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Vollmar S, Haas V, Schmid M, Preuß S, Joshi R, Rodehutscord M, Bennewitz J. Mapping genes for phosphorus utilization and correlated traits using a 4k SNP linkage map in Japanese quail (Coturnix japonica). Anim Genet 2020; 52:90-98. [PMID: 33140443 DOI: 10.1111/age.13018] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 10/09/2020] [Indexed: 12/17/2022]
Abstract
A large F2 cross with 920 Japanese quail was used to map QTL for phosphorus utilization, calcium utilization, feed per gain and body weight gain. In addition, four bone ash traits were included, because it is known that they are genetically correlated with the focal trait of phosphorus utilization. Trait recording was done at the juvenile stage of the birds. The individuals were genotyped genome-wide for about 4k SNPs and a linkage map constructed, which agreed well with the reference genome. QTL linkage mapping was performed using multimarker regression analysis in a line cross model. Single marker association mapping was done within the mapped QTL regions. The results revealed several genome-wide significant QTL. For the focal trait phosphorus utilization, a QTL on chromosome CJA3 could be detected by linkage mapping, which was substantiated by the results of the SNP association mapping. Four candidate genes were identified for this QTL, which should be investigated in future functional studies. Some overlap of QTL regions for different traits was detected, which is in agreement with the corresponding genetic correlations. It seems that all traits investigated are polygenic in nature with some significant QTL and probably many other small-effect QTL that were not detectable in this study.
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Affiliation(s)
- S Vollmar
- Institute of Animal Science, University of Hohenheim, Stuttgart, 70599, Germany
| | - V Haas
- Institute of Animal Science, University of Hohenheim, Stuttgart, 70599, Germany
| | - M Schmid
- Institute of Animal Science, University of Hohenheim, Stuttgart, 70599, Germany
| | - S Preuß
- Institute of Animal Science, University of Hohenheim, Stuttgart, 70599, Germany
| | - R Joshi
- Department of Animal and Aquacultural Sciences, Faculty of Biosciences, Norwegian University of Life Sciences, Ås, N-1432, Norway
| | - M Rodehutscord
- Institute of Animal Science, University of Hohenheim, Stuttgart, 70599, Germany
| | - J Bennewitz
- Institute of Animal Science, University of Hohenheim, Stuttgart, 70599, Germany
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Semenov GA, Basheva EA, Borodin PM, Torgasheva AA. High rate of meiotic recombination and its implications for intricate speciation patterns in the white wagtail (Motacilla alba). Biol J Linn Soc Lond 2018. [DOI: 10.1093/biolinnean/bly133] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Georgy A Semenov
- Ecology and Evolutionary Biology, University of Colorado, Ramaley Hall, Boulder, CO, USA
- Institute of Systematics and Ecology of Animals, Frunze, Novosibirsk, Russian Federation
- Ecology and Evolutionary Biology, University of Colorado, Ramaley Hall, Boulder, CO, USA
| | - Ekaterina A Basheva
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Lavrentiev Ave., Novosibirsk, Russian Federation
| | - Pavel M Borodin
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Lavrentiev Ave., Novosibirsk, Russian Federation
- Novosibirsk State Research University, Department of Cytology and Genetics, Pirogova st., Novosibirsk, Russian Federation
| | - Anna A Torgasheva
- Institute of Systematics and Ecology of Animals, Frunze, Novosibirsk, Russian Federation
- Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences, Lavrentiev Ave., Novosibirsk, Russian Federation
- Novosibirsk State Research University, Department of Cytology and Genetics, Pirogova st., Novosibirsk, Russian Federation
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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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Moradian H, Esmailizadeh AK, Sohrabi SS, Nasirifar E, Askari N, Mohammadabadi MR, Baghizadeh A. Genetic analysis of an F2 intercross between two strains of Japanese quail provided evidence for quantitative trait loci affecting carcass composition and internal organs. Mol Biol Rep 2014; 41:4455-62. [PMID: 24590740 DOI: 10.1007/s11033-014-3316-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2013] [Accepted: 02/24/2014] [Indexed: 10/25/2022]
Abstract
The purpose of this study was to identify genomic regions, quantitative trait loci (QTL), affecting carcass traits on chromosome 1 in an F2 population of Japanese quail. For this purpose, two white and wild strains of Japanese quail (16 birds) were crossed reciprocally and F1 generation (34 birds) was created. The F2 generation was produced by intercrossing of the F1 birds. Phenotypic data including carcass weight, internal organs and carcass parts were collected on F2 animals (422 birds). The total mapping population (472 birds) was genotyped for 8 microsatellite markers on chromosome 1. QTL analysis was performed with interval mapping method applying the line-cross model. Significant QTL were identified for breast weight at 0 (P < 0.01), 172 (P < 0.05) and 206 (P < 0.01), carcass weight at 91 (P < 0.05), carcass fatness at 0 (P < 0.01), pre-stomach weight at 206 (P < 0.01) and uropygial weight gland at 197 (P < 0.01) cM on chromosome 1. There was also evidence for imprinted QTL affecting breast weight (P < 0.01) on chromosome 1. The proportion of the F2 phenotypic variation explained by the significant additive, dominance and imprinted QTL effects ranged from 1.0 to 7.3%, 1.2 to 3.3% and 1.4 to 2.2%, respectively.
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Affiliation(s)
- Hasan Moradian
- Department of Animal Science, Faculty of Agriculture, Shahid Bahonar University of Kerman, PB 76169-133, Kerman, Iran,
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Gomes ML, Hatanaka T, Campos WND, Wasko AP. Assessing paternity in japanese quails (Coturnix japonica) using microsatellite markers - inferences for its mating system and reproductive success. BRAZILIAN JOURNAL OF POULTRY SCIENCE 2013. [DOI: 10.1590/s1516-635x2013000400007] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Affiliation(s)
- ML Gomes
- São Paulo State University, Brazil
| | - T Hatanaka
- Federal University of São Carlos, Brazil
| | | | - AP Wasko
- São Paulo State University, Brazil
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Sun W, Chen H, Lei C, Lei X, Zhang Y. Study on population genetic characteristics of Qinchuan cows using microsatellite markers. J Genet Genomics 2009; 34:17-25. [PMID: 17469774 DOI: 10.1016/s1673-8527(07)60003-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/17/2006] [Accepted: 06/25/2006] [Indexed: 11/20/2022]
Abstract
To evaluate the genetic polymorphisms and to search for available molecular markers for Qinchuan cattle, 90 Qinchuan cows were genotyped with 12 microsatellite markers. A total of 247 alleles were detected, with the number of alleles ranging from 13 (INRA005) to 33 (HEL13), giving a mean number of 21 alleles per locus. The total and mean effective allele number were 142.6229 and 11.8852, respectively. Mean sampling variance of the allele frequency was 2.6036 x 10(-4). Allele size ranges of the 12 microsatellite loci were different. The observed heterozygosity and expected heterozygosity were from 0.7842 (INRA005) to 0.9775 (BM315) and 0.7952 (BM315) to 0.9446 (HEL13), respectively. Mean observed heterozygosity and mean expected heterozygosity were 0.9117 and 0.9047, respectively. Polymorphism information content values were from 0.7653 (INRA005) to 0.9420 (HEL13), and mean polymorphism information content of the 12 microsatellite loci was 0.8965. All the 12 microsatellite loci were highly polymorphic, which showed that there were rich genetic polymorphisms at these detected microsatellite loci in Qinchuan cows. At the 12 microsatellite loci, the mean fixation index was -0.0076, reflecting that the degree of heterozygote defect at these loci was not high and deviations from Hardy-Weinberg equilibrium were not significant.
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Affiliation(s)
- Weibin Sun
- College of Animal Science and Technology, Northwest A & F University, Shaanxi Key Laboratory of Molecular Biology for Agriculture, Yangling 712100, China
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Huang CW, Cheng YS, Rouvier R, Yang KT, Wu CP, Huang HL, Huang MC. Duck (Anas platyrhynchos) linkage mapping by AFLP fingerprinting. Genet Sel Evol 2009; 41:28. [PMID: 19291328 PMCID: PMC2666072 DOI: 10.1186/1297-9686-41-28] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2009] [Accepted: 03/17/2009] [Indexed: 11/10/2022] Open
Abstract
Amplified fragment length polymorphism (AFLP) with multicolored fluorescent molecular markers was used to analyze duck (Anas platyrhynchos) genomic DNA and to construct the first AFLP genetic linkage map. These markers were developed and genotyped in 766 F2 individuals from six families from a cross between two different selected duck lines, brown Tsaiya and Pekin. Two hundred and ninety-six polymorphic bands (64% of all bands) were detected using 18 pairs of fluorescent TaqI/EcoRI primer combinations. Each primer set produced a range of 7 to 29 fragments in the reactions, and generated on average 16.4 polymorphic bands. The AFLP linkage map included 260 co-dominant markers distributed in 32 linkage groups. Twenty-one co-dominant markers were not linked with any other marker. Each linkage group contained three to 63 molecular markers and their size ranged between 19.0 cM and 171.9 cM. This AFLP linkage map provides important information for establishing a duck chromosome map, for mapping quantitative trait loci (QTL mapping) and for breeding applications.
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Affiliation(s)
- Chang-Wen Huang
- Department of Animal Science, National Chung Hsing University, 250 Kuo-Kung Road, Taichung 402, Taiwan
- Institute of Cellular and Organism Biology, Academia Sinica, 128 Section 2, Academia Road, Nankang, Taipei 115, Taiwan
| | - Yu-Shin Cheng
- Livestock Research Institute, Council of Agriculture, Hsin-Hua, Tainan 712, Taiwan
| | - Roger Rouvier
- Institut National de la Recherche Agronomique, Station d'Amélioration Génétique des Animaux, Centre de Recherches de Toulouse, BP52627, F31326 Castanet-Tolosan Cedex, France
| | - Kuo-Tai Yang
- Department of Animal Science, National Chung Hsing University, 250 Kuo-Kung Road, Taichung 402, Taiwan
- Institute of Biomedical Sciences, Academia Sinica, 128 Section 2, Academia Road, Nankang, Taipei 115, Taiwan
| | - Chean-Ping Wu
- Department of Animal Science, National Chung Hsing University, 250 Kuo-Kung Road, Taichung 402, Taiwan
- Department of Animal Science, National Chiayi University, 300 Syuefu Road, Chiayi 600, Taiwan
| | - Hsiu-Lin Huang
- Department of Animal Science, National Chung Hsing University, 250 Kuo-Kung Road, Taichung 402, Taiwan
| | - Mu-Chiou Huang
- Department of Animal Science, National Chung Hsing University, 250 Kuo-Kung Road, Taichung 402, Taiwan
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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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Poynter G, Huss D, Lansford R. Japanese quail: an efficient animal model for the production of transgenic avians. Cold Spring Harb Protoc 2009; 2009:pdb.emo112. [PMID: 20147007 DOI: 10.1101/pdb.emo112] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
The ability to generate transgenic mice has been a powerful tool in studying functional genomics, and much of our knowledge about developmental biology has come from the study of chicken embryology. Unfortunately, the availability of molecular genetic techniques, such as transgenics and knockouts, has been limited for developmental biologists using avian animal models. Efforts to develop a system for the rapid production of transgenic chickens have met with many obstacles, including high animal husbandry costs and long generational times. Recently, the Japanese quail has proven to be an excellent model organism for the production of transgenic avians using lentiviral vectors. The relatively small size of the adults, short time to sexual maturity, and prodigious egg production of the Japanese quail make development of transgenic lines less labor- and space-intensive compared to chickens. The high degree of homology between chicken and quail genomes allows researchers to design highly specific DNA constructs for the production of transgenic birds. In addition, transgenic quail offer all of the advantages of the classic avian developmental model system, such as the ability to readily produce quail:chick transplant chimeras. Finally, Japanese quail are ideal for in ovo imaging of embryos expressing fluorescent reporters introduced from a transgene and/or electroporation. Here, we provide detailed methods for generating transgenic quail using high-titer lentivirus.
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Affiliation(s)
- Greg Poynter
- Division of Biology and Biological Imaging Center, Beckman Institute, California Institute of Technology, Pasadena, CA 91125, USA
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A multilocus assay reveals high nucleotide diversity and limited differentiation among Scandinavian willow grouse (Lagopus lagopus). BMC Genet 2008; 9:89. [PMID: 19099558 PMCID: PMC2628942 DOI: 10.1186/1471-2156-9-89] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2008] [Accepted: 12/19/2008] [Indexed: 12/02/2022] Open
Abstract
Background There is so far very little data on autosomal nucleotide diversity in birds, except for data from the domesticated chicken and some passerines species. Estimates of nucleotide diversity reported so far in birds have been high (~10-3) and a likely explanation for this is the generally higher effective population sizes compared to mammals. In this study, the level of nucleotide diversity has been examined in the willow grouse, a non-domesticated bird species from the order Galliformes, which also holds the chicken. The willow grouse (Lagopus lagopus) has an almost circumpolar distribution but is absent from Greenland and the north Atlantic islands. It primarily inhabits tundra, forest edge habitats and sub-alpine vegetation. Willow grouse are hunted throughout its range, and regionally it is a game bird of great cultural and economical importance. Results We sequenced 18 autosomal protein coding loci from approximately 15–18 individuals per population. We found a total of 127 SNP's, which corresponds to 1 SNP every 51 bp. 26 SNP's were amino acid replacement substitutions. Total nucleotide diversity (πt) was between 1.30 × 10-4 and 7.66 × 10-3 (average πt = 2.72 × 10-3 ± 2.06 × 10-3) and silent nucleotide diversity varied between 4.20 × 10-4and 2.76 × 10-2 (average πS = 9.22 × 10-3 ± 7.43 × 10-4). The synonymous diversity is approximately 20 times higher than in humans and two times higher than in chicken. Non-synonymous diversity was on average 18 times lower than the synonymous diversity and varied between 0 and 4.90 × 10-3 (average πa = 5.08 × 10-4 ± 7.43 × 103), which suggest that purifying selection is strong in these genes. FST values based on synonymous SNP's varied between -5.60 × 10-4 and 0.20 among loci and revealed low levels of differentiation among the four localities, with an overall value of FST = 0.03 (95% CI: 0.006 – 0.057) over 60 unlinked loci. Non-synonymous SNP's gave similar results. Low levels of linkage disequilibrium were observed within genes, with an average r2 = 0.084 ± 0.110, which is expected for a large outbred population with no population differentiation. The mean per site per generation recombination parameter (ρ) was comparably high (0.028 ± 0.018), indicating high recombination rates in these genes. Conclusion We found unusually high levels of nucleotide diversity in the Scandinavian willow grouse as well as very little population structure among localities with up to 1647 km distance. There are also low levels of linkage disequilibrium within the genes and the population recombination rate is high, which is indicative of an old panmictic population, where recombination has had time to break up any haplotype blocks. The non-synonymous nucleotide diversity is low compared with the silent, which is in agreement with effective purifying selection, possibly due to the large effective population size.
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A linkage map of the zebra finch Taeniopygia guttata provides new insights into avian genome evolution. Genetics 2008; 179:651-67. [PMID: 18493078 DOI: 10.1534/genetics.107.086264] [Citation(s) in RCA: 85] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
Passeriformes are the largest order of birds and one of the most widely studied groups in evolutionary biology and ecology. Until recently genomic tools in passerines relied on chicken genomic resources. Here we report the construction and analysis of a whole-genome linkage map for the zebra finch (Taeniopygia guttata) using a 354-bird pedigree. The map contains 876 SNPs dispersed across 45 linkage groups and we found only a few instances of interchromosomal rearrangement between the zebra finch and the chicken genomes. Interestingly, there was a greater than expected degree of intrachromosomal rearrangements compared to the chicken, suggesting that gene order is not conserved within avian chromosomes. At 1068 cM the map is approximately only one quarter the length of the chicken linkage map, providing further evidence that the chicken has an unusually high recombination rate. Male and female linkage-map lengths were similar, suggesting no heterochiasmy in the zebra finch. This whole-genome map is the first for any passerine and a valuable tool for the zebra finch genome sequence project and for studies of quantitative trait loci.
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Correlation between Microsatellite Loci and Onset of Lay and Egg Quality Traits in Chinese Silkies, Gallus gallus. J Poult Sci 2008. [DOI: 10.2141/jpsa.45.241] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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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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Akesson M, Hansson B, Hasselquist D, Bensch S. Linkage mapping of AFLP markers in a wild population of great reed warblers: importance of heterozygosity and number of genotyped individuals. Mol Ecol 2007; 16:2189-202. [PMID: 17561884 DOI: 10.1111/j.1365-294x.2007.03290.x] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Amplified fragment length polymorphisms (AFLP) are dominant markers frequently used to build linkage maps where heterozygosity could be inferred by a backcross breeding strategy. In the present study, we describe the utilization of an unmanipulated great reed warbler, Acrocephalus arundinaceus pedigree to infer heterozygous genotypes of AFLP markers in order to map these markers to a partial linkage map previously based on microsatellites. In total, 50 of the 83 autosomal AFLPs (60%) and 4 of 5 Z-linked AFLPs (80%) were mapped. For each marker, on average, 88% of the expected number of heterozygote parents was detected. The likelihood of map assignment was to a large extent due to the number and density of microsatellite markers already in the map. The 'parsimonious linkage map', that is the map based on the most parsimonious location of all significantly linked markers, consisted of 21 autosomal linkage groups with 2 to 15 markers and had a total map size of 552 cM in males and 858 cM in females. The Z-chromosome linkage group with 12 markers had a size of 155 cM. The autosomal 'framework linkage map', that is the map based only on markers with an unambiguous position, had a total size of 237 cM in males and 440 cM in females, respectively. The inclusion of AFLPs enlarged the previous map substantially (e.g. the autosomal parsimonious linkage map became 441 cM and 621 cM larger for male and female recombination, respectively). The probability that an AFLP became mapped increased with increasing level of heterozygosity, whereas the probability of mapping into a framework position increased with both heterozygosity and number of genotyped individuals. Our results suggest that AFLP provides a fast and inexpensive means of enlarging genetic maps already composed of markers with high polymorphism, also in wild populations with unmanipulated pedigrees.
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Affiliation(s)
- Mikael Akesson
- Department of Animal Ecology, Ecology Building, Lund University, S-223 62 Lund, Sweden.
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15
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Burt DW, White SJ. Avian genomics in the 21st century. Cytogenet Genome Res 2007; 117:6-13. [PMID: 17675839 DOI: 10.1159/000103159] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2007] [Accepted: 02/01/2007] [Indexed: 11/19/2022] Open
Abstract
The chicken has long been an important model organism for developmental biology, as well as a major source of protein with billions of birds used in meat and egg production each year. Chicken genomics has been transformed in recent years, with the characterisation of large EST collections and most recently with the assembly of the chicken genome sequence. As the first livestock genome to be fully sequenced it leads the way for others to follow--with zebra finch later this year. The genome sequence and the availability of three million genetic polymorphisms are expected to aid the identification of genes that control traits of importance in poultry. As the first bird genome to be sequenced it is a model for the remaining 9,600 species thought to exist today. Many of the features of avian biology and organisation of the chicken genome make it an ideal model organism for phylogenetics and embryology, along with applications in agriculture and medicine. The availability of new tools such as whole-genome gene expression arrays and SNP panels, coupled with information resources on the genes and proteins are likely to enhance this position.
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Affiliation(s)
- D W Burt
- Department of Genomics and Genetics, Roslin Institute (Edinburgh), Roslin, Midlothian, UK.
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16
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Huang CW, Cheng YS, Rouvier R, Yang KT, Wu CP, Huang MC. AFLP fingerprinting for paternity testing in ducks. Br Poult Sci 2007; 48:323-30. [PMID: 17578695 DOI: 10.1080/00071660701370459] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
1. The accuracy and reproducibility of AFLP fingerprinting was investigated in the duck (Anas Platyrhynchos), using a multicolour fluorescent labeling technique. The fluorescent labelling fragments were separated on a capillary electrophoresis-base ABI PRISM 3100 Genetic Analyzer. 2. A total of 337 AFLP peaks with 103 of them being polymorphic markers were generated by 16 sets consisting of EcoRI/TaqI primer pair combinations. The number and size range of AFLP polymorphisms detected per primer pair varied from 3 to 11 and 58 to 290 bp, respectively. About 30.6% (103/337) of AFLP peaks were detected polymorphisms, with an average of 6.4 polymorphic markers per primer pair. 3. The clear polymorphic peaks were amplified with EcoR+AC/Taq+AC primer combinations. The AFLP peaks showed high reproducibility. From the family testing, we found that the fingerprints of all the offspring were derived from one or other parent. Therefore, we conclude that AFLP fingerprinting might be a suitable method for duck paternity testing.
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Affiliation(s)
- C-W Huang
- Department of Animal Science, National Chung Hsing University, Taichung, Taiwan
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17
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Sasazaki S, Hinenoya T, Lin B, Fujiwara A, Mannen H. A comparative map of macrochromosomes between chicken and Japanese quail based on orthologous genes. Anim Genet 2006; 37:316-20. [PMID: 16879339 DOI: 10.1111/j.1365-2052.2006.01454.x] [Citation(s) in RCA: 20] [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
In order to develop a comparative map between chicken and quail, we identified orthologous gene markers based on chicken genomic sequences and localized them on the Japanese quail Kobe-NIBS linkage map, which had previously been constructed with amplified fragment length polymorphisms. After sequencing the intronic regions of 168 genes located on chicken chromosomes 1-8, polymorphisms among Kobe-NIBS quail family parents were detected in 51 genes. These orthologous markers were mapped on eight Japanese quail linkage groups (JQG), and they allowed the comparison of JQG to chicken macrochromosomes. The locations of the genes and their orders were quite similar between the two species except within a previously reported inversion on quail chromosome 2. Therefore, we propose that the respective quail linkage groups are macrochromosomes and designated as quail chromosomes CJA 1-8.
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Affiliation(s)
- S Sasazaki
- Graduate School of Science and Technology, Kobe University, Kobe 657-8501, Japan
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18
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Backström N, Brandström M, Gustafsson L, Qvarnström A, Cheng H, Ellegren H. Genetic mapping in a natural population of collared flycatchers (Ficedula albicollis): conserved synteny but gene order rearrangements on the avian Z chromosome. Genetics 2006; 174:377-86. [PMID: 16783008 PMCID: PMC1569790 DOI: 10.1534/genetics.106.058917] [Citation(s) in RCA: 84] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023] Open
Abstract
Data from completely sequenced genomes are likely to open the way for novel studies of the genetics of nonmodel organisms, in particular when it comes to the identification and analysis of genes responsible for traits that are under selection in natural populations. Here we use the draft sequence of the chicken genome as a starting point for linkage mapping in a wild bird species, the collared flycatcher - one of the most well-studied avian species in ecological and evolutionary research. A pedigree of 365 flycatchers was established and genotyped for single nucleotide polymorphisms in 23 genes selected from (and spread over most of) the chicken Z chromosome. All genes were also found to be located on the Z chromosome in the collared flycatcher, confirming conserved synteny at the level of gene content across distantly related avian lineages. This high degree of conservation mimics the situation seen for the mammalian X chromosome and may thus be a general feature in sex chromosome evolution, irrespective of whether there is male or female heterogamety. Alternatively, such unprecedented chromosomal conservation may be characteristic of most chromosomes in avian genome evolution. However, several internal rearrangements were observed, meaning that the transfer of map information from chicken to nonmodel bird species cannot always assume conserved gene orders. Interestingly, the rate of recombination on the Z chromosome of collared flycatchers was only approximately 50% that of chicken, challenging the widely held view that birds generally have high recombination rates.
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Affiliation(s)
- Niclas Backström
- Department of Evolutionary Biology, Evolutionary Biology Centre, Uppsala University, SE-752 36 Uppsala, Sweden
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SASAZAKI S, HINENOYA T, FUJIMA D, KIKUCHI S, FUJIWARA A, MANNEN H. Mapping of expressed sequence tag markers with a cDNA-amplified fragment length polymorphism method in Japanese quail (Coturnix japonica). Anim Sci J 2006. [DOI: 10.1111/j.1740-0929.2006.00318.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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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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