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Wu H, Chuang TC, Liao WC, Chi KJ, Ng CS, Cheng HC, Juan WT. Modification of Keratin Integrations and the Associated Morphogenesis in Frizzling Chicken Feathers. BIOLOGY 2024; 13:464. [PMID: 39056659 PMCID: PMC11273737 DOI: 10.3390/biology13070464] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2024] [Revised: 06/02/2024] [Accepted: 06/21/2024] [Indexed: 07/28/2024]
Abstract
The morphological and compositional complexities of keratinized components make feathers ingenious skin appendages adapted to diverse ecological needs. Frizzling feathers, characterized by their distinct curling phenotypes, offer a unique model to explore the intricate morphogenesis in developing a keratin-based bioarchitecture over a wide range of morphospace. Here, we investigated the heterogeneous allocation of α- and β-keratins in flight feather shafts of homozygous and heterozygous frizzle chickens by analyzing the medulla-cortex integrations using quantitative morphology characterizations across scales. Our results reveal the intriguing construction of the frizzling feather shaft through the modified medulla development, leading to a perturbed balance of the internal biomechanics and, therefore, introducing the inherent natural frizzling compared to those from wild-type chickens. We elucidate how the localized developmental suppression of the α-keratin in the medulla interferes with the growth of the hierarchical keratin organization by changing the internal stress in the frizzling feather shaft. This research not only offers insights into the morphogenetic origin of the inherent bending of frizzling feathers but also facilitates our in-depth understanding of the developmental strategies toward the diverse integuments adapted for ecological needs.
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Affiliation(s)
- Hao Wu
- Graduate Institute of Biomedical Sciences, China Medical University, Taichung 40402, Taiwan
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan; (K.-J.C.)
| | - Tsao-Chi Chuang
- Department of Biomedical Imaging and Radiological Science, China Medical University, Taichung 40402, Taiwan
| | - Wan-Chi Liao
- Department of Biomedical Imaging and Radiological Science, China Medical University, Taichung 40402, Taiwan
| | - Kai-Jung Chi
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan; (K.-J.C.)
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan
- Department of Physics, National Chung Hsing University, Taichung 40227, Taiwan
| | - Chen-Siang Ng
- Institute of Molecular and Cellular Biology, National Tsing Hua University, Hsinchu 30013, Taiwan;
| | - Hsu-Cheng Cheng
- Department of Life Sciences, National Chung Hsing University, Taichung 40227, Taiwan; (K.-J.C.)
- The iEGG and Animal Biotechnology Center, National Chung Hsing University, Taichung 40227, Taiwan
| | - Wen-Tau Juan
- Department of Biomedical Imaging and Radiological Science, China Medical University, Taichung 40402, Taiwan
- Department of Medical Research, China Medical University Hospital, Taichung 40447, Taiwan
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Ng CS, Wu P, Foley J, Foley A, McDonald ML, Juan WT, Huang CJ, Lai YT, Lo WS, Chen CF, Leal SM, Zhang H, Widelitz RB, Patel PI, Li WH, Chuong CM. The chicken frizzle feather is due to an α-keratin (KRT75) mutation that causes a defective rachis. PLoS Genet 2012; 8:e1002748. [PMID: 22829773 PMCID: PMC3400578 DOI: 10.1371/journal.pgen.1002748] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2011] [Accepted: 04/19/2012] [Indexed: 12/15/2022] Open
Abstract
Feathers have complex forms and are an excellent model to study the development and evolution of morphologies. Existing chicken feather mutants are especially useful for identifying genetic determinants of feather formation. This study focused on the gene F, underlying the frizzle feather trait that has a characteristic curled feather rachis and barbs in domestic chickens. Our developmental biology studies identified defects in feather medulla formation, and physical studies revealed that the frizzle feather curls in a stepwise manner. The frizzle gene is transmitted in an autosomal incomplete dominant mode. A whole-genome linkage scan of five pedigrees with 2678 SNPs revealed association of the frizzle locus with a keratin gene-enriched region within the linkage group E22C19W28_E50C23. Sequence analyses of the keratin gene cluster identified a 69 bp in-frame deletion in a conserved region of KRT75, an α-keratin gene. Retroviral-mediated expression of the mutated F cDNA in the wild-type rectrix qualitatively changed the bending of the rachis with some features of frizzle feathers including irregular kinks, severe bending near their distal ends, and substantially higher variations among samples in comparison to normal feathers. These results confirmed KRT75 as the F gene. This study demonstrates the potential of our approach for identifying genetic determinants of feather forms. With the availability of a sequenced chicken genome, the reservoir of variant plumage genes found in domestic chickens can provide insight into the molecular mechanisms underlying the diversity of feather forms. In this paper, we identify the molecular basis of the distinctive frizzle (F) feather phenotype that is caused by a single autosomal incomplete dominant gene in which heterozygous individuals show less severe phenotypes than homozygous individuals. Feathers in frizzle chickens curve backward. We used computer-assisted analysis to establish that the rachis of the frizzle feather was irregularly kinked and more severely bent than normal. Moreover, microscopic evaluation of regenerating feathers found reduced proliferating cells that give rise to the frizzle rachis. Analysis of a pedigree of frizzle chickens showed that the phenotype is linked to two single-nucleotide polymorphisms in a cluster of keratin genes within the linkage group E22C19W28_E50C23. Sequencing of the gene cluster identified a 69-base pair in-frame deletion of the protein coding sequence of the α-keratin-75 gene. Forced expression of the mutated gene in normal chickens produced a twisted rachis. Although chicken feathers are primarily composed of beta-keratins, our findings indicate that alpha-keratins have an important role in establishing the structure of feathers.
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Affiliation(s)
- Chen Siang Ng
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Ping Wu
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - John Foley
- Department of Anatomy and Cell Biology, Indiana University School of Medicine, Bloomington, Indiana, United States of America
- Department of Dermatology, Indiana University School of Medicine, Bloomington, Indiana, United States of America
| | - Anne Foley
- Department of Anatomy and Cell Biology, Indiana University School of Medicine, Bloomington, Indiana, United States of America
- Department of Dermatology, Indiana University School of Medicine, Bloomington, Indiana, United States of America
| | - Merry-Lynn McDonald
- Department of Molecular and Human Genetics, Baylor College of Medicine, Houston, Texas, United States of America
| | - Wen-Tau Juan
- Institute of Physics, Academia Sinica, Taipei, Taiwan
| | - Chih-Jen Huang
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Taiwan International Graduate Program, Academia Sinica, Taipei, Taiwan
- Graduate Institute of Biotechnology, National Chung Hsing University, Taichung, Taiwan
| | - Yu-Ting Lai
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Wen-Sui Lo
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
| | - Chih-Feng Chen
- Department of Animal Sciences, National Chung Hsing University, Taichung, Taiwan
| | - Suzanne M. Leal
- Department of Dermatology, Indiana University School of Medicine, Bloomington, Indiana, United States of America
| | - Huanmin Zhang
- Avian Disease and Oncology Laboratory, Agriculture Research Service, United States Department of Agriculture, East Lansing, Michigan, United States of America
| | - Randall B. Widelitz
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
| | - Pragna I. Patel
- Institute for Genetic Medicine and Center for Craniofacial Molecular Biology, University of Southern California, Los Angeles, California, United States of America
| | - Wen-Hsiung Li
- Biodiversity Research Center, Academia Sinica, Taipei, Taiwan
- Department of Ecology and Evolution, University of Chicago, Chicago, Illinois, United States of America
- * E-mail: (W-HL); (C-MC)
| | - Cheng-Ming Chuong
- Department of Pathology, Keck School of Medicine, University of Southern California, Los Angeles, California, United States of America
- Research Center for Developmental Biology and Regenerative Medicine, National Taiwan University, Taipei, Taiwan
- * E-mail: (W-HL); (C-MC)
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Rosário MF, Margarido GRA, Boschiero C, Moura ASAMT, Ledur MC, Coutinho LL, Garcia AAF. Precision of distances and ordering of microsatellite markers in consensus linkage maps of chromosomes 1, 3 and 4 from two reciprocal chicken populations using bootstrap sampling. GENETICS AND MOLECULAR RESEARCH 2010; 9:1357-76. [PMID: 20645260 DOI: 10.4238/vol9-3gmr842] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
Some factors complicate comparisons between linkage maps from different studies. This problem can be resolved if measures of precision, such as confidence intervals and frequency distributions, are associated with markers. We examined the precision of distances and ordering of microsatellite markers in the consensus linkage maps of chromosomes 1, 3 and 4 from two F(2) reciprocal Brazilian chicken populations, using bootstrap sampling. Single and consensus maps were constructed. The consensus map was compared with the International Consensus Linkage Map and with the whole genome sequence. Some loci showed segregation distortion and missing data, but this did not affect the analyses negatively. Several inversions and position shifts were detected, based on 95% confidence intervals and frequency distributions of loci. Some discrepancies in distances between loci and in ordering were due to chance, whereas others could be attributed to other effects, including reciprocal crosses, sampling error of the founder animals from the two populations, F(2) population structure, number of and distance between microsatellite markers, number of informative meioses, loci segregation patterns, and sex. In the Brazilian consensus GGA1, locus LEI1038 was in a position closer to the true genome sequence than in the International Consensus Map, whereas for GGA3 and GGA4, no such differences were found. Extending these analyses to the remaining chromosomes should facilitate comparisons and the integration of several available genetic maps, allowing meta-analyses for map construction and quantitative trait loci (QTL) mapping. The precision of the estimates of QTL positions and their effects would be increased with such information.
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Affiliation(s)
- M F Rosário
- Departamento de Genética, Escola Superior de Agricultura Luiz de Queiroz, Universidade de São Paulo, Piracicaba, SP, Brasil.
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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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5
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Valdez MB, Mizutani M, Fujiwara A, Yazawa H, Yamagata T, Shimada K, Namikawa T. Histocompatible chicken inbred lines: homogeneities in the major histocompatibility complex antigens of the GSP, GSN/1, PNP/DO and BM-C inbred lines assessed by hemagglutination, mixed lymphocyte reaction and skin transplantation. Exp Anim 2008; 56:329-38. [PMID: 18075192 DOI: 10.1538/expanim.56.329] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022] Open
Abstract
Chicken inbred lines of the GSP, GSN/1, PNP/DO and BM-C have been established by selection of a specific allele at the B blood group locus (MHC B-G region) and other polymorphic loci through pedigree mating. To extend the potential of these inbred lines as experimental animals in Aves, we assessed the antigenic homogeneities of the MHC antigens by three immunological methods. Antigenic variations of red blood cells (RBCs) were surveyed in the inbred lines and a random-bred line (NG) derived from the Nagoya breed by using ten kinds of intact antisera produced in the inbred line of chickens against RBCs of a red junglefowl and hybrids. In the hemagglutination test, no individual variations were found within the inbred line at all, while all the ten antisera detected highly heterogeneous reactions in individuals of the NG. The reciprocal one-way mixed lymphocyte reactions gave constantly higher stimulation responses (P<0.01) between individual pairs from the inbred lines having different B alleles compared to pairs within the inbred line, while lower stimulation was observed between pairs of the GSP and GSN/1 inbred lines both having the B(21) allele. In reciprocal skin transplantation, the transplanted skingrafts within the inbred line and between individuals from the GSP and GSN/1 inbred lines survived more than 100 days, while all the skingrafts showed signs of rejection within 7 days among the inbred lines having different B alleles. The results obtained by the three practical methods coincidentally indicated that the individuals in the respective four inbred lines were histocompatible, and further, that the GSP and GSN/1 individuals were histocompatible.
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Affiliation(s)
- Marcos B Valdez
- Laboratory of Animal Genetics, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Japan
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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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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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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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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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10
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Smith J, Speed D, Hocking PM, Talbot RT, Degen WGJ, Schijns VEJC, Glass EJ, Burt DW. Development of a chicken 5 K microarray targeted towards immune function. BMC Genomics 2006; 7:49. [PMID: 16533398 PMCID: PMC1440325 DOI: 10.1186/1471-2164-7-49] [Citation(s) in RCA: 30] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2005] [Accepted: 03/13/2006] [Indexed: 11/17/2022] Open
Abstract
BACKGROUND The development of microarray resources for the chicken is an important step in being able to profile gene expression changes occurring in birds in response to different challenges and stimuli. The creation of an immune-related array is highly valuable in determining the host immune response in relation to infection with a wide variety of bacterial and viral diseases. RESULTS Here we report the development of chicken immune-related cDNA libraries and the subsequent construction of a microarray containing 5190 elements (in duplicate). Clones on the array originate from tissues known to contain high levels of cells related to the immune system, namely Bursa, Peyers patch, thymus and spleen. Represented on the array are genes that are known to cluster with existing chicken ESTs as well as genes that are unique to our libraries. Some of these genes have no known homologies and represent novel genes in the chicken collection. A series of reference genes (ie. genes of known immune function) are also present on the array. Functional annotation data is also provided for as many of the genes on the array as is possible. CONCLUSION Six new chicken immune cDNA libraries have been created and nearly 10,000 sequences submitted to GenBank [GenBank: AM063043-AM071350; AM071520-AM072286; AM075249-AM075607]. A 5 K immune-related array has been developed from these libraries. Individual clones and arrays are available from the ARK-Genomics resource centre.
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Affiliation(s)
- Jacqueline Smith
- Division of Genetics and Genomics, Roslin Institute, Roslin (Edinburgh), Midlothian, EH25 9PS, UK
| | - David Speed
- Division of Genetics and Genomics, Roslin Institute, Roslin (Edinburgh), Midlothian, EH25 9PS, UK
| | - Paul M Hocking
- Division of Genetics and Genomics, Roslin Institute, Roslin (Edinburgh), Midlothian, EH25 9PS, UK
| | - Richard T Talbot
- Ark-Genomics, Roslin Institute, Roslin (Edinburgh), Midlothian, EH25 9PS, UK
| | - Winfried GJ Degen
- Intervet International B.V., Dept. of Vaccine Technology and Immunology R&D, P.O. Box 31, 5830 AA, Boxmeer, The Netherlands
| | - Virgil EJC Schijns
- Intervet International B.V., Dept. of Vaccine Technology and Immunology R&D, P.O. Box 31, 5830 AA, Boxmeer, The Netherlands
| | - Elizabeth J Glass
- Division of Genetics and Genomics, Roslin Institute, Roslin (Edinburgh), Midlothian, EH25 9PS, UK
| | - David W Burt
- Division of Genetics and Genomics, Roslin Institute, Roslin (Edinburgh), Midlothian, EH25 9PS, UK
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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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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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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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Rabie TSKM, Crooijmans RPMA, Morisson M, Andryszkiewicz J, van der Poel JJ, Vignal A, Groenen MAM. A radiation hybrid map of chicken Chromosome 4. Mamm Genome 2005; 15:560-9. [PMID: 15366376 DOI: 10.1007/s00335-004-2362-8] [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: 10/26/2022]
Abstract
The mapping resolution of the physical map for chicken Chromosome 4 (GGA4) was improved by a combination of radiation hybrid (RH) mapping and bacterial artificial chromosome (BAC) mapping. The ChickRH6 hybrid panel was used to construct an RH map of GGA4. Eleven microsatellites known to be located on GGA4 were included as anchors to the genetic linkage map for this chromosome. Based on the known conserved synteny between GGA4 and human Chromosomes 4 and X, sequences were identified for the orthologous chicken genes from these human chromosomes by BLAST analysis. These sequences were subsequently used for the development of STS markers to be typed on the RH panel. Using a logarithm of the odds (LOD) threshold of 5.0, nine linkage groups could be constructed which were aligned with the genetic linkage map of this chromosome. The resulting RH map consisted of the 11 microsatellite markers and 50 genes. To further increase the number of genes on the map and to provide additional anchor points for the physical BAC map of this chromosome, BAC clones were identified for 22 microsatellites and 99 genes. The combined RH and BAC mapping approach resulted in the mapping of 61 genes on GGA4 increasing the resolution of the chicken-human comparative map for this chromosome. This enhanced comparative mapping resolution enabled the identification of multiple rearrangements between GGA4 and human Chromosomes 4q and Xp.
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Affiliation(s)
- Tarik S K M Rabie
- Wageningen Institute of Animal Sciences, Animal Breeding and Genetics Group, Wageningen University, Marijkeweg 40, 6709 PG Wageningen, The Netherlands.
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Wallis JW, Aerts J, Groenen MAM, Crooijmans RPMA, Layman D, Graves TA, Scheer DE, Kremitzki C, Fedele MJ, Mudd NK, Cardenas M, Higginbotham J, Carter J, McGrane R, Gaige T, Mead K, Walker J, Albracht D, Davito J, Yang SP, Leong S, Chinwalla A, Sekhon M, Wylie K, Dodgson J, Romanov MN, Cheng H, de Jong PJ, Osoegawa K, Nefedov M, Zhang H, McPherson JD, Krzywinski M, Schein J, Hillier L, Mardis ER, Wilson RK, Warren WC. A physical map of the chicken genome. Nature 2005; 432:761-4. [PMID: 15592415 DOI: 10.1038/nature03030] [Citation(s) in RCA: 161] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2004] [Accepted: 09/17/2004] [Indexed: 11/10/2022]
Abstract
Strategies for assembling large, complex genomes have evolved to include a combination of whole-genome shotgun sequencing and hierarchal map-assisted sequencing. Whole-genome maps of all types can aid genome assemblies, generally starting with low-resolution cytogenetic maps and ending with the highest resolution of sequence. Fingerprint clone maps are based upon complete restriction enzyme digests of clones representative of the target genome, and ultimately comprise a near-contiguous path of clones across the genome. Such clone-based maps are used to validate sequence assembly order, supply long-range linking information for assembled sequences, anchor sequences to the genetic map and provide templates for closing gaps. Fingerprint maps are also a critical resource for subsequent functional genomic studies, because they provide a redundant and ordered sampling of the genome with clones. In an accompanying paper we describe the draft genome sequence of the chicken, Gallus gallus, the first species sequenced that is both a model organism and a global food source. Here we present a clone-based physical map of the chicken genome at 20-fold coverage, containing 260 contigs of overlapping clones. This map represents approximately 91% of the chicken genome and enables identification of chicken clones aligned to positions in other sequenced genomes.
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Affiliation(s)
- John W Wallis
- Genome Sequencing Center, Washington University School of Medicine, Campus Box 8501, 4444 Forest Park Avenue, St Louis, Missouri 63108, USA
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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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