Progress 04/15/05 to 04/14/09
Outputs
OUTPUTS: We are developing a robust BAC physical and comparative map of the turkey to estimate its sequence repertoire, compare its genome with those of chicken and human, and provide a platform for functional analysis and genome sequencing. We developed a universal, one-tube and one-step fluorescent labeling kit well suited for BAC fingerprint analysis with capillary electrophoresis using any enzyme combinations. We fingerprinted over 46,000 BACs randomly selected from the turkey CHORI-260 library. We developed a widely applicable computer program (named FPE for Fingerprint Editor) that is capable of automatically and manually collecting, transforming and editing BAC fingerprint data generated on capillary sequencers. From the fingerprints, we assembled our first version of the turkey genome physical map using FingerPrinted Contig software. We also sequenced over 21,000 ends of CHORI-260 BACs and aligned them to the chicken genome sequence using automated and manual annotation techniques. Unique orthologous locations in the chicken genome have been identified for a large majority of the sequenced turkey BACs. Over 20,000 turkey BACs have been assigned to turkey genes or markers via overgo hybridization. These data (available at http://poultry.mph.msu.edu/resources/Resources.htm) allow for integration of the physical map with the turkey genetic map and chicken genome sequence and further merging of contigs. This process is currently underway, involving additional manual annotation, overgo hybridization, the construction and analysis of a second turkey BAC library and cytogenetic analysis. The resulting map will provide a platform for turkey genome sequencing and tools for genetic improvement of an important agricultural species, along with novel insights into the evolution of avian genomes. PARTICIPANTS: Jerry Dodgson, P.I., Michigan State U. Hongbin-Zhang, co-P.I., Texas A&M U. Bill Payne, research associate, Michigan State U. Dr. Xiaojun Zhang, postdoctoral research scientist, Texas A&M U. Dr. Mi-Kyung Lee, assistant research scientist, Texas A&M U. Jennifer J. Dong, research assistant, TAMU, Texas A&M U. Chantel Scheuring, research associate, TAMU, Texas A&M U. Dr. Yang Zhang, postdoctoral research scientist, Texas A&M U. Interaction with the Turkey Genome Sequencing Consortium: Otto Folkerts, Ed Smith, Rami Dallouel, Audrey McElroy, Eric Wong, Oswald Crasta, Rick Jensen and Clive Evans, Virginia Tech; Dave Burt, Roslin Institute; Roger Coulombe, Utah State; Kent Reed, U. of Minnesota TARGET AUDIENCES: Poultry scientists, animal geneticists, turkey breeders. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
A turkey BAC contig map, integrated with its linkage map, will be aligned with the chicken sequence to create a high density turkey-chicken comparative map, a "one sequence - two genomes" strategy. This will not only provide a unique resource for research in molecular genetics of the turkey, an important agricultural species in its own right, it would also enhance the utility of the chicken genome sequence and its relevance to agriculture. Turkey breeders and researchers will be able to test genes and polymorphisms shown to be important in desirable traits in chickens for their applicability to turkeys and vice versa. A platform will be provided for further genetic analysis of the turkey and sequencing the turkey genome, outcomes that are now underway.
Publications
- Cheng, H., M. Niikura, T. Kim, W. Mao, K.S. MacLea, H. Hunt, J. Dodgson, J. Burnside, R. Morgan, M. Ouyang, S. Lamont, J. Dekkers, J. Fulton, M. Soller, and W. Muir. 2008. Using integrative genomics to elucidate genetic resistance to Marek's disease in chickens. Dev Biol (Basel). 132:365-372.
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Progress 04/15/07 to 04/14/08
Outputs
OUTPUTS: We are developing a robust BAC physical and comparative map of the turkey to estimate its sequence repertoire, compare its genome with those of chicken and human, and provide a platform for functional analysis and genome sequencing. We developed a universal, one-tube and one-step fluorescent labeling kit well suited for BAC fingerprint analysis with capillary electrophoresis using any enzyme combinations. We fingerprinted > 46,000 BACs (6.0 x) randomly selected from the turkey CHORI-260 library. We developed a widely applicable computer program (named FPE for Fingerprint Editor) that is capable of automatically and manually collecting, transforming and editing BAC fingerprint data generated on capillary sequencers. From the fingerprints, we assembled our first version of the turkey genome physical map using FingerPrinted Contig (FPC) software. We also sequenced >21,000 ends of CHORI-260 BACs and aligned them to the chicken genome sequence using automated and manual
annotation techniques. Unique orthologous locations in the chicken genome have been identified for a large majority of the sequenced turkey BACs. Nearly 18,000 turkey BACs have been assigned to 1,429 genes or markers via overgo hybridization. These data (available at http://poultry.mph.msu.edu/resources/Resources.htm) allow for integration of the physical map with the turkey genetic map and chicken genome sequence and further merging of contigs. This process is currently underway, involving additional manual annotation, overgo hybridization, the construction and analysis of a second turkey BAC library and cytogenetic analysis. The resulting map will provide a platform for turkey genome sequencing and tools for genetic improvement of an important agricultural species, along with novel insights into the evolution of avian genomes.
PARTICIPANTS: Jerry Dodgson, P.I. William Payne, technical research associate. Texas A&M University, partner organization. Hongbin Zhang, collaborator. M.-K. Lee, postdoctoral associate.
TARGET AUDIENCES: Poultry breeders, poultry geneticists.
PROJECT MODIFICATIONS: No Project Modifications information reported.
Impacts
A turkey BAC contig map, integrated with its linkage map, will be aligned with the chicken sequence to create a high density turkey-chicken comparative map, a "one sequence - two genomes" strategy. This will not only provide a unique resource for research in molecular genetics of the turkey, an important agricultural species in its own right, it would also enhance the utility of the chicken genome sequence and its relevance to agriculture. Turkey breeders and researchers will be able to test genes and polymorphisms shown to be important in desirable traits in chickens for their applicability to turkeys and vice versa. A platform will be provided for further genetic analysis of the turkey and sequencing the turkey genome.
Publications
- Dodgson, J.B. 2007. The chicken genome: some good news and some bad news. Poultry Science 86:1453-1459.
- Cogburn, L.A., Porter, T.E., Duclos, M.J., Simon, J., Burgess, S.C., Cheng, H., Dodgson, J.B., and Burnside, J. 2007. Functional genomics of the chicken, a model organism. Poultry Science 86:2059-2094.
- Lee, M.-K., Payne, B., Dong, J., Park, H.J., Zhang, X., Dodgson, J., and Zhang, H.-B. 2008. First-generation physical and comparative map of the turkey genome constructed by BAC fingerprint analysis with capillary electrophoresis. Proceedings, Plant and Animal Genome XVI, p. 68.
- Sazanova, A.L., Romanov, M.N., Blagoveshenski, I.Y., Fomichev, K.A., Stekolnikova, V.A., Nefedov, M., Modi, W.S., Ryder, O.A., Dodgson, J.B., and Sazanov, A.A. 2008. Cytogenetic localization of avian Z- and W-linked genes using large-insert BAC clones. Proceedings, Plant and Animal Genome XVI, p. 257.
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Progress 04/15/06 to 04/15/07
Outputs
The goal of this proposal is the generation of a comparative turkey-chicken genome map based on a BAC contig map of the turkey genome and the draft chicken genome sequence. A comparative turkey-chicken map should provide fundamental evolutionary and agricultural insights for all poultry species. We proposed to: 1. Fingerprint approximately 40,000 BACs (6.3X genome coverage) from the CHORI-260 turkey BAC library, 2. Generate 20,000 BAC end sequences (BES) for use in both assembling the turkey map and construction of the chicken-turkey comparative map, and 3. Integrate the BAC contig map with linkage and comparative genome maps by mapping turkey genes and linkage map markers, chicken genes and BAC end sequences using a high throughput overgo mapping strategy. We have now met or exceeded these basic goals and are in process of assembling and refining our physical map. We have sequenced a total 21,000 BAC ends and assembled the first version of the contig map. We
fingerprinted 46,080 clones, 41,179 of which provided usable data (12% insert-empty clones were found in this library). Of the 41,179 clones, 41,169 (6.5 x) were used in the contig map assembly. 35,861 of the clones (5.7 x) were assembled into 2,544 contigs, with each consisting of 2 - 200 clones, whereas 5,308 clones remained as singletons. The 2,544 contigs collectively span a total of 1.100 Mb in physical length, covering >91% of the 1,200-Mb turkey genome. The average length of the contigs is 432 kb in physical length, with 4,000 kb for the largest contig. We have also selected 100 contigs and sequenced all ends of the contig BACs. Now we are conducting comparative analysis with the chicken sequences using these 100 contigs. We have also assigned 9358 turkey BACs to specific linkage map or gene markers that they contain (777 markers in total). This will allow BAC contigs to be assembled along the genetic linkage map and assist in the comparative analysis to the chicken genome
sequence. The initial alignment with the chicken will allow us to develop tests that will allow us to extend and improve the turkey assembly.
Impacts
A turkey BAC contig map, integrated with its linkage map, will be aligned with the chicken sequence to create a high density turkey-chicken comparative map, a "one sequence - two genomes" strategy. This will not only provide a unique resource for research in molecular genetics of the turkey, an important agricultural species in its own right, it would also enhance the utility of the chicken genome sequence and its relevance to agriculture. Turkey breeders and researchers will be able to test genes and polymorphisms shown to be important in desirable traits in chickens for their applicability to turkeys and vice versa. A platform will be provided for further genetic analysis of the turkey.
Publications
- Romanov, M.N., Dodgson, J.B. 2006. Cross-species overgo hybridization and comparative physical mapping within avian genomes. Animal Genetics 37:397-399.
- Siegel, P.B., Dodgson, J.B., Andersson, L. 2006. Progress from chicken genetics to the chicken genome. Poultry Science 85:2050-2060.
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Progress 04/15/05 to 04/14/06
Outputs
The goal of this project is the generation of a comparative turkey-chicken genome map based on a BAC contig map of the turkey genome and the draft chicken genome sequence. To date, we have generated over half our goal of 40,000 BACs from the CHORI-260 turkey BAC library (6.3X genome coverage) and hope to exceed this goal to a total of 45,000 soon. We will then begin to generate 20,000 BAC end sequences (BES) for use in both assembling the turkey map and construction of the chicken-turkey comparative map. We are integrating the BAC contig map with linkage and comparative genome maps by mapping turkey genes and linkage map markers, chicken genes and BAC end sequences using a high throughput overgo mapping strategy. To date we've identified nearly 4000 turkey BACs containing a total of nearly 350 markers. A manuscript describing this work is in press. Additional overgo mapping is continuing. In summary, we are well on our way to achieving our goals that will allow us to
develop a physical map for the turkey genome and a comparative turkey-chicken aligned map.
Impacts
Although it is an important agricultural species, limited gene mapping and other genomic resources and data are available for the turkey. Our research, when completed, will allow turkey breeders to utilize the information of the chicken genome sequence using our turkey-chicken comparative map, a one sequence - two genomes strategy. This will not only provide a unique resource for research into the breeding and molecular genetics of the turkey, it will also enhance the utility of the chicken genome sequence and its relevance to agriculture. A comparative turkey-chicken map should provide fundamental evolutionary and agricultural insights for all poultry species.
Publications
- No publications reported this period
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