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Recoquillay J, Pitel F, Arnould C, Leroux S, Dehais P, Moréno C, Calandreau L, Bertin A, Gourichon D, Bouchez O, Vignal A, Fariello MI, Minvielle F, Beaumont C, Leterrier C, Le Bihan-Duval E. A medium density genetic map and QTL for behavioral and production traits in Japanese quail. BMC Genomics 2015; 16:10. [PMID: 25609057 PMCID: PMC4307178 DOI: 10.1186/s12864-014-1210-9] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2014] [Accepted: 12/30/2014] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND Behavioral traits such as sociability, emotional reactivity and aggressiveness are major factors in animal adaptation to breeding conditions. In order to investigate the genetic control of these traits as well as their relationships with production traits, a study was undertaken on a large second generation cross (F2) between two lines of Japanese Quail divergently selected on their social reinstatement behavior. All the birds were measured for several social behaviors (social reinstatement, response to social isolation, sexual motivation, aggression), behaviors measuring the emotional reactivity of the birds (reaction to an unknown object, tonic immobility reaction), and production traits (body weight and egg production). RESULTS We report the results of the first genome-wide QTL detection based on a medium density SNP panel obtained from whole genome sequencing of a pool of individuals from each divergent line. A genetic map was constructed using 2145 markers among which 1479 could be positioned on 28 different linkage groups. The sex-averaged linkage map spanned a total of 3057 cM with an average marker spacing of 2.1 cM. With the exception of a few regions, the marker order was the same in Japanese Quail and the chicken, which confirmed a well conserved synteny between the two species. The linkage analyses performed using QTLMAP software revealed a total of 45 QTLs related either to behavioral (23) or production (22) traits. The most numerous QTLs (15) concerned social motivation traits. Interestingly, our results pinpointed putative pleiotropic regions which controlled emotional reactivity and body-weight of birds (on CJA5 and CJA8) or their social motivation and the onset of egg laying (on CJA19). CONCLUSION This study identified several QTL regions for social and emotional behaviors in the Quail. Further research will be needed to refine the QTL and confirm or refute the role of candidate genes, which were suggested by bioinformatics analysis. It can be hoped that the identification of genes and polymorphisms related to behavioral traits in the quail will have further applications for other poultry species (especially the chicken) and will contribute to solving animal welfare issues in poultry production.
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Affiliation(s)
| | - Frédérique Pitel
- UMR INRA/Génétique Physiologie et Systèmes d'Elevage, INRA, F-31326, Castanet-Tolosan, France.
- INPT ENSAT / Génétique Physiologie et Systèmes d'Elevage, INRA, F-31326, Castanet-Tolosan, France.
- INPT ENVT Génétique Physiologie et Systèmes d'Elevage, INRA, F-31326, Castanet-Tolosan, France.
| | - Cécile Arnould
- INRA, UMR85 Physiologie de la Reproduction et des Comportements, F-37380, Nouzilly, France.
- CNRS, UMR7247, F-37380, Nouzilly, France.
- Université François Rabelais de Tours, F-37000, Tours, France.
- IFCE, F-37380, Nouzilly, France.
| | - Sophie Leroux
- UMR INRA/Génétique Physiologie et Systèmes d'Elevage, INRA, F-31326, Castanet-Tolosan, France.
- INPT ENSAT / Génétique Physiologie et Systèmes d'Elevage, INRA, F-31326, Castanet-Tolosan, France.
- INPT ENVT Génétique Physiologie et Systèmes d'Elevage, INRA, F-31326, Castanet-Tolosan, France.
| | - Patrice Dehais
- UMR INRA/Génétique Physiologie et Systèmes d'Elevage, INRA, F-31326, Castanet-Tolosan, France.
- INPT ENSAT / Génétique Physiologie et Systèmes d'Elevage, INRA, F-31326, Castanet-Tolosan, France.
- INPT ENVT Génétique Physiologie et Systèmes d'Elevage, INRA, F-31326, Castanet-Tolosan, France.
- INRA, Sigenae UR875 Biométrie et Intelligence Artificielle, F-31326, Castanet-Tolosan, France.
| | - Carole Moréno
- UMR INRA/Génétique Physiologie et Systèmes d'Elevage, INRA, F-31326, Castanet-Tolosan, France.
- INPT ENSAT / Génétique Physiologie et Systèmes d'Elevage, INRA, F-31326, Castanet-Tolosan, France.
- INPT ENVT Génétique Physiologie et Systèmes d'Elevage, INRA, F-31326, Castanet-Tolosan, France.
| | - Ludovic Calandreau
- INRA, UMR85 Physiologie de la Reproduction et des Comportements, F-37380, Nouzilly, France.
- CNRS, UMR7247, F-37380, Nouzilly, France.
- Université François Rabelais de Tours, F-37000, Tours, France.
- IFCE, F-37380, Nouzilly, France.
| | - Aline Bertin
- INRA, UMR85 Physiologie de la Reproduction et des Comportements, F-37380, Nouzilly, France.
- CNRS, UMR7247, F-37380, Nouzilly, France.
- Université François Rabelais de Tours, F-37000, Tours, France.
- IFCE, F-37380, Nouzilly, France.
| | - David Gourichon
- UE1295 Pôle d'Expérimentation Avicole de Tours, F-37380, Nouzilly, France.
| | - Olivier Bouchez
- UMR INRA/Génétique Physiologie et Systèmes d'Elevage, INRA, F-31326, Castanet-Tolosan, France.
- INPT ENSAT / Génétique Physiologie et Systèmes d'Elevage, INRA, F-31326, Castanet-Tolosan, France.
- INPT ENVT Génétique Physiologie et Systèmes d'Elevage, INRA, F-31326, Castanet-Tolosan, France.
- INRA, GeT-PlaGe Genotoul, F-31326, Castanet-Tolosan, France.
| | - Alain Vignal
- UMR INRA/Génétique Physiologie et Systèmes d'Elevage, INRA, F-31326, Castanet-Tolosan, France.
- INPT ENSAT / Génétique Physiologie et Systèmes d'Elevage, INRA, F-31326, Castanet-Tolosan, France.
- INPT ENVT Génétique Physiologie et Systèmes d'Elevage, INRA, F-31326, Castanet-Tolosan, France.
| | - Maria Ines Fariello
- UMR INRA/Génétique Physiologie et Systèmes d'Elevage, INRA, F-31326, Castanet-Tolosan, France.
- INPT ENSAT / Génétique Physiologie et Systèmes d'Elevage, INRA, F-31326, Castanet-Tolosan, France.
- INPT ENVT Génétique Physiologie et Systèmes d'Elevage, INRA, F-31326, Castanet-Tolosan, France.
- Institut Pasteur, Montevideo, Uruguay.
| | - Francis Minvielle
- INRA, UMR1313 GABI Génétique Animale et Biologie Intégrative, F-78530, Jouy-en-Josas, France.
| | | | - Christine Leterrier
- INRA, UMR85 Physiologie de la Reproduction et des Comportements, F-37380, Nouzilly, France.
- CNRS, UMR7247, F-37380, Nouzilly, France.
- Université François Rabelais de Tours, F-37000, Tours, France.
- IFCE, F-37380, Nouzilly, France.
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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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Amirinia C, Emrani H, Arbabe MAR, Torshizi RV, Javaremi AN. Evaluation of eight microsatellite loci polymorphism in four Japanese quail (Coturnix japonica) strain in Iran. Pak J Biol Sci 2009; 10:1195-9. [PMID: 19069916 DOI: 10.3923/pjbs.2007.1195.1199] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
Allele frequencies of eight microsatellite loci as GUJ0001, GUJ0021, GUJ0034, GUJ0041, GUJ0049, GUJ0059, GUJ0070 and GUJ0097 was estimated for four strain of Japanese quail in Iran. Whole blood samples were collected from 200 individuals belonging to four strain (Pharach, Panda, Tuxedo and Golden).Total Genomic DNA was extracted by the GUSN-Silica Gel kit. The extracted DNA was amplified through Polymerase Chain Reaction (PCR). Of the eight microsatellite loci used in this study, two loci ( GUJ0001 and GUJ0041 ) were monomorphic in Panda and Texedo, respectively. The highest and the lowest PIC values belonged to GUJ0059 in Golden (0.815) and GUJ0041 in Panda strain (0.427), respectively. The expected heterozygosity varied between 0.708 and 0.849. All locus-strain combinations deviated from Hardy-Weinberg equilibrium except GUJ0041 in Pharach strain, GUJ0021, GUJ0034, GUJ0041 and GUJ0097 in Panda strain and GUJ0034, GUJ0049 and GUJ0070 in Golden strain (p < 0.001). Results suggest the effectiveness of this set of loci for testing genetic relatedness.
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Affiliation(s)
- C Amirinia
- Department of Biotechnology, Animal Science Research Institute of Iran, Karaj, Iran
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5
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Mutations of Japanese Quail ( Coturnix japonica) and Recent Advances of Molecular Genetics for This Species. J Poult Sci 2008. [DOI: 10.2141/jpsa.45.159] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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6
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Kayang BB, Fillon V, Inoue-Murayama M, Miwa M, Leroux S, Fève K, Monvoisin JL, Pitel F, Vignoles M, Mouilhayrat C, Beaumont C, Ito S, Minvielle F, Vignal A. Integrated maps in quail (Coturnix japonica) confirm the high degree of synteny conservation with chicken (Gallus gallus) despite 35 million years of divergence. BMC Genomics 2006; 7:101. [PMID: 16669996 PMCID: PMC1534036 DOI: 10.1186/1471-2164-7-101] [Citation(s) in RCA: 63] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2005] [Accepted: 05/02/2006] [Indexed: 12/01/2022] Open
Abstract
BACKGROUND By comparing the quail genome with that of chicken, chromosome rearrangements that have occurred in these two galliform species over 35 million years of evolution can be detected. From a more practical point of view, the definition of conserved syntenies helps to predict the position of genes in quail, based on information taken from the chicken sequence, thus enhancing the utility of this species in biological studies through a better knowledge of its genome structure. A microsatellite and an Amplified Fragment Length Polymorphism (AFLP) genetic map were previously published for quail, as well as comparative cytogenetic data with chicken for macrochromosomes. Quail genomics will benefit from the extension and the integration of these maps. RESULTS The integrated linkage map presented here is based on segregation analysis of both anonymous markers and functional gene loci in 1,050 quail from three independent F2 populations. Ninety-two loci are resolved into 14 autosomal linkage groups and a Z chromosome-specific linkage group, aligned with the quail AFLP map. The size of linkage groups ranges from 7.8 cM to 274.8 cM. The total map distance covers 904.3 cM with an average spacing of 9.7 cM between loci. The coverage is not complete, as macrochromosome CJA08, the gonosome CJAW and 23 microchromosomes have no marker assigned yet. Significant sequence identities of quail markers with chicken enabled the alignment of the quail linkage groups on the chicken genome sequence assembly. This, together with interspecific Fluorescence In Situ Hybridization (FISH), revealed very high similarities in marker order between the two species for the eight macrochromosomes and the 14 microchromosomes studied. CONCLUSION Integrating the two microsatellite and the AFLP quail genetic maps greatly enhances the quality of the resulting information and will thus facilitate the identification of Quantitative Trait Loci (QTL). The alignment with the chicken chromosomes confirms the high conservation of gene order that was expected between the two species for macrochromosomes. By extending the comparative study to the microchromosomes, we suggest that a wealth of information can be mined in chicken, to be used for genome analyses in quail.
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Affiliation(s)
- Boniface B Kayang
- Laboratoire de Génétique Cellulaire, Centre INRA de Toulouse, BP 52627 Auzeville, 31326 Castanet Tolosan, France
- Department of Animal Science, University of Ghana, Legon, Accra, Ghana
| | - Valérie Fillon
- Laboratoire de Génétique Cellulaire, Centre INRA de Toulouse, BP 52627 Auzeville, 31326 Castanet Tolosan, France
| | - Miho Inoue-Murayama
- Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan
| | - Mitsuru Miwa
- Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan
| | - Sophie Leroux
- Laboratoire de Génétique Cellulaire, Centre INRA de Toulouse, BP 52627 Auzeville, 31326 Castanet Tolosan, France
| | - Katia Fève
- Laboratoire de Génétique Cellulaire, Centre INRA de Toulouse, BP 52627 Auzeville, 31326 Castanet Tolosan, France
| | - Jean-Louis Monvoisin
- UMR Génétique et Diversité Animales, INRA bât 211, 78352 Jouy-en-Josas Cedex, France
| | - Frédérique Pitel
- Laboratoire de Génétique Cellulaire, Centre INRA de Toulouse, BP 52627 Auzeville, 31326 Castanet Tolosan, France
| | - Matthieu Vignoles
- Laboratoire de Génétique Cellulaire, Centre INRA de Toulouse, BP 52627 Auzeville, 31326 Castanet Tolosan, France
| | - Céline Mouilhayrat
- Laboratoire de Génétique Cellulaire, Centre INRA de Toulouse, BP 52627 Auzeville, 31326 Castanet Tolosan, France
| | | | - Shin'ichi Ito
- Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan
| | - Francis Minvielle
- UMR Génétique et Diversité Animales, INRA bât 211, 78352 Jouy-en-Josas Cedex, France
| | - Alain Vignal
- Laboratoire de Génétique Cellulaire, Centre INRA de Toulouse, BP 52627 Auzeville, 31326 Castanet Tolosan, France
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Chaves LD, Knutson TP, Krueth SB, Reed KM. Using the chicken genome sequence in the development and mapping of genetic markers in the turkey (Meleagris gallopavo). Anim Genet 2006; 37:130-8. [PMID: 16573527 DOI: 10.1111/j.1365-2052.2005.01396.x] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The efficacy of employing the chicken genome sequence in developing genetic markers and in mapping the turkey genome was studied. Eighty previously uncharacterized microsatellite markers were identified for the turkey using BLAST alignment to the chicken genome. The chicken sequence was then used to develop primers for polymerase chain reaction where the turkey sequence was either unavailable or insufficient. A total of 78 primer sets were tested for amplification and polymorphism in the turkey, and informative markers were genetically mapped. Sixty-five (83%) amplified turkey genomic DNA, and 33 (42%) were polymorphic in the University of Minnesota/Nicholas Turkey Breeding Farms mapping families. All but one marker genetically mapped to the position predicted from the chicken genome sequence. These results demonstrate the usefulness of the chicken sequence for the development of genomic resources in other avian species.
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Affiliation(s)
- L D Chaves
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St Paul, MN 55108, USA
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Miwa M, Inoue-Murayama M, Kobayashi N, Kayang BB, Mizutani M, Takahashi H, Ito S. Mapping of panda plumage color locus on the microsatellite linkage map of the Japanese quail. BMC Genet 2006; 7:2. [PMID: 16405738 PMCID: PMC1361776 DOI: 10.1186/1471-2156-7-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2005] [Accepted: 01/12/2006] [Indexed: 11/10/2022] Open
Abstract
Background Panda (s) is an autosomal recessive mutation, which displays overall white plumage color with spots of wild-type plumage in the Japanese quail (Coturnix japonica). In a previous study, the s locus was included in the same linkage group as serum albumin (Alb) and vitamin-D binding protein (GC) which are mapped on chicken (Gallus gallus) chromosome 4 (GGA4). In this study, we mapped the s locus on the microsatellite linkage map of the Japanese quail by linkage analysis. Results Segregation data on the s locus were obtained from three-generation families (n = 106). Two microsatellite markers derived from the Japanese quail chromosome 4 (CJA04) and three microsatellite markers derived from GGA4 were genotyped in the three-generation families. We mapped the s locus between GUJ0026 and ABR0544 on CJA04. By comparative mapping with chicken, this locus was mapped between 10.0 Mb and 14.5 Mb region on GGA4. In this region, the endothelin receptor B subtype 2 gene (EDNRB2), an avian-specific paralog of the mammalian endothelin receptor B gene (EDNRB), is located. Because EDNRB is responsible for aganglionic megacolon and spot coat color in mouse, rat and equine, EDNRB2 is suggested to be a candidate gene for the s locus. Conclusion The s locus and the five microsatellite markers were mapped on CJA04 of the Japanese quail. EDNRB2 was suggested to be a candidate gene for the s locus.
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Affiliation(s)
- Mitsuru Miwa
- Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan
| | - Miho Inoue-Murayama
- Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan
| | - Naoki Kobayashi
- Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan
| | - Boniface Baboreka Kayang
- Department of Animal Science, College of Agriculture and Consumer Sciences, University of Ghana, Legon, Ghana
| | - Makoto Mizutani
- Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya 464-8601, Japan
| | - Hideaki Takahashi
- National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan
| | - Shin'ichi Ito
- Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan
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Zou F, Yue B, Xu L, Zhang Y. Isolation and characterization of microsatellite loci from forest musk deer (Moschus berezovskii). Zoolog Sci 2005; 22:593-8. [PMID: 15930833 DOI: 10.2108/zsj.22.593] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
This study reported the isolation and characterization of eight polymorphic microsatellite loci in endangered forest musk deer Moschus berezovskii. An improved enrichment protocol was used to isolate microsatellites, and polymorphism was explored with samples from wild musk deer population collected in Miyalo of Sichuan Province in China. Approximately 70% of clones from the genomic library constructed in current study contained dinucleotide (AC) repeats. Eight microsatellite loci amplified were highly polymorphic within forest musk deer population. The number of alleles per locus ranged from 6 to 14, and the observed and expected heterozygosities ranged from 0.41 approximately 1.0 and from 0.8 approximately 0.9, respectively. The average polymorphic information content (PIC) value for these markers was 0.82. This demonstrated that the eight microsatellite loci developed here are highly polymorphic, and can be used as genetic markers for further investigation of musk deer. Also, the results showed that the musk deer distributed in Miyalo had a relatively higher level of genetic variation.
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Affiliation(s)
- Fangdong Zou
- Sichuan Key Laboratory for Reproduction and Conservation Genetics of Endangered Wild Life, College of Life Science, Sichuan University, Japan
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Kikuchi S, Fujima D, Sasazaki S, Tsuji S, Mizutani M, Fujiwara A, Mannen H. Construction of a genetic linkage map of Japanese quail (Coturnix japonica) based on AFLP and microsatellite markers. Anim Genet 2005; 36:227-31. [PMID: 15932402 DOI: 10.1111/j.1365-2052.2005.01295.x] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The Japanese quail (Coturnix japonica) is a notably valuable egg and meat producer but has also been used as a laboratory animal. In the present study, we constructed a Japanese quail linkage map with 1735 polymorphic amplified fragment length polymorphisms markers, and nine chicken microsatellite (MS) markers, as well as sex and phenotypes of two genetic diseases; a muscular disorder (LWC) and neurofilament-deficient mutant (Quv). Linkage analysis revealed 578 independent loci. The resulting linkage map contained 44 multipoint linkage groups covering 2597.8 cM and an additional 218.2 cM was contained in 21 two-point linkage groups. The total map was 2816 cM in length with an average marker interval of 5.5 cM. The Quv locus was located on linkage group 5, but linkage was not found between the LWC locus and any of the markers. Comparative mapping with chicken using orthologous markers revealed chromosomal assignments of the quail linkage group 1 to chicken chromosome 2 (GGA2), 5 to GGA22, 2 to GGA5, 8 to GGA7, 27 to GGA11, 29 to GGA1 and 45 to GGA4.
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Affiliation(s)
- S Kikuchi
- Graduate School of Science and Technology, Kobe University, Kobe 657-8501, Japan
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Miwa M, Inoue-Murayama M, Kayang BB, Vignal A, Minvielle F, Monvoisin JL, Takahashi H, Ito S. Mapping of plumage colour and blood protein loci on the microsatellite linkage map of the Japanese quail. Anim Genet 2005; 36:396-400. [PMID: 16167982 DOI: 10.1111/j.1365-2052.2005.01335.x] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The objective of this work was to map classical markers (plumage colours and blood proteins) on the microsatellite linkage map of the Japanese quail (Coturnix japonica). The segregation data on two plumage colours and three blood proteins were obtained from 25 three-generation families (193 F2 birds). Linkage analysis was carried out for these five classical markers and 80 microsatellite markers. A total of 15 linkage groups that included the five classical loci and 69 of the 80 microsatellite markers were constructed. Using the BLAST homology search against the chicken genome sequence, three quail linkage groups, QL8, QL10 and QL13, were suggested to be homologous to chicken chromosomes GGA9, GGA20 and GGA24, respectively. Two plumage colour loci, black at hatch (Bh) and yellow (Y), and the three blood protein loci, transferrin (Tf), haemoglobin (Hb-1) and prealbumin-1 (Pa-1), were assigned to CJA01, QL10, QL8, CJA14 and QL13, respectively.
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Affiliation(s)
- M Miwa
- Faculty of Applied Biological Sciences, Gifu University, Gifu 501-1193, Japan
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12
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Development and Mapping of Microsatellite Markers Derived from cDNA in Japanese Quail (Coturnix japonica). J Poult Sci 2005. [DOI: 10.2141/jpsa.42.263] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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13
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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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14
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Shiina T, Shimizu S, Hosomichi K, Kohara S, Watanabe S, Hanzawa K, Beck S, Kulski JK, Inoko H. Comparative Genomic Analysis of Two Avian (Quail and Chicken) MHC Regions. THE JOURNAL OF IMMUNOLOGY 2004; 172:6751-63. [PMID: 15153492 DOI: 10.4049/jimmunol.172.11.6751] [Citation(s) in RCA: 122] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
We mapped two different quail Mhc haplotypes and sequenced one of them (haplotype A) for comparative genomic analysis with a previously sequenced haplotype of the chicken Mhc. The quail haplotype A spans 180 kb of genomic sequence, encoding a total of 41 genes compared with only 19 genes within the 92-kb chicken Mhc. Except for two gene families (B30 and tRNA), both species have the same basic set of gene family members that were previously described in the chicken "minimal essential" Mhc. The two Mhc regions have a similar overall organization but differ markedly in that the quail has an expanded number of duplicated genes with 7 class I, 10 class IIB, 4 NK, 6 lectin, and 8 B-G genes. Comparisons between the quail and chicken Mhc class I and class II gene sequences by phylogenetic analysis showed that they were more closely related within species than between species, suggesting that the quail Mhc genes were duplicated after the separation of these two species from their common ancestor. The proteins encoded by the NK and class I genes are known to interact as ligands and receptors, but unlike in the quail and the chicken, the genes encoding these proteins in mammals are found on different chromosomes. The finding of NK-like genes in the quail Mhc strongly suggests an evolutionary connection between the NK C-type lectin-like superfamily and the Mhc, providing support for future studies on the NK, lectin, class I, and class II interaction in birds.
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Affiliation(s)
- Takashi Shiina
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa, Japan
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15
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Tang B, Huang YH, Lin L, Hu XX, Feng JD, Yao P, Zhang L, Li N. Isolation and characterization of 70 novel microsatellite markers from ostrich (Struthiocamelus) genome. Genome 2003; 46:833-40. [PMID: 14608400 DOI: 10.1139/g03-059] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Microsatellite markers are widely used in linkage mapping, parentage testing, population genetic studies, and molecular evolution studies in many agricultural species, while only a limited number of ostrich (Struthio camelus) microsatellites have been isolated. Thus, we constructed a random small-insert genomic library and a microsatellite-enriched library containing CA repeats. Fourteen clones containing CA repeats were isolated from 3462 clones in the non-enriched library by radioactive screening and 248 positive clones were isolated from 300 sequenced clones from the enriched library by PCR screening. After the enrichment procedures, the proportion of clones containing CA repeats was raised to 78.8%, compared with 0.4% in the non-enriched libraries, indicating that the enrichment value approaches 200 fold, which decreased the time and cost of cloning. The number of complete simple CA repeats in these positive clones ranged from 5 to 29. The primers for 94 of these microsatellites were developed and used to detect polymorphisms, of which 61 loci exhibited length polymorphisms in 17 unrelated ostrich individuals. The new polymorphic microsatellite markers we have identified and characterized will contribute to the ostrich genetic map, parentage testing, and comparative genomics between avian species.Key words: ostrich, microsatellite markers, enriched library, polymorphism.
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Affiliation(s)
- Bo Tang
- The College of Animal Science and Technology, China Agricultural University, Beijing, China
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16
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KAYANG BB, INOUE-MURAYAMA M, TAKAHASHI H, MINEZAWA M, TSUDZUKI M, MIZUTANI M, ITO S. Twenty-eight new microsatellite loci in chicken and their cross-species amplification in Japanese quail and helmeted guinea fowl. Anim Sci J 2003. [DOI: 10.1046/j.1344-3941.2003.00114.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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