsatellite markers was estimated by the CRIMAP program. The program QTL Express was used for QTL detection. Significance levels were obtained using the permutation test. For the 8 traits, a total of 18 and 13 significant QTL were detected at a 1% chromosome-wise significance level, of which 17 and 10 were significant at the 5% genome-wise level for the broiler-Leghorn cross and broiler-Fayoumi cross, respectively. Highly correlated growth traits showed similar QTL profiles within each cross but different QTL profiles between the 2 crosses. Most QTL for growth traits in the current study were detected in Gga 1, 2, 4, 7, and 14 for the broiler-Leghorn cross and Gga 1, 2, 4, 5, 8, and 13 for the broiler-Fayoumi cross. Potential candidate genes within the QTL region for growth traits at 1% chromosome-wise significance level were discussed. The results in the current study lay the foundations for fine mapping these traits in the advanced intercross lines and provide a start point for identification causative genes responsible for growth traits in chickens.
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Affiliation(s)
- H Zhou
- Department of Animal Science, Iowa State University, Ames 50011, USA
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29
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Abstract
Poultry genetic resources, which are valuable for research, span an impressive gamut from breeds to highly specialized inbred lines. The community of scientists utilizing specialized lines is broad, including researchers in medicine, basic biology, and agricultural science. The majority of specialized research lines used by such scientists are held at land grant universities. Over the prior 2 decades, hundreds of lines were eliminated. This pattern continues today with no evidence of abatement. Awareness and visibility of the causes and ongoing problems have been highlighted via a number of high-profile forums. Given the large community of scientists and the negative impact on future advances in biological, medical, and agricultural research as these genetic resources dwindle, the issue is of national interest and warrants federal funding to support a united network of avian and poultry stocks centers.
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Affiliation(s)
- M E Delany
- Department of Animal Science, University of California, Davis 95616, USA.
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30
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Huang Y, Zhao Y, Haley CS, Hu S, Hao J, Wu C, Li N. A genetic and cytogenetic map for the duck (Anas platyrhynchos). Genetics 2006; 173:287-96. [PMID: 16510785 PMCID: PMC1461431 DOI: 10.1534/genetics.105.053256] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
A genetic linkage map for the duck (Anas platyrhynchos) was developed within a cross between two extreme Peking duck lines by linkage analysis of 155 polymorphic microsatellite markers, including 84 novel markers reported in this study. A total of 115 microsatellite markers were placed into 19 linkage groups. The sex-averaged map spans 1353.3 cM, with an average interval distance of 15.04 cM. The male map covers 1415 cM, whereas the female map covers only 1387.6 cM. All of the flanking sequences of the 155 polymorphic loci--44 monomorphic loci and a further 41 reported microsatellite loci for duck--were blasted against the chicken genomic sequence, and corresponding orthologs were found for 49. To integrate the genetic and cytogenetic map of the duck genome, 28 BAC clones were screened from a chicken BAC library using the specific PCR primers and localized to duck chromosomes by FISH, respectively. Of 28 BAC clones, 24 were detected definitely on duck chromosomes. Thus, 11 of 19 linkage groups were localized to 10 duck chromosomes. This genetic and cytogenetic map will be helpful for the mapping QTL in duck for breeding applications and for conducting genomic comparisons between chicken and duck.
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Affiliation(s)
- Yinhua Huang
- State Key Laboratory for Agrobiotechnology, China Agricultural University, Beijing 100094, People's Republic of China
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31
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O'Hare TH, Delany ME. Telomerase gene expression in the chicken: Telomerase RNA (TR) and reverse transcriptase (TERT) transcript profiles are tissue-specific and correlate with telomerase activity. AGE (DORDRECHT, NETHERLANDS) 2005; 27:257-266. [PMID: 23598659 PMCID: PMC3455884 DOI: 10.1007/s11357-005-4558-6] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2005] [Revised: 08/31/2005] [Accepted: 09/05/2005] [Indexed: 06/02/2023]
Abstract
Telomerase is the specialized enzyme which replicates the telomeres, thus maintaining the integrity of the chromosome ends; in absence of enzyme activity telomere lengths decrease, ultimately impacting genome stability. In this study, we examined the mRNA expression of both enzyme components, the RNA template (TR) and catalytic subunit (TERT) during growth and development of the chicken to better understand mechanisms which regulate telomerase activity in vertebrates. Quantitative real-time PCR was used to establish transcript profiles for six ages ranging from pre-blastula to two-year old adults. Organ-specific profiles were established for brain, heart, liver, intestine, spleen and gonad. The pre-blastula and gastrula stages exhibited very high transcript levels of both telomerase components; organs from the embryos and adult showed transcript levels either similar or down-regulated relative to the early differentiation embryo stages. Organs which are known to become negative for telomerase activity between the embryo and adult stages (brain, heart, liver) exhibited down-regulation of TR and either no change or an increase in TERT transcripts. Whereas, organs which maintain high telomerase activity even in adults (intestine, spleen, gonad), generally exhibited up-regulation of transcripts for both components. However, there were some tissue-specific differences between telomerase-positive tissues. These results show that TERT and TR transcript levels correlate with telomerase activity profiles and suggest that TR is the rate-limiting component in telomerase-negative tissues.
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Affiliation(s)
- Thomas H. O'Hare
- Department of Animal Science, University of California, 2131D Meyer Hall, One Shields Avenue, Davis, CA 95616 USA
| | - Mary E. Delany
- Department of Animal Science, University of California, 2131D Meyer Hall, One Shields Avenue, Davis, CA 95616 USA
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32
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Benkel BF, Nguyen T, Uno Y, Ponce de León FA, Hickey DA. Structural organization and chromosomal location of the chicken alpha-amylase gene family. Gene 2005; 362:117-24. [PMID: 16226407 DOI: 10.1016/j.gene.2005.07.030] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2005] [Revised: 05/19/2005] [Accepted: 06/29/2005] [Indexed: 11/30/2022]
Abstract
Characterization of the Gallus gallus alpha-amylase gene family revealed that the chicken genome contains two distinct amy loci. One of the two loci is expressed in the chicken pancreas while cDNA clones for the second locus were detected in a library constructed from liver mRNA. Fluorescent in situ hybridization to chromosome spreads showed that the two loci are both located on chromosome 8 within the chicken genome. Moreover, each locus contains both an intact, expressed gene copy as well as a pseudogene. The expressed gene and the pseudogene are arranged in a divergent configuration in the pancreatic amy locus, while in the hepatic locus the intact gene and the pseudogene are arranged in tandem. The data suggest a complex pattern of evolution for the chicken amylase gene family which includes multiple gene duplication events, insertion/deletion events, as well as changes in spatial expression patterns.
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Affiliation(s)
- Bernhard F Benkel
- Agriculture and Agri-Food Canada, Lethbridge Research Centre, Lethbridge, Alberta, Canada, T1J 4B1.
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33
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Rodrigue KL, May BP, Famula TR, Delany ME. Meiotic instability of chicken ultra-long telomeres and mapping of a 2.8 megabase array to the W-sex chromosome. Chromosome Res 2005; 13:581-91. [PMID: 16170623 DOI: 10.1007/s10577-005-0984-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2005] [Indexed: 11/27/2022]
Abstract
The objective of this research was to study the meiotic stability of a subset of chicken telomere arrays, which are the largest reported for any vertebrate species. Inheritance of these ultra-long telomere arrays (200 kb to 3 mb) was studied in a highly homozygous inbred line, UCD 003 (F >or= 99.9). Analysis of array transmission in four families indicated unexpected heterogeneity and non-Mendelian segregation including high-frequency-generation of novel arrays. Additionally, the largest array detected (2.8 Mb) was female-specific and correlated to the most intense telomeric DNA signal on the W-sex chromosome by fluorescence in situ hybridization (FISH). These results are discussed in regard to the potential functions of the ultra-long telomere arrays in the chicken genome including generation of genetic variation through enhanced recombination, protection against erosion by providing a buffer for gene-dense regions, and sex-chromosome organization.
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Affiliation(s)
- K L Rodrigue
- Department of Animal Science, University of California, 2131D Meyer Hall, Davis, CA 95616, USA
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34
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Smith J, Paton IR, Hughes DC, Burt DW. Isolation and mapping the chicken zona pellucida genes: an insight into the evolution of orthologous genes in different species. Mol Reprod Dev 2005; 70:133-45. [PMID: 15570621 DOI: 10.1002/mrd.20197] [Citation(s) in RCA: 56] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
Abstract
The avian oocyte is surrounded by a specialized extracellular glycoproteinaceous matrix, the perivitelline membrane, which is equivalent to the zona pellucida (ZP) in mammals and the chorion in teleosts. A number of related ZP genes encode the proteins that make up this matrix. These proteins play an important role in the sperm/egg interaction and may be involved in speciation. The human genome is known to contain ZP1, ZP2, ZP3, and ZPB genes, while a ZPAX gene has also been identified in Xenopus. The rapid evolution of these genes has confused the nomenclature and thus orthologous relationships across species. In order to clarify these homologies, we have identified ZP1, ZP2, ZPC, ZPB, and ZPAX genes in the chicken and mapped them to chromosomes 5, 14, 10, 6, and 3, respectively, establishing conserved synteny with human and mouse. The amino acid sequences of these genes were compared to the orthologous genes in human, mouse, and Xenopus, and have given us an insight into the evolution of these genes in a variety of different species. The presence of the ZPAX gene in the chicken has highlighted a pattern of probable gene loss by deletion in mouse and gene inactivation by deletion, and base substitution in human.
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Affiliation(s)
- Jacqueline Smith
- Division of Genomics and Bioinformatics, Roslin Institute, Roslin (Edinburgh), Midlothian EH25 9PS, Scotland, United Kingdom.
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35
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Aerts JA, Veenendaal T, van der Poel JJ, Crooijmans RPMA, Groenen MAM. Chromosomal assignment of chicken clone contigs by extending the consensus linkage map. Anim Genet 2005; 36:216-22. [PMID: 15932400 DOI: 10.1111/j.1365-2052.2005.01289.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The bacterial artificial clone-based physical map for chicken plays an important role in the integration of the consensus linkage map and the whole-genome shotgun sequence. It also provides a valuable resource for clone selection within applications such as fluorescent in situ hybridization and positional cloning. However, a substantial number of clone contigs have not yet been assigned to a chromosomal location or have an ambiguous chromosome assignment. In this study, 86 single nucleotide polymorphism markers derived from 86 clones were mapped on the genetic map. These markers added anchoring information for 56 clone contigs and 13 individual clones, covering a total of 57,145 clones.
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Affiliation(s)
- J A Aerts
- Division of Genetics and Genomics, Bioinformatics Group, Roslin Institute, Roslin, Midlothian, UK.
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36
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Schmid M, Nanda I, Hoehn H, Schartl M, Haaf T, Buerstedde JM, Arakawa H, Caldwell RB, Weigend S, Burt DW, Smith J, Griffin DK, Masabanda JS, Groenen MAM, Crooijmans RPMA, Vignal A, Fillon V, Morisson M, Pitel F, Vignoles M, Garrigues A, Gellin J, Rodionov AV, Galkina SA, Lukina NA, Ben-Ari G, Blum S, Hillel J, Twito T, Lavi U, David L, Feldman MW, Delany ME, Conley CA, Fowler VM, Hedges SB, Godbout R, Katyal S, Smith C, Hudson Q, Sinclair A, Mizuno S. Second report on chicken genes and chromosomes 2005. Cytogenet Genome Res 2005; 109:415-79. [PMID: 15905640 DOI: 10.1159/000084205] [Citation(s) in RCA: 103] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/23/2023] Open
Affiliation(s)
- M Schmid
- Department of Human Genetics, University of Würzburg, Würzburg, Germany.
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37
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Reed KM, Holm J, Morisson M, Leroux S, Vignal A. Assignment of non-informative turkey genetic markers through comparative approaches. Cytogenet Genome Res 2005; 109:527-32. [PMID: 15905649 DOI: 10.1159/000084214] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2004] [Accepted: 09/08/2004] [Indexed: 11/19/2022] Open
Abstract
Molecular markers such as microsatellites, provide genetic signposts for navigating genomes. In general, genetic markers that are monomorphic or non-informative in mapping populations typically remain unmapped and as such are less likely to be included in future studies. The use of hybrid cell panels and in silico mapping via whole genome sequences allow for positional mapping of non-segregating markers. This study utilizes the INRA ChickRH6 whole-genome radiation hybrid panel and chicken whole-genome shotgun sequence to map microsatellite markers from the turkey (Meleagris gallopavo). Thirty-three of the 41 markers typed on the RH panel had significant linkage to at least one other marker and 83 of 100 sequences returned significant BLAST similarities. Positioning of these markers provides additional sequence tagged sites in the turkey genome and increases the potential use of these markers for future genetic studies.
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Affiliation(s)
- K M Reed
- Department of Veterinary and Biomedical Sciences, University of Minnesota, St. Paul, MN 55108, USA.
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38
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OKUMURA F, SHIMOGIRI T, SHINBO Y, YOSHIZAWA K, KAWABE K, MANNEN H, OKAMOTO S, CHENG HH, MAEDA Y. Linkage mapping of four chicken calpain genes. Anim Sci J 2005. [DOI: 10.1111/j.1740-0929.2005.00246.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Burt DW. The chicken genome and the developmental biologist. Mech Dev 2005; 121:1129-35. [PMID: 15296976 DOI: 10.1016/j.mod.2004.04.020] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2004] [Revised: 04/27/2004] [Accepted: 04/27/2004] [Indexed: 01/28/2023]
Abstract
Recently the initial draft sequence of the chicken genome was released. The reasons for sequencing the chicken were to boost research and applications in agriculture and medicine, through its use as a model of vertebrate development. In addition, the sequence of the chicken would provide an important anchor species in the phylogenetic study of genome evolution. The chicken genome project has its roots in a decade of map building by genetic and physical mapping methods. Chicken genetic markers for map building have generally depended on labour intensive screening procedures. In recent years this has all changed with the availability of over 450,000 EST sequences, a draft sequence of the entire chicken genome and a map of over 1 million SNPs. Clearly, the future for the chicken genome and developmental biology is an exciting one. Through the integration of these resources, it will be possible to solve challenging scientific questions exploiting the power of a chicken model. In this paper we review progress in chicken genomics and discuss how the new tools and information on the chicken genome can help the developmental biologists now and in the future.
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Affiliation(s)
- David W Burt
- Department of Genomics and Bioinformatics, Roslin Institute (Edinburgh), Midlothian EH25 9PS, UK.
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40
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Kinoshita K, Shimogiri T, Okamoto S, Yoshizawa K, Mannen H, Ibrahim HR, Cheng HH, Maeda Y. Linkage mapping of chicken ovoinhibitor and ovomucoid genes to chromosome 13. Anim Genet 2004; 35:356-8. [PMID: 15265086 DOI: 10.1111/j.1365-2052.2004.01159.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- K Kinoshita
- The United Graduate School of Agricultural Sciences, Kagoshima University, Korimoto, Kagoshima 890-0065, Japan
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41
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Delany ME. Genetic variants for chick biology research: from breeds to mutants. Mech Dev 2004; 121:1169-77. [PMID: 15296980 DOI: 10.1016/j.mod.2004.05.018] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2004] [Revised: 05/30/2004] [Accepted: 05/31/2004] [Indexed: 11/16/2022]
Abstract
The availability of the draft sequence of the chicken genome will undoubtedly propel an already important vertebrate research model, the domestic chicken, to a new level. This review describes aspects of chicken natural history and cross-disciplinary biological value. The diversity of extant genetic variants available to researchers is reviewed along with institutional stock locations for North America. An overview of the problem of lack of long-term stability for these resources is presented.
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Affiliation(s)
- Mary E Delany
- Department of Animal Science, 2131D Meyer Hall, One Shields Avenue, University of California, Davis, CA 95616, USA.
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Elleder D, Plachý J, Hejnar J, Geryk J, Svoboda J. Close linkage of genes encoding receptors for subgroups A and C of avian sarcoma/leucosis virus on chicken chromosome 28. Anim Genet 2004; 35:176-81. [PMID: 15147387 DOI: 10.1111/j.1365-2052.2004.01118.x] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
Avian sarcoma and leucosis viruses (ASLV) are classified into six major subgroups (A to E and J) according to the properties of the viral envelope proteins and the usage of cellular receptors for virus entry. Subgroup A and B receptors are identified molecularly and their genomic positions TVA and TVB are mapped. The subgroup C receptor is unknown, its genomic locus TVC is reported to be genetically linked to TVA, which resides on chicken chromosome 28. In this study, we used two chicken inbred lines that carry different alleles coding for resistance (TVC(R) and sensitivity (TVC(S)) to infection by subgroup C viruses. A backross population of these lines was tested for susceptibility to subgroup C infection and genotyped for markers from chicken chromosome 28. We confirmed the close linkage between TVA and TVC loci. Further, we have described the position of TVC on chromosome 28 relative to markers from the consensus map of the chicken genome.
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Affiliation(s)
- D Elleder
- Department of Cellular and Viral Genetics, Institute of Molecular Genetics, Academy of Sciences of the Czech Republic, Flemingovo nam. 2, Prague, 166 37, Czech Republic
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43
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Niikura M, Liu HC, Dodgson JB, Cheng HH. A Comprehensive Screen for Chicken Proteins that Interact with Proteins Unique to Virulent Strains of Marek's Disease Virus. Poult Sci 2004; 83:1117-23. [PMID: 15285502 DOI: 10.1093/ps/83.7.1117] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023] Open
Abstract
Genetic resistance to Marek's disease (MD) has been proposed as a method to augment current vaccinal control of MD. Although it is possible to identify QTL and candidate genes that are associated with MD resistance, it is necessary to integrate functional screens with linkage analysis to confirm the identity of true MD resistance genes. To help achieve this objective, a comprehensive 2-hybrid screen was conducted using genes unique to virulent Marek's disease virus (MDV) strains. Potential MDV-host protein interactions were tested by an in vitro binding assay to confirm the initial two-hybrid results. As a result, 7 new MDV-chicken protein interactions were identified and included the chicken proteins MHC class II beta (BLB) and invariant (Ii) chain (CD74), growth-related translationally controlled tumor protein (TPT1), complement component Clq-binding protein (C1QBP), retinoblastoma-binding protein 4 (RBBP4), and alpha-enolase (ENO1). Mapping of the encoding chicken genes suggests that BLB, the gene for MHC class II beta chain, is a positional candidate gene. In addition, the known functions of the chicken proteins suggest mechanisms that MDV might use to evade the chicken immune system and alter host gene regulation. Taken together, our results indicate that integrated genomic methods provide a powerful strategy to gain insights on complex biological processes and yield a manageable number of genes and pathways for further characterization.
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Affiliation(s)
- M Niikura
- Department of Microbiology and Molecular Genetics, Michigan State University, East Lansing, Michigan 48824, USA
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Kayang BB, Vignal A, Inoue-Murayama M, Miwa M, Monvoisin JL, Ito S, Minvielle F. A first-generation microsatellite linkage map of the Japanese quail. Anim Genet 2004; 35:195-200. [PMID: 15147390 DOI: 10.1111/j.1365-2052.2004.01135.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
A linkage map of the Japanese quail (Coturnix japonica) genome was constructed based upon segregation analysis of 72 microsatellite loci in 433 F(2) progeny of 10 half-sib families obtained from a cross between two quail lines of different genetic origins. One line was selected for long duration of tonic immobility, a behavioural trait related to fearfulness, while the other was selected based on early egg production. Fifty-eight of the markers were resolved into 12 autosomal linkage groups and a Z chromosome-specific linkage group, while the remaining 14 markers were unlinked. The linkage groups range from 8 cM (two markers) to 206 cM (16 markers) and cover a total map distance of 576 cM with an average spacing of 10 cM between loci. Through comparative mapping with chicken (Gallus gallus) using orthologous markers, we were able to assign linkage groups CJA01, CJA02, CJA05, CJA06, CJA14 and CJA27 to chromosomes. This map, which is the first in quail based solely on microsatellites, is a major step towards the development of a quality molecular genetic map for this valuable species. It will provide an important framework for further genetic mapping and the identification of quantitative trait loci controlling egg production and fear-related behavioural traits in quail.
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Affiliation(s)
- B B Kayang
- Laboratoire de Génétique Cellulaire, Centre INRA de Toulouse, BP 27 Auzeville, 31326 Castanet Tolosan, France
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Goodenbour JM, Kaiser MG, Lamont SJ. Linkage mapping of inhibitor of apoptosis protein-1 (IAP 1) to chicken chromosome 1. Anim Genet 2004; 35:158-9. [PMID: 15025589 DOI: 10.1111/j.1365-2052.2004.01111.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- J M Goodenbour
- Department of Animal Science, Iowa State University, Ames, Iowa 50011-3150, USA
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46
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Zhang HM, Cheng HH. Chicken tubby-like protein 1 (TULP1) gene maps to chromosome 26. Anim Genet 2004; 35:165-6. [PMID: 15025594 DOI: 10.1111/j.1365-2052.2004.01107.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- H M Zhang
- United States Department of Agriculture, Agriculture Research Service, Avian Disease and Oncology Laboratory, 3606 E. Mount Hope Road, East Lansing, MI 48823, USA.
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47
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Zhang HM, Cheng HH. SNP identification and genetic mapping of chicken ephrin type-B receptor 2 gene to linkage group E54. Anim Genet 2004; 35:162-3. [PMID: 15025591 DOI: 10.1111/j.1365-2052.2004.01108.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Affiliation(s)
- H M Zhang
- United States Department of Agriculture, Agriculture Research Service, Avian Disease and Oncology Laboratory, 3606 E. Mount Hope Road, East Lansing, Michigan 48823, USA
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Dodgson JB, Romanov MN. Use of Chicken Models for the Analysis of Human Disease. ACTA ACUST UNITED AC 2004; Chapter 15:Unit 15.5. [DOI: 10.1002/0471142905.hg1505s40] [Citation(s) in RCA: 16] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/07/2022]
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49
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Yang J, Kirby JD, Scarbrough K, Okimoto R. Assignment of the chicken glycoprotein hormones, alpha polypeptide (CGA) gene to chromosome 3. Anim Genet 2004; 35:67-8. [PMID: 14731235 DOI: 10.1046/j.1365-2052.2003.01073.x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- J Yang
- Department of Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA
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50
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Cisar CR, Balog JM, Okimoto R, Anthony NB, Donoghue AM. The chicken bone morphogenetic protein receptor type II (BMPR2) gene maps to chromosome 7. Anim Genet 2004; 34:475-6. [PMID: 14687089 DOI: 10.1046/j.1365-2052.2003.01065.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Affiliation(s)
- C R Cisar
- Poultry Production and Product Safety Research Unit, Agricultural Research Service, United States Department of Agriculture, Fayetteville, AR, USA.
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