NATIONAL ANIMAL GENOME RESEARCH PROGRAM

• Sponsoring Institution: National Institute of Food and Agriculture
• Project Status: TERMINATED
• Funding Source: HATCH
• Reporting Frequency: Annual
• Accession No.: 0163267
• Project No.: MICL01728
• Multistate No.: NRSP-_OLD8
• Project Start Date: Oct 1, 2008
• Project End Date: Sep 30, 2013

Project Director
Dodgson, JE.

Recipient Organization
MICHIGAN STATE UNIV
(N/A)
EAST LANSING,MI 48824

Performing Department
Microbiology & Molecular Genetics

Non Technical Summary
In order to realize the combined agricultural and biomedical potential of livestock and aquaculture species, a thorough knowledge of the structure and organization of individual genomes is crucial to sustain and accelerate future genetic improvement. The current resolution of genome sequence across these species is highly variable, ranging from 'minimal or non-existent' in sheep and aquaculture species to 'reasonably sequenced' in species like cattle and chicken. In addition, a variety of powerful tools are necessary for dissection of the genetic architecture of complex traits in livestock. Importantly, these approaches are most beneficial when coordinated synergistically in an integrated discovery program. Despite the mapping of many QTL for a variety of economically relevant traits in several species, elucidation of the identity and nature of the underlying polygenes remains elusive. Bridging the gap between genotype and phenotype will be important in order to enhance genetic improvement programs and increase our understanding of the biological ramifications of genetic variation in commercial populations. Recent technological advancements have greatly reduced the cost of genotyping animals. Currently phenotype collection is easily the most cost intensive portion of an experiment. Furthermore, in some species, numerous QTL and some causal mutations have been identified in moderately to highly heritable traits. Future efforts will most likely be focused on lowly heritable or expensive-to-measure traits (e.g., disease resistance, fertility). In order to identify the mechanisms controlling these traits, a large number of intensively phenotyped individuals will be required. Advances in structural and functional genomics have allowed researchers to rapidly acquire vast amounts of experimental data. To understand the biological meaning of the genome, bioinformatic tools are necessary to extract information from public databases, analyze and store experimental data, and disseminate information. It is too costly for each scientist to individually develop these tools. Thus, there is a need to develop bioinformatic resources and facilitate access to freely available resources.

Animal Health Component

(N/A)

Research Effort Categories

Basic

(N/A)

Applied

(N/A)

Developmental

(N/A)

Classification

Knowledge Area (KA)	Subject of Investigation (SOI)	Field of Science (FOS)	Percent
303	3910	1080	40%
304	3910	1080	60%

Knowledge Area
303 - Genetic Improvement of Animals; 304 - Animal Genome;

Subject Of Investigation
3910 - Cross-commodity research--multiple animal species;

Field Of Science
1080 - Genetics;

Keywords

genome

animal breeding

quantitative trait loci

bioinformatics

genomic tools

coordination

comparative genomics

single nucleotide polymorphisms

phenotypes

mapping populations

genome sequences

physical genome maps

Goals / Objectives
Create shared genomic tools and reagents and sequence information to enhance the understanding and discovery of genetic mechanisms affecting traits of interest. Facilitate the development and sharing of animal populations and the collection and analysis of new, unique and interesting phenotypes. Develop, integrate and implement bioinformatics resources to support the discovery of genetic mechanisms that underlie traits of interest.

Project Methods
The purpose of NRSP-8 is to provide or enhance infrastructure for the genome community as a whole. NRSP-8 accomplishes its mission by working with a structure that is divided by species and managed by species coordinators. The six species coordinators for aquaculture, cattle, horse, poultry, sheep and swine also are joined by a bioinformatics coordinator. The coordinators facilitate the availability of shared genomic resources (tools, reagents and data) to the members of each species committee, often by leveraging the limited resources of the coordinator with those available from Federal (e.g., NIH, USDA-NRI), international, industry and State sources. The coordinators, working with the members of their respective committees and amongst themselves, also help to develop, stimulate and coordinate new initiatives by providing national leadership that is recognized nationally and internationally. Finally, NRSP-8 fosters communication among its members and stakeholders through, among other things, several email newsletters and participation in meetings and conferences. Species coordinators both stimulate this communication and provide focal points for input from the committee members and other stakeholders.

Progress 10/01/08 to 09/30/13

Outputs
Target Audience: Animal scientists. Poultry, cattle, swine, horse and aquaculture breeders. Animal industry representatives. Consumers of animal products. Genome biologists. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Training and mentoring have been provided to 5 graduate students, 5 undergraduate students and 4 postdoctoral associates. How have the results been disseminated to communities of interest? Publications. Annual meetings well attended by stakeholders. Quarterly newsletters. Email listserver. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? A new build, Galgal4.0, of the chicken genome sequence which combines the original reads, next generation sequencing (NGS) reads (Roche and Illumina) and the near-finished quality of the Z sequence done by Bellott et al. (Nature 466:612-616, 2010) was released late in 2011 and is now on browser sites. This still has not captured the roughly 5% of missing sequence (believed to be predominantly on the microchromosomes). Methods to fill gaps and obtain the missing sequence are being pursued (e.g., optical mapping, PacBio and Moleculo sequence methods, new assembly algorithms). Optical mapping and Moleculo sequencing of the reference genome was supported this year through coordination funds. In addition, Cobb-Vantress Inc. made a ~$150,000 commitment to this effort being led by The Genome Institute at Washington U., and additional support has been obtained this year from a USDA-NIFA-AFRI grant submission. A number of additional chicken genomes have been sequenced via NGS. This year coordination funds supported a project to sequence 19 different chicken lines of interest to NRSP-8 members, following up on a similar effort two years ago. That project is currently in progress with data availability anticipated by the end of 2013. The Turkey Genome Sequencing Consortium generated a draft sequence of the turkey genome using a combination of NGS reads, along with the turkey BAC contig map. Coordination funds aided in this effort which also enjoyed support from VaTech, BARC and U. of Minn., among others. Efforts are on-going to improve the annotation of genes and fill gaps in the turkey sequence. Previously, coordination funds provided microarrays for transcriptional profiling and comparative genome hybridization. Some coordination support also was committed to Illumina RNA-sequencing and Agilent chip-based transcriptional profiling, partly in hopes of filling in missing sequences. Database activities are led by the NRSP-8 Bioinformatics Coordinator, Jim Reecy, and Susan Lamont, along with Shane Burgess, represent poultry interests on the advisory committee for this group. Poultry bioinformatics has also benefitted from support at several other locations. We maintain a homepage for the NRSP-8 U.S. Poultry Genome project (http://poultry.mph.msu.edu) that provides a variety of genome mapping resources, including our newsletter archive. The Poultry Genome Newsletter has been published quarterly and is distributed through our Homepage and on the angenmap email discussion group. Research activities in pigs have focused on use of high density and low density SNP platforms with imputation for genomic selection and QTL discovery. Genotype imputation of high density SNP genotypes can improve cost efficiency of genomic breeding value prediction. Phenotypes and genotypes obtained with the PorcineSNP60 BeadChip (60K) for 983 Yorkshire boars were used, and SNP effects estimated using de-regressed breeding values as response variables. Genotypes of selection candidates were masked and imputed using tagSNP in the GeneSeek Genomic Profiler for Porcine LD (~9K). Imputation was performed using 128 or 1800 haplotypes as reference panels. Accuracy of genomic evaluation using observed genotypes was high for all traits (0.65-0.68). Using genotypes imputed from a large reference panel for genomic evaluation did not significantly decrease accuracy (R2 = 0:95), whereas genotypes imputed from a small reference panel decreased accuracy (R2 = 0:88). Optimal imputation strategies were also developed for F2 populations to allow the wealth of phenotypic information available from experimental resource populations to be further mined for QTL, and to facilitate meta-analysis of several populations to increase power and resolution for QTL fine mapping.

Publications

• Type: Journal Articles Status: Accepted Year Published: 2013 Citation: Arceo, M.E., C.W. Ernst, J.K. Lunney, I. Choi, N.E. Raney, T. Huang, C.K. Tuggle, R.R.R. Rowland and J.P. Steibel. 2013. Characterizing differential individual response to Porcine Reproductive and Respiratory Syndrome Virus infection through statistical and functional analysis of gene expression. Frontiers in Genetics (Livestock Genomics). 3:321. Badke, Y.M., R.O. Bates, C.W. Ernst, C. Schwab, J. Fix, C.P. Van Tassell and J.P. Steibel. 2013. Methods of tagSNP selection and other variables affecting imputation accuracy in swine. BMC Genet. 14:8. Ernst, C.W. and J.P. Steibel. 2013. Molecular advances in QTL discovery and application in pig breeding. Trends Genet. 29:215-224. Gualdron Duarte, J.L., R.O. Bates, C.W. Ernst, N.E. Raney, R.J. Cantet and J.P. Seibel. 2013. Genotype imputation accuracy in a F2 pig population using high density and low density SNP panels. BMC Genet. 14:38. Dodgson, J.B. 2013. Genomics of food animals. In N. Van Alfen (ed.), Encyclopedia of Agriculture and Food Systems, Elsevier, Oxford, UK, in press. Dodgson, J.B. 2013. Avian genomics. In C. Scanes, (ed.), Sturckies Avian Physiology, 6th ed., Elsevier, in press.

Progress 01/01/12 to 12/31/12

Outputs
OUTPUTS: Poultry coordination funds have been committed to SNP chip development and distribution. Very high density SNP mapping (ca. 600,000 SNP) panels have been developed and are being employed in genome-wide marker-assisted selection (GMAS). This year, 192 Affymetrix 600K genotypes are being obtained from DNA Landmarks for various members. A new build, Galgal4.0, of the chicken genome sequence which combines the original reads, next generation sequencing (NGS) reads and the near-finished quality of the Z sequence was released late last year and is now available on some browsers. This still has not captured the roughly 5% of missing sequence (believed to be predominantly on the microchromosomes). Methods to fill gaps and obtain the missing sequence are being pursued. A number of additional chicken genomes have been or are being sequenced with NGS technology. Coordination funds previously supported a project to sequence 20 different chicken lines of interest to NRSP-8 members. Those data and NGS data for genomes from the DF1 and DT40 chicken cell lines are currently being analyzed and pursued further. The Turkey Genome Sequencing Consortium generated a draft sequence of the turkey genome using a combination of NGS reads, along with the turkey BAC contig map. Coordination funds aided in this effort which also enjoyed support from VaTech, BARC and U. of Minn., among others. Efforts are on-going to improve the annotation of genes and fill gaps in the turkey sequence. Previously, coordination funds provided microarrays for transcriptional profiling and comparative genome hybridization. Some coordination support also was committed to Illumina RNA-sequencing and Agilent chip-based transcriptional profiling, partly in hopes of filling in missing sequences. Database activities are led by the NRSP-8 Bioinformatics Coordinator, Jim Reecy, and Susan Lamont, along with Shane Burgess, represent poultry interests on the advisory committee for this group. Poultry bioinformatics has also benefitted from support at several other locations. We maintain a homepage for the NRSP-8 U.S. Poultry Genome project (http://poultry.mph.msu.edu) that provides a variety of genome mapping resources, including our newsletter archive. The Poultry Genome Newsletter is published quarterly and is distributed through our Homepage and on the angenmap email discussion group. Efforts at the Michigan Station in pigs included utilization of the Illumina Porcine SNP60 Beadchip to determine estimates of linkage disequilibrium (LD) in Duroc, Hampshire, Landrace and Yorkshire breeds in the US. Average r2 (estimate of LD) for adjacent SNP ranged from 0.36 (Landrace) to 0.46 (Duroc), and for markers 1 Mb apart ranged from 0.15 (Landrace) to 0.20 (Hampshire). Results support application of low density SNP panels with genotype imputation for cost efficient genomic association and marker assisted selection applications. Other efforts in pigs involved evaluation of genotyping strategies using combinations of high and low density SNP genotypes to estimate imputation accuracy in an F2 pig population, and evaluation of QTL regions using SNP markers in commercial pig populations. PARTICIPANTS: Jerry Dodgson, project director. Hans Cheng, co-P.I. Cathy Ernst, co-P.I. Partner Organizations: U. of California, Davis, USDA-ARS Avian Disease and Oncology Lab, Purdue University, Iowa State University, Utah State University, Auburn University, U. of Kentucky. TARGET AUDIENCES: Animal scientists. Poultry, cattle, swine, horse and aquaculture breeders. Animal industry representatives. Consumers of animal products. Genome biologists. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
This project is generating tools through which genome sequences can be improved and used to locate inherited production trait alleles and to ascertain the physiological basis for those traits. It has resulted, among other things, in the generation of the complete sequence of the genomes of chicken, turkey, swine, sheep, cattle and other agricultural animals. Commercial breeders are using the sequence and SNP we generated to characterize and improve production lines using GMAS. In simpler terms, we are now moving closer to understanding the cause of phenotypic variation that is relevant to the agricultural use of animal products.

Publications

• Badke, Y.M., Bates, R.O., Ernst, C.W., Schwab, C. and Steibel, J.P. 2012. Estimation of linkage disequilibrium in four US pig breeds. BMC Genomics. 13:24.
• Choi, I., Bates, R.O., Raney, N.E., Steibel, J.P. and Ernst, C.W. 2012. Evaluation of QTL for carcass merit and meat quality traits in a US commercial Duroc population. Meat Sci. 92:132-138.

Progress 01/01/11 to 12/31/11

Outputs
OUTPUTS: Linkage mapping is now primarily via high throughput SNP assays. Coordination funds have been committed to SNP chip development and distribution. Very high density SNP mapping (ca. 600,000 SNP) panels have been developed and are being employed in genome-wide marker-assisted selection (GMAS). A new build, Galgal4.0, of the chicken genome sequence which combines the original reads, next generation sequencing (NGS) reads (Roche and Illumina) and the near-finished quality of the Z sequence recently has been released (11/22/11). NGS technology appears not to have captured the roughly 5% of missing sequence (believed to be predominantly on the microchromosomes) in the current chicken assembly. A number of additional chicken genomes have been or are being sequenced with NGS technology. Coordination funds are supporting a project with DNA Landmarks to sequence 20 different chicken lines of interest to NRSP-8 members. NGS data for genomes from the DF1 and DT40 chicken cell lines have also been obtained and are currently being analyzed and compared to the new reference Galgal4.0 chicken genome assembly. The Turkey Genome Sequencing Consortium generated a draft sequence of the turkey genome using a combination of NGS reads, along with the turkey BAC contig map noted above. Coordination funds were committed to aid in this effort which also enjoyed support from VaTech, BARC and U. of Minn., among others. Efforts are on-going to improve the annotation of genes and fill gaps in the turkey sequence. Previously, coordination funds were used to provide microarrays for transcriptional profiling and comparative genome hybridization. Some coordination support also was committed to Illumina RNA-sequencing and Agilent chip-based transcriptional profiling, partly in hopes of filling in missing sequences. Database activities are led by the NRSP-8 Bioinformatics Coordinator, Jim Reecy, and Susan Lamont, along with Shane Burgess, represent poultry interests on the advisory committee for this group. Poultry bioinformatics has also benefitted from support at several other locations. We maintain a homepage for the NRSP-8 U.S. Poultry Genome project (http://poultry.mph.msu.edu) that provides a variety of genome mapping resources, including our newsletter archive. The Poultry Genome Newsletter is published quarterly and is distributed through our Homepage and on the angenmap email discussion group. Efforts in pigs included completion of an expression QTL (eQTL) study which utilized a whole genome microarray and the MSU resource population to conduct a global eQTL analysis for loin muscle tissue. Sixty-two unique eQTL (FDR<0.10) were found and 13 genomic regions had overlapping eQTL and phenotypic QTL involving 14 cis-acting eQTL. Results of this analysis provide novel candidate genes for important complex pig phenotypes. PARTICIPANTS: Jerry Dodgson, project director. Hans Cheng, co-P.I. Cathy Ernst, co-P.I. Partner Organizations: U. of California, Davis, USDA-ARS Avian Disease and Oncology Lab, Iowa State University, Utah State University, Auburn University, U. of Kentucky TARGET AUDIENCES: Animal scientists. Poultry, cattle, swine, horse and aquaculture breeders. Animal industry representatives. Consumers of animal products. Genome biologists. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
This project is generating tools through which genome sequences can be used to locate inherited production trait alleles and apply the DNA sequence to ascertain the physiological basis for those traits. It has resulted, among other things, in the generation of the complete sequence of the genomes of chicken, turkey, swine, sheep, cattle and other agricultural animals. Commercial breeders are using the sequence and SNP we generated to characterize and improve production lines using GMAS. In simpler terms, we are now moving closer to understanding the cause of phenotypic variation that is relevant to the agricultural use of animal products.

Publications

• Dodgson, J.B., M.E. Delany and H.H. Cheng. 2011. Poultry genome sequences: progress and outstanding challenges. Cytogenetics and Genome Research 134:19-26.
• Meydan, H., M. A. Yildiz, J. B. Dodgson, and H. H. Cheng. 2011. Allele-specific expression analysis reveals CD79B has a cis-acting regulatory element that responds to Marek's disease virus infection in chicken, Poultry Science 90:1206-1211.
• Romanov, M.N., J.B. Dodgson, R.A. Gonser, and E.M. Tuttle. 2011. Comparative BAC-based mapping in the white-throated sparrow, a novel behavioral genomics model, using interspecies overgo hybridization, BMC Research Notes 4:211.
• Zhang, Y., X. Zhang, T.H. O'Hare, W.S. Payne, J.J. Dong, C.F. Scheuring, M. Zhang, J.J. Huang, M.-K. Lee, M.E. Delany, H.-B. Zhang and J.B. Dodgson. 2011. A comparative physical map reveals the pattern of chromosomal evolution between the turkey (Meleagris gallopavo) and chicken (Gallus gallus) genomes, BMC Genomics, 12:447.
• Choi, I., Steibel, J.P., Bates, R.O., Raney, N.E., Rumph, J.M. and Ernst, C.W. 2011. Identification of carcass and meat quality QTL in an F2 Duroc x Pietrain pig resource population using different least-squares analysis models. Frontiers in Genetics (Livestock Genomics). 2:18.
• Ernst, C.W., Steibel, J.P., Sollero, B.P., Strasburg, G.M., Guimaraes,S.E.F. and Raney, N.E. 2011. Transcriptional profiling during pig fetal skeletal muscle development using direct high-throughput sequencing and cross-platform comparison with gene expression microarrays. J. Anim. Sci. 89(E-Suppl. 1):ii.
• Sollero, B.P., Guimaraes, S.E.F., Rilington, V.D., Tempelman, R.J., Raney, N.E., Steibel, J.P., Guimaraes, J.D., Lopes, P.S., Lopes, M.S. and Ernst, C.W. 2011. Transcriptional profiling during foetal skeletal muscle development of Piau and Yorkshire-Landrace crossbred pigs. Anim. Genet. 42:600-612.
• Steibel, J.P., Bates, R.O., Rosa, G.J.M., Tempelman, R.J., Rilington, V.D., Ragavendran, A., Raney, N.E., Ramos, A.M., Cardoso, F.F., Edwards, D.B. and Ernst, C.W. 2011. Genome-wide linkage analysis of global gene expression in loin muscle tissue identifies candidate genes in pigs. PLoS ONE. 6:e16766.

Progress 01/01/10 to 12/31/10

Outputs
OUTPUTS: Linkage mapping has transitioned almost solely into high throughput SNP (single nucleotide polymorphism) assays. Such techniques not only have greatly enhanced the reference map, but they are also essential components for trait mapping and genome-wide marker assisted selection. Coordination funds have been committed to SNP chip development and distribution. Very high density SNP mapping (ca. 500,000 SNP) panels have been developed and are being employed in genome-assisted selection efforts. Physical mapping of the turkey genome is essentially complete, along with the construction of a detailed comparative chicken-turkey BAC contig-based comparative map that was used for the assembly of the first draft turkey genome sequence (see below). The first assembly of the draft 6.6X chicken sequence was done at the Washington U. Genome Sequencing Center and released on March 1, 2004. Next generation (next gen) sequencing now has been applied in hopes of obtaining the roughly 5% of missing sequence (predominantly on the microchromosomes) in the current chicken assembly, but so far this has made limited progress in filling the gaps. A new build of the chicken genome sequence which combines the original reads, next gen reads (Roche and Illumina) and the near-finished quality of the Z sequence done by Bellott et al. (Nature 466:612-616, 2010) is being completed by the U. of Md. Center for Bioinformatics and Computational Biology and should be available on browsers early next year. Further efforts to capture missing, microchromosomal sequence have been proposed. The Turkey Genome Sequencing Consortium has generated a first draft sequence of the turkey genome (Dalloul et al., PLoS Biology 8(9):e1000475) using a combination of next gen reads, along with the turkey BAC contig-based comparative map alignments noted above. A number of additional chicken genomes have been or are being sequenced (e.g., Rubin et al., Nature 464:587-591, 2010). The cost of next gen sequencing is now low enough that coordination funds have been committed to add new genomes of wide interest to participants. Some coordination support has also been committed to Illumina RNA-sequencing and Agilent chip-based transcriptional profiling, partly in hopes of filling in missing sequences, especially those on GGA16. PARTICIPANTS: Jerry Dodgson, project director. Hans Cheng, co-P.I. Cathy Ernst, co-P.I. Partner Organizations: Texas A&M University. USDA-ARS Avian Disease and Oncology Lab, Iowa State University, Utah State University, Auburn University, U. of Kentucky. TARGET AUDIENCES: Animal scientists. Poultry, cattle, swine, horse and aquaculture breeders. Animal industry representatives. Consumers of animal products. Genome biologists. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
This project is generating tools through which the genome sequence can be used to locate inherited production trait alleles and apply the DNA sequence to ascertain the physiological basis for those traits. It has resulted, among other things, in the generation of the complete sequence of the chicken and now the turkey genome. Industries have begun to apply the sequence and SNP we generated to characterizing and improving production lines using genome-wide marker-assisted selection. Since publication of the first draft of the chicken genome sequence, a shift has been made from providing and supporting physical genomics resources to those focused on gene expression and function. In simpler terms, we are now moving closer to understanding the cause of phenotypic variation that is relevant to the agricultural use of poultry.

Publications

• Dalloul RA, Long JA, Zimin AV, Aslam L, Beal K, Ann Blomberg L, Bouffard P, Burt DW, Crasta O, Crooijmans RP, Cooper K, Coulombe RA, De S, Delany ME, Dodgson JB, Dong JJ, Evans C, Frederickson KM, Flicek P, Florea L, Folkerts O, Groenen MA, Harkins TT, Herrero J, Hoffmann S, Megens HJ, Jiang A, de Jong P, Kaiser P, Kim H, Kim KW, Kim S, Langenberger D, Lee MK, Lee T, Mane S, Marcais G, Marz M, McElroy AP, Modise T, Nefedov M, Notredame C, Paton IR, Payne WS, Pertea G, Prickett D, Puiu D, Qioa D, Raineri E, Ruffier M, Salzberg SL, Schatz MC, Scheuring C, Schmidt CJ, Schroeder S, Searle SM, Smith EJ, Smith J, Sonstegard TS, Stadler PF, Tafer H, Tu ZJ, Van Tassell CP, Vilella AJ, Williams KP, Yorke JA, Zhang L, Zhang HB, Zhang X, Zhang Y, Reed KM.. 2010. Multi-platform next-generation sequencing of the domestic turkey (Meleagris gallopavo): genome assembly and analysis. PLoS Biology 8(9):e1000475.
• Dodgson, J.B. 2010. Comparative genome sequencing: low price-high value. Proceedings, Plant and Animal Genome XVIII. (abstract).

Progress 01/01/09 to 12/31/09

Outputs
OUTPUTS: Linkage mapping has transitioned almost solely into high throughput SNP (single nucleotide polymorphism) assays. Such techniques not only have greatly enhanced the reference map, but they are also essential components for trait mapping and genome-wide marker assisted selection. A 60K SNP Illumina iSelect genotyping array has been developed, and coordination funding has aided in its use to enhance the SNP linkage map by genotyping the Wageningen reference panel. Another related project, currently underway, is to develop an even more dense SNP map specifically useful for the East Lansing reference linkage map population by employing reduced representation, high throughput sequencing of the UCD003 genome to generate additional SNP between the UCD001 and UCD003 parents of that population. Physical mapping of the turkey genome is nearly complete, along with the construction of a detailed comparative chicken-turkey BAC contig-based comparative map that was essential for the assembly of the first draft turkey genome sequence (see below). The first assembly of the draft 6.6X chicken sequence was done at the Washington U. Genome Sequencing Center and released on March 1, 2004. High throughput next generation sequencing now has been used to obtain the ~5% of missing sequence (predominantly on the microchromosomes) in the current chicken assembly and to otherwise improve it. A third build of the chicken genome was released in November, 2009, based on 12x 454-Roche reads, but this is not yet on the major genome browsers. The 60K SNP chip, mentioned above, included 1211 SNP from unassigned sequence contigs in hopes of linking them to chromosomes and thereby improving the sequence assembly. Unfortunately, this generally was unsuccessful (suggesting that much of chr_Un derives from small unplaced microchromosomes, chromosome W, and repetitive elements or CNV regions). The Turkey Genome Sequencing Consortium has generated a first draft sequence of the turkey genome (Dalloul et al., submitted for publication) using a novel combination of "Next Generation" sequencing platforms (454-Roche and Illumina reads), along with the turkey BAC contig-based comparative map alignments noted above. Coordination funds were committed to aid in this effort which also enjoyed support from VaTech, BARC and U. of Minn., among others. In the past, coordination funds have been used to provide samples of the 44K element long oligonucleotide chicken array made by Agilent Corp. to several NRSP-8 participants, along with a new 244K whole genome long oligo array that can be used for comparative genome hybridization and whole genome transcriptional profiles. Alternatively, other participants chose to be provided GeneChip Chicken Genome arrays from Affymetrix, Inc. Further transcriptomics support is anticipated in future years. PARTICIPANTS: Jerry Dodgson, project director. Hans Cheng, co-P.I. Cathy Ernst, co-P.I. Partner Organizations: Texas A&M University. USDA-ARS Avian Disease and Oncology Lab, Iowa State University, Utah State University, Auburn University, U. of Kentucky. TARGET AUDIENCES: Animal scientists. Poultry, cattle, swine, horse and aquaculture breeders. Animal industry representatives. Consumers of animal products. Genome biologists. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
This project is generating tools through which the genome sequence can be used to locate inherited production trait alleles and apply the DNA sequence to ascertain the physiological basis for those traits. It has resulted, among other things, in the generation of the complete sequence of the chicken and now the turkey genome. Industries have begun to apply the sequence and SNP we generated to characterizing and improving production lines using genome-wide marker-assisted selection. Since publication of the first draft of the chicken genome sequence, a shift has been made from providing and supporting physical genomics resources to those focused on gene expression and function. In simpler terms, we are now moving closer to understanding the cause of phenotypic variation that is relevant to the agricultural use of poultry.

Publications

• Chen, M., W.S. Payne, J.R. Dunn, S. Chang, H. Hunt, H. Zhang, and J.B. Dodgson. 2009. Retroviral delivery of RNA interference against Marek's Disease virus in vivo. Poultry Science 88:1373-1380.
• Lee, M.-K., X. Zhang, Y. Zhang, B. Payne, H.J. Park, J.J. Dong, C. Scheuring, M.E. Delany, J. Dodgson, and H.-B. Zhang. 2009. Toward a robust BAC-based physical and comparative map of the turkey genome. Proceedings, Plant and Animal Genome XVII. (abstract).
• Chang, S., J. Dunn, M. Heidari, L.F. Lee, J. Song, J.B. Dodgson, C.W. Ernst, Z. Ding, and H. Zhang. 2009. Non-MHC genomic variation affecting Marek's disease resistance and vaccine protective efficiency. Proceedings, Plant and Animal Genome XVII. (abstract).
• Dodgson, J.B. 2009. Post-genomic chicken nuggets: an acquired taste. Proceedings, Plant and Animal Genome XVII. (abstract).

Progress 01/01/08 to 12/31/08

Outputs
OUTPUTS: The genetic linkage map of the chicken has provided a framework for numerous QTL and other mapping experiments. In work supported by a consortium of funding entities, Illumina was contracted to obtain 3000 SNP genotypes from over 5300 birds. These data greatly enhanced the chicken linkage map and were critical in the second build of the sequence. The data also provide the most thorough picture to date of the genetic diversity of commercial breeding stock, worldwide. Currently, a 60K SNP Illumina iSelect genotyping array is being developed. Another related project is to develop an even denser SNP map specifically useful for the East Lansing reference linkage map population by employing reduced representation, high throughput sequencing of the UCD003 genome. The first assembly of the draft 6.6X chicken sequence was done at the Washington U. Genome Sequencing Center (WUGSC) and released on March 1, 2004. Additional sequence data, physical, RH and SNP data were used to assemble a second, improved build of the chicken genome, released in May, 2006. High throughput sequencing now is being used at WUGSC in hopes of obtaining the 5% of missing sequence (predominantly on the microchromosomes) in the current chicken assembly and improving coverage in the next assembly. Physical mapping of the turkey genome is also on-going. A second turkey BAC library has been constructed to supplement the existing turkey CHORI-260 library. Both libraries have been used to generate over 43,000 BAC end sequences, along with over 23,000 BAC overgo hybridization assignments on the CHORI-260 library to distinct markers or genes. Over 85,000 turkey BAC fingerprints have also been generated, allowing the construction of a first generation BAC contig physical map and a comparative chicken-turkey BAC map. Colleagues at Virginia Tech have begun a pilot project to begin high throughput sequencing of the turkey genome. These sequence data will be aligned with the chicken sequence and the comparative turkey-chicken BAC map described above. We maintain a homepage for the NRSP-8 U.S. Poultry Genome project that provides a variety of genome mapping resources, including the latest EL maps and mapping data, descriptions of available resources, and access to a host of other information relating to both genetic and physical maps, including our newsletter archive. The Poultry Genome Newsletter is published quarterly and is distributed through our Homepage, electronically on the angenmap email discussion group and via direct email. In this past FY, coordination funds again were used to provide samples of the 44K element long oligonucleotide chicken array made by Agilent Corp to several NRSP-8 participants, along with a new 244K whole genome long oligo array that can be used for comparative genome hybridization and whole genome transcriptional profiles. Alternatively, other participants chose to be provided GeneChip Chicken Genome arrays from Affymetrix, Inc. We also helped support the annual NRSP-8 meeting in conjunction with the Plant and Animal Genome XVI meeting, attended by over 2000 scientists. PARTICIPANTS: Participants: Jerry Dodgson, project director. Hans Cheng, co-P.I. Cathy Ernst, co-P.I. Partner Organizations: Texas A&M University. USDA-ARS Avian Disease and Oncology Lab, Iowa State University, Utah State University, Auburn University, U. of Kentucky. TARGET AUDIENCES: Animal scientists. Poultry, cattle, swine, horse and aquaculture breeders. Animal industry representatives. Consumers of animal products. Genome biologists. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
This project is generating tools through which the genome sequence can be used to locate inherited production trait alleles and apply the DNA sequence to ascertain the physiological basis for those traits. It has resulted, among other things, in the generation of the complete sequence of the chicken genome. Industries have begun to apply the sequence and SNP we generated to characterizing and improving production lines. Since publication of the first draft of the chicken genome sequence, a shift has been made from providing and supporting physical genomics resources to those focused on gene expression and function. In simpler terms, we are now moving closer to understanding the cause of phenotypic variation that is relevant to the agricultural use of poultry. Initial application of dense SNP maps to genome-wide marker-assisted selection is now under study.

Publications

• Muir, W.M., Wong, G.K., Zhang, Y., Wang, J., Groenen, M.A., Crooijmans, R.P., Megens, H.J., Zhang, H., Okimoto, R., Vereijken, A., Jungerius, A., Albers, G.A., Lawley, C.T., Delany, M.E., MacEachern, S., and Cheng, H.H. 2008. Genome-wide assessment of worldwide chicken SNP genetic diversity indicates significant absence of rare alleles in commercial breeds. Proc. Natl. Acad. Sci. U. S. A. 105:17312-17317.
• Chen, M., W.S. Payne, H. Hunt, H. Zhang, S.L. Holmen, and J.B. Dodgson. 2008. Inhibition of Marek's disease virus replication by vector-based RNA interference, Virology 377: 265-272.
• Sazanova, A.L., M.N. Romanov, I.Y. Blagoveshenski, K.A. Fomichev, V.A. Stekol'nikova, M. Nefedov, W.S. Modi, O.A. Ryder, J.B. Dodgson, and A.A. Sazanov. 2008. Cytogenetic localization of avian Z- and W-linked genes using large-insert BAC clones. Proceedings, Plant and Animal Genome XVI. (abstract).
• Chen, Mo. 2008. Ph.D. thesis. Michigan State University, East Lansing, MI.
• Chen, M., W.S. Payne, H. Hunt, H. Zhang, S.L. Holmen, and J.B. Dodgson. 2008. Inhibition of avian tumor viruses by vector-based RNA interference. Proceedings, Plant and Animal Genome XVI. (abstract).
• Lee, M.-K., B. Payne, J. Dong, H.J. Park, X. Zhang, J. Dodgson, and H.-B. Zhang. 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. (abstract).

Progress 01/01/07 to 12/31/07

Outputs
OUTPUTS: The genetic linkage map of the chicken has provided a framework for numerous QTL and other mapping experiments and a platform on which genome sequences have been assembled and linked to chromosomes. In work supported by a consortium of industry, NRI Tools & Reagent grant, ARS and NRSP-8 funding, Illumina Corp was contracted to obtain ~3000 SNP genotypes, each, from ~5300 birds (about half the birds and data will be in the public domain). About 88% (2733) of the SNP assays worked and almost all of the submitted DNAs were successfully typed. Since members of the East Lansing and Wageningen reference linkage families were included among the panel, these data greatly enhanced the chicken linkage map, more than doubling the number of markers, and were critical in the second build of the genome sequence. During the previous year, coordination funds contributed to another Illumina Corp. SNP typing consortium initiated by NRSP-8 members. Together, the rapid expansion of SNP data will provide a high density linkage map and should aid numerous on-going attempts to identify the causative genetic changes involved in many chicken QTL. The chicken BAC contig physical map was updated in parallel with the second build of the chicken genome sequence. Similar efforts applied to the turkey CHORI-260 library are underway in hopes of generating a BAC contig physical map of the turkey genome and a comparative chicken-turkey map. These efforts have generated over 21,000 BAC end sequences and over 15,200 BAC overgo hybridization assignments to 1248 distinct markers or genes. Over 40,000 turkey BAC fingerprints have also been generated, allowing the construction of a first generation BAC contig physical map for the turkey made up of 2,544 contigs containing 35,861 BACs (5.6X genome coverage). The first assembly of the draft 6.6X chicken sequence was done at the Washington U. Genome Sequencing Center (WUGSC) and released on March 1, 2004. Additional sequence data, physical, RH and SNP data were used to assemble a second, improved "build" of the chicken genome, released in May, 2006. Ongoing sequence improvement efforts at WUGSC will act to enhance the quality of the draft assembly, and this new assembly will be available soon. We maintain a homepage for the NRSP-8 U.S. Poultry Genome project that provides a variety of genome mapping resources, including the latest EL maps and mapping data, descriptions of available resources, the latest cytogenetic map, and access to a host of other information relating to both genetic and physical maps, including our newsletter archive. The Poultry Genome Newsletter is published quarterly and is distributed through our Homepage, electronically on the angenmap email discussion group and via direct email. Reference panel DNAs, primer kits, BAC libraries and filters and chicken microarrays have been provided to colleagues as part of the poultry genome coordination effort. PARTICIPANTS: Participants: Jerry Dodgson, project director. Hans Cheng, co-P.I. Cathy Ernst, co-P.I. Partner Organizations: Texas A&M University. USDA-ARS Avian Disease and Oncology Lab, Iowa State University, Utah State University, Auburn University, U. of Kentucky. TARGET AUDIENCES: Animal scientists. Poultry, cattle, swine, horse and aquaculture breeders. Animal industry representatives. Consumers of animal products. Genome biologists.

Impacts
This project is generating tools through which the genome sequence can be used to locate inherited production trait alleles and apply the DNA sequence to ascertain the physiological basis for those traits. It has resulted, among other things, in the generation of the complete sequence of the chicken genome. Industries have begun to apply the sequence and SNP we generated to characterizing and improving production lines. Since publication of the first draft of the chicken genome sequence, a shift has been made from providing and supporting physical genomics resources to those focused on gene expression and function. In simpler terms, we are now moving closer to understanding the cause of phenotypic variation that is relevant to the agricultural use of poultry.

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.
• Romanov, M.N., Ryder, O.A., Koriabine, M., Nefedov, M., de Jong, P.J., Modi, W.S., and Dodgson, J.B. 2007. Genomic resources and tools to investigate factors associated with chondrodystrophy in California condors. Proceedings, Plant and Animal Genome XV. W345, p. 78 (abstract).
• Lee, M.-K., Park, H.J., Dodgson, J., and Zhang, H.-B. 2007. Toward a BAC-based physical and comparative map of the turkey genome. Proceedings, Plant and Animal Genome XV. P569, p. 243 (abstract).

Progress 01/01/06 to 12/31/06

Outputs
The genetic linkage map of the chicken has provided a framework for numerous QTL and other mapping experiments and a platform on which genome sequences have been assembled and linked to chromosomes. In work supported by a consortium of industry, NRI Tools & Reagent grant, ARS and NRSP-8 funding, Illumina Corp was contracted to obtain 3000 SNP genotypes, each, from 5300 birds (about half the birds and data are or will be in the public domain). About 88% (2733) of the SNP assays worked and almost all of the submitted DNAs were successfully typed. Since members of the East Lansing and Wageningen reference linkage families were included among the panel, these data will greatly enhance the chicken linkage map, more than doubling the number of markers. The data were also used to enhance the second build of the draft genome sequence. During the past year, coordination funds contributed to another Illumina Corp. SNP typing consortium initiated by NRSP-8 members. This project could only have occurred with the re-use of the SNP genotyping reagents developed by the first Illumina consortium. The BAC contig physical map was updated in parallel with the second build of the chicken genome sequence. Similar efforts applied to the turkey CHORI-260 library are udnerway in hopes of generating a BAC contig physical map of the turkey genome and a comparative chicken-turkey map. The second build of the chicken genome sequence was released in May, 2006. The second build moved a large portion of the previously unplaced sequence contigs into specific chromosomal locations and enhanced the general contiguity and accuracy of the sequence assembly. In addition, the National Human Genome Research Institute has approved funding that will allow additional directed sequencing to bring the chicken genome to a finished state. This will likely be done next year. Nearly 600,000 chicken ESTs have been deposited in NCBI's dbEST. Microarrays are now available in several formats and from several sources. Coordination funds have contributed to the availability of both a 13K cDNA and a 44K spotted oligo array for NRSP-8 members. We maintain a WWW homepage for the Poultry Genome which links to ChickGBASE, the Roslin Institute homepage, and a variety of other genome mapping resources. Several kits of microsatellite primer pairs have been made available for free distribution. Filter arrays of BAC clones are being distributed for both the Texas A&M and CHORI-261 chicken BAC libraries. Filter arrays of the turkey CHORI-260 library are also now available. A quarterly newsletter is distributed and the annual NAGRP meeting and other key meetings are used to enhance communication on poultry genomics.

Impacts
This project is generating tools through which the genome sequence can be used to locate inherited production trait alleles and apply the DNA sequence to ascertain the physiological basis for those traits. It has resulted, among other things, in the generation of the complete sequence of the chicken genome. Industries have begun to apply the sequence and SNP we generated to characterizing and improving production lines. Since publication of the first draft of the chicken genome sequence, a shift has been made from providing and supporting physical genomics resources to those focused on gene expression and function. In simpler terms, we are now moving closer to understanding the cause of phenotypic variation that is relevant to the agricultural use of poultry.

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.

Progress 01/01/05 to 12/31/05

Outputs
The genetic linkage map of the chicken has provided a framework for numerous QTL and other mapping experiments and a platform on which genome sequences have been assembled and linked to chromosomes. Updates brought the number of markers on the consensus map to over 2200. In connection with the genome sequence, the Beijing Genomics Institute randomly sequenced 0.25X, each, of a broiler, layer and Silkie genome, generating 2.8 million potential SNPs for high resolution linkage mapping experiments. In work supported by a consortium of industry, NRI Tools & Reagent grant, ARS and NRSP-8 funding, Illumina Corp was contracted to obtain 3000 SNP genotypes, each, from 5300 birds (about half the birds and data are or will be in the public domain). About 88% (2733) of the SNP assays worked and almost all of the submitted DNAs were successfully typed. Since members of the East Lansing and Wageningen reference linkage families were included among the panel, these data will greatly enhance the chicken linkage map, more than doubling the number of markers. The data are also being used to enhance the second build of the draft genome sequence. The BAC contig physical map is being updated in parallel with the second build of the chicken genome sequence that will be made public in late 2005. Similar efforts applied to the turkey CHORI-260 library have begun in hopes of generating a BAC contig physical map of the turkey genome and a comparative chicken-turkey map. The first assembly of the draft 6.6X chicken sequence was released on March 1, 2004. The initial analysis and annotation of the sequence was published late that year. In addition, the National Human Genome Research Institute has approved funding that will allow additional directed sequencing to bring the chicken genome to a "finished" state. This will likely be done in 2006. The NCBI dbEST presently lists 531,351 chicken ESTs. As a result, a 13K chicken spotted cDNA glass slide array has been made available for transcriptional profiling. Affymetrix, Inc. is now marketing a chicken gene chip that measures levels of 32,773 chicken transcripts and 684 chicken viral transcripts from 17 different avian viruses. We maintain a WWW homepage for the Poultry Genome which links to ChickGBASE, the Roslin Institute homepage, and a variety of other genome mapping resources. Several kits of microsatellite primer pairs have been made available for free distribution. At least three public BAC libraries for chicken and one for turkey are now available. Filter arrays of BAC clones are being distributed for both the Texas A&M and CHORI-261 chicken BAC libraries. Filter arrays of the turkey CHORI-260 library are also now available. A quarterly newsletter is distributed and the annual NAGRP meeting and other key meetings are used to enhance communication on poultry genomics.

Impacts
This project is generating tools through which the genome sequence can be used to locate inherited production trait alleles and apply the DNA sequence to ascertain the physiological basis for those traits. It has resulted, among other things, in the generation of the complete sequence of the chicken genome. Industries have begun to apply the sequence and SNP we generated to characterizing and improving production lines.

Publications

• Sazanov, A. A., Romanov, M. N., Wardcka, B., Sazanova, A.L., Korczak, M., Stekolnikova, V.A., Kozyreva, A.A., Smirnov, A.F., Jaszczak, K. and Dodgson, J.B. 2005. Chromosomal localization of fifteen large insert BAC clones containing three microsatellites on chicken chromosome 4 (GGA4) which refine its centromere position. Animal Genetics 36:161-163.
• Romanov, M.N., Daniels, L., Dodgson, J.B. and Delany, M.E. 2005. Integration of the cytogenetic and physical maps of chicken chromosome 17. Chromosome Research 13:215-222.
• Burnside, J., Cogburn, L., Talbot, R. and Dodgson, J.B. 2005. Genomic tools for endocrine research. In A. Dawson and P.J. Sharp (eds), Functional avian endocrinology, Narosa Publishing House, New Delhi, India.
• Sazanov, A.A., Sazanova, A.L., Stekolnikova, V.A., Trukhina, A.V., Kozyreva, A.A., Smirnov, A.F., Romanov, M.N., Lawson-Handley, L.-J., Malewski, T. and Dodgson, J.B. 2005. Chromosomal localization of the UBAP2Z and UBAP2W genes in chicken. Animal Genetics, in press.
• Sazanov, A.A., Romanov, M.N., Sazanova, A.L., Stekol'nikova, V.A., Kozyreva, A.A., Smirnov A.F. and Dodgson, J.B. 2005. Localisation of seven HSA3q13-q23 NotI linking clones on the chicken microchromosomes 14 and 15 by double-color FISH. Proceedings, Plant and Animal Genome XIII. P550, p. 208 (abstract).
• H. Zhang, Hunt, H.D., Cheng, H.H., Dodgson, J.B., Romanov, M.N. and Bacon, L.D. 2005. Identification and evaluation of SNPs at the 3' end of the tva gene that segregate among ALVA resistant and susceptible lines of chickens. Proceedings, Plant and Animal Genome XIII. P197, p. 123 (abstract).
• Romanov, M.N. and Dodgson, J.B. 2005. Development of a physical and comparative map of the turkey genome. Proceedings, Plant and Animal Genome XIII. W297, p. 69 (abstract).
• Zhang, H.-B., Yan, B., Chang, Y.-L., Dodgson, J.B., Lee, M.-K., Li, Y., Lightfoot, D.A., Liu, D., Meksem, K., Nguyen, H.T., Ren, C., Stelly, D.M., Sun, S., Wu, C., Xu, Z. and Zhang, A. 2005. Whole genome physical mapping with BACs by fingerprint analysis: lessons and tips. Proceedings, Plant and Animal Genome XIII. W201, p. 48 (abstract).

Progress 01/01/04 to 12/31/04

Outputs
The consensus chicken linkage map has expanded to 2204 markers, covering nearly 4000 cM. The East Lansing map contains 1276 markers on 42 linkage groups. In connection with the genome sequence, 2.8 million potential SNPs were generated for future high resolution linkage mapping experiments. A second generation BAC contig map physical map of the chicken has been developed, comprised of 260 contigs, 226 of which have been anchored to the genetic linkage/chromosome map. Over 7800 BAC assignments to over 900 distinct markers or genes have been made in support of map development and sequence assembly. Recently, similar efforts applied to the turkey have generated over 2400 BAC assignments for 176 markers/genes. The NCBI dbEST presently lists 531,351 chicken ESTs. As a result, a 13K chicken spotted cDNA glass slide array has been made available for transcriptional profiling. Affymetrix, Inc. is now marketing a chicken gene chip that measures levels of 32,773 chicken transcripts and 684 chicken viral transcripts from 17 different avian viruses. The Washington U. Genome Sequencing Center (WUGSC) has completed 6.6X sequencing of the chicken genome (primarily whole genome shotgun) and the first assembly of the draft chicken sequence was released on March 1, 2004. The initial analysis and annotation of the sequence was recently published, along with papers describing the BAC contig map and SNP discovery efforts described above. The sequence, along with a variety of options and tools, can be accessed at three different browsers: the UCSC Chicken Genome Browser Gateway, the NCBI Chicken Genome Resources website, and the EBI's Ensembl Chicken Genome Browser. We maintain a WWW homepage for the Poultry Genome which links to ChickGBASE, the Roslin Institute homepage, and a variety of other genome mapping resources. Several kits of microsatellite primer pairs have been made available for free distribution. At least three public BAC libraries for chicken and one for turkey are now available. Filter arrays of BAC clones are being distributed for both the Texas A&M and CHORI-261 chicken BAC libraries. Filter arrays of the turkey CHORI-260 library are also now available. A quarterly newsletter is distributed and the annual NAGRP meeting and other key meetings are used to enhance communication on poultry genomics.

Impacts
This project is generating tools through which the genome sequence can be used to locate inherited production trait alleles and apply the DNA sequence to ascertain the physiological basis for those traits. It has resulted, among other things, in the generation of the complete sequence of the chicken genome. The availability of a high quality genome sequence will be of enormous benefit to avian biology.

Publications

• Dodgson, J.B. Romanov, M.N. Rondelli, C.M. 2004. Integration of the chicken linkage and physical maps and sequence alignment using overgo hybridization. Proceedings, Plant and Animal Genome XII. p. 59.
• Dodgson, J.B. Romanov, M.N. Rondelli, C.M. 2004. Alignment of the linkage map, physical map, and sequence of the chicken genome. Proceedings, Plant and Animal Genome XII. p. 233.
• Sazanov, A. A. Romanov, M.N. Sazanova, A. L. Tzareva, V. A. Kozyreva, A. A. Smirnov, A. F. Price, J. A. Dodgson, J. B. 2004. Chromosomal localization of large insert clones of the chicken genome: expanding the comparative map. Proceedings, Plant and Animal Genome XII. p. 234.
• Sazanov, A.A. Romanov, M.N. Wardecka, B. Sazanova, A.L. Korczak, M. Stekolnikova, V.A. Kozyreva, A.A. Smirnov, A.F. Dodgson, J.B. Jaszczak, K. 2004. Chromosomal localization of GGA4 BACs containing QTL-linked microsatellites. Proceedings, 16th European Colloquium on Animal Cytogenetics and Gene Mapping. Cytogenetics and Genome Research 106: 19.
• Wallis, J.W. Aerts, J. Groenen, M. Crooijmans, R. Layman, D. Graves, T. Scheer, D. Kremitzki, C. Higgenbotham, J. Gaige, T. Mead, K. Walker, J. Albracht, D. Divito, J. Yang, S.-P. Leong, S. Chinwalla, A. Hillier, L. Sekhon, M. Dodgson, J. Romanov, M.N. Cheng, H. de Jong, P.J. Zhang, H. McPherson, J.D. Krzywinski, M. Schein, J. Mardis, E. Wilson, R. Warren, W.C. 2004. A physical map of the chicken genome. Nature 432:761-764.
• Dodgson, J.B. Romanov, M.N. 2004. Use of chicken models for the analysis of human disease. In Current Protocols in Human Genetics. John Wiley & Sons, Hoboken, NJ 15.5:1-11.
• Sazanov, A. A. Sazanova, A. L. Tzareva, V. A. Kozyreva, A. A. Smirnov, A. F. Romanov, M. N. Price, J. A. Dodgson, J. B. 2004. Refined localization of the chicken KITLG, MGP and TYR genes on GGA1 by FISH mapping using BACs. Animal Genetics 35:148-150.
• Sazanov, A. A. Sazanova, A. L. Tzareva, V. A. Kozyreva, A. A. Smirnov, A. F. Romanov, M. N. Price, J. A. Dodgson, J. B. 2004. Chromosomal localization of three GGA4 genes using BAC-based FISH mapping: a region of conserved synteny between the chicken and human genomes. Hereditas 140:250-252.
• Sazanov, A. A. Sazanova, A. L. Stekolnikova, V. A. Kozyreva, A. A. Smirnov, A. F. Romanov, M. N. Dodgson, J. B. 2004. Chromosomal localisation of CTSL: expanding of the region of evolutionary conservatism between GGAZ and HSA9. Animal Genetics 35:260.
• International Chicken Genome Sequencing Consortium. 2004. Sequence and comparative analysis of the chicken genome provide unique perspectives on vertebrate evolution. Nature 432:695-716.

Progress 01/01/03 to 12/31/03

Outputs
The consensus chicken linkage map has expanded to nearly 2000 markers, placed into 50 linkage groups, covering around 4000 cM. The East Lansing map has 1249 markers on 43 linkage groups. Over 320 genes have been mapped in the East Lansing map. Several chicken (and one turkey) BAC libraries have been generated and fingerprinted to create detailed BAC contig maps of the chicken. A first generation physical map of the chicken genome containing 2331 contigs has been published. The Washington U. Genome Sequencing Center (WUGSC) has been provided copies of the chicken BAC libraries and has fingerprinted 188,369 of them, generating over 133,000 useable BAC fingerprints. These have been used to generate a second generation BAC contig map comprised of about 230 contigs, two-thirds of which have been anchored to the genetic linkage/chromosome map. The map should be submitted for publication and become publically available in January. The Dodgson lab has been integrating the BAC contigs with the linkage map primarily by screening the libraries for genetic markers using overgo hybridization. Their efforts, plus those of cooperating scientists who've been provided BAC filters, have led to over 5700 BAC assignments to over 720 distinct markers or genes. Burnside, Cogburn, Morgan, Cheng, Reed and Neiman in the U.S. and several European groups have generated EST collections and applied them to microarray analysis. Nearly 450,000 public ESTs are available. Radiation hybrid (RH) panels have been constructed by Vignal and colleagues at INRA, and a framework RH map is in the process of being constructed. The Washington U. Genome Sequencing Center (WUGSC) has completed 6.6X sequencing of the chicken genome (primarily whole genome shotgun) and this is now being assembled. The complete chicken genome sequence is expected to be announced early in 2004. The chicken gene database, ChickGBASE, is available in the Arkdb format at http://www.ri.bbsrc.ac.uk/chickmap/chickgbase/chickgbase.html and a mirror site for the database is maintained at Iowa State, http://www.genome.iastate.edu/. We maintain a WWW homepage for the Poultry Genome which links to ChickGBASE, the Roslin Institute homepage, and a variety of other genome mapping resources. The Homepage provides the latest EL maps and mapping data, an updated list of published microsatellites, descriptions of available resources, the latest cytogenetic map, and access to a host of other information relating to both genetic and physical maps. It can be accessed at http://poultry.mph.msu.edu. Resources distributed include reference linkage map panel DNA, two microsatellite primer pair kits (one covering the full genome and one for rapid monitoring of gene flow in populations), two chicken gene primer pair kits (300 genes in total), filter arrays of robot-spotted BAC clones (nearly 190,000 in total), and a new chicken gene expression microarray of 13,000 spotted cDNA clones, developed, in part, with NAGRP support. A quarterly newsletter is distributed and the annual NAGRP meeting and other key meetings are used to enhance communication on poultry genomics.

Impacts
This project is generating tools through which the genome sequence can be used to locate inherited production trait alleles and apply the DNA sequence to ascertain the physiological basis for those traits. It has resulted, among other things, in the generation of the complete sequence of the chicken genome.

Publications

• Lee, M.-K., C.W. Ren, B. Yan, B. Cox, H.-B. Zhang, M.N. Romanov, F.G. Sizemore, S.P. Suchyta, E. Peters, and J.B. Dodgson 2003. Construction and characterization of three BAC libraries for analysis of the chicken genome, Animal Genetics 34:151-152.
• Dodgson, J.B. 2003. The future of molecular genetics in poultry breeding. In W. M. Muir and S.E. Aggrey (eds.), Poultry genetics, breeding and biotechnology. CABI Publishing, New York, NY, pp. 685-695.
• Romanov M.N., J.A. Price, and J.B. Dodgson. 2003. Integration of animal linkage and BAC contig maps using overgo hybridization. Cytogenetics and Genome Research, in press.
• Dodgson, J.B. 2003. Chicken genome sequence: a centennial gift to poultry genetics. Cytogenetics and Genome Research, in press.
• Ren C., M.K. Lee, B. Yan, K. Ding, B. Cox, M.N. Romanov, J.A. Price, J.B. Dodgson and H.B. Zhang. 2003. A BAC-based physical map of the chicken genome. Genome Research 13:2754-2758.
• Dodgson, J.B., M.N. Romanov, and J. Price. 2003. Integration of the chicken genetic map with BAC contig-based physical maps using overgo hybridization. Proceedings, Plant and Animal Genome XI. p. 49 (abstract)
• Romanov, M.N., J.A. Price, F.G. Sizemore, and J.B. Dodgson. 2003. Chicken BAC library screening using conventional and overgo probes. Proceedings, Plant and Animal Genome XI. p. 225 (abstract)
• Ren, C., M.-K. Lee, B. Yan, P. Ling, K. Ding, B. Cox, J.B. Dodgson, and H.-B. Zhang. 2003. A BAC-based physical map of the chicken genome. Proceedings, Plant and Animal Genome XI. p. 225 (abstract).
• Dodgson, J.B., M.N. Romanov, F.G. Sizemore, and Price, J. 2003. Integration of genetic and physical maps of the chicken genome. Proceedings, Advances in Genome Biology & Technology p. 25 (abstract)
• Dodgson, J.B. 2003. Linking the physical map and sequence of the chicken to the genetic map. Proceedings, Chicken Genome Sequence Symposium, Atlanta, GA (abstract)

Progress 01/01/02 to 12/31/02

Outputs
The consensus map contains 1965 markers, placed into 50 linkage groups, covering around 4000 cM. The East Lansing map has expanded to 1230 markers on 43 linkage groups. Of these, 514 are microsatellite markers. Over 310 genes have been mapped in the East Lansing map. These provide evidence that gene order is conserved between the human and chicken genomes to a remarkable extent. Thirty of the 38 autosomes are now marked by hybridization tags, and 24 autosomes have been associated with the appropriate linkage group. Physical mapping resources, such as chicken large insert bacterial artificial chromosome (BAC) libraries, have been expanded. Zhang, Dodgson and colleagues have generated a library of over 115,000 BACs (15X) at Texas A&M and have fingerprinted 65,000 of these. Preliminary BAC contig building has been done, and these contigs are now in the process of being editted. On-line, interactive contig building for the fingerprinted Texas A&M BACs is now available at http://hbz.tamu.edu. P. de Jong has generated a 10X BAC library (CHORI-261) with extra large inserts and a large insert turkey BAC library (CHORI-260). The Washington U. Genome Center has been provided copies of the Texas A&M and CHORI-261 chicken BAC libraries, and they are fingerprinting both libraries completely. Dodgson and Cheng are integrating the BAC contigs with the linkage map by screening the libraries for genetic markers using overgo hybridization and 3-dimensional PCR, respectively. Their efforts, plus those of cooperating scientists who've been provided BAC filters, have led to over 1200 BAC assignments to nearly 400 distinct markers or genes. These linkages will be an essential part of the contig and sequence assembly processes. Burnside, Cogburn, Morgan, Cheng, Reed and Neiman in the U.S. and several European groups are generating EST collections and beginning to apply them for microarray analysis. Boardman et al. (Current Biology 12:1965-19-69, 2002) announced the sequencing of over 300,000 chicken ESTs from a wide variety of tissues and developmental stages. Radiation hybrid (RH) panels have been constructed by Vignal and colleagues at INRA. In response to a request from the National Human Genome Research Institute, a white paper proposing full sequence analysis of the chicken genome was submitted by McPherson, Dodgson, Krumlauf and Pourquie. The NHGRI review panel subsequently placed the chicken genome among the high priority sequencing targets. ChickGBASE is available in the Arkdb format at http://www.ri.bbsrc.ac.uk/chickmap/chickgbase/chickgbase.html. A mirror site for the poultry database is being mounted at the Iowa State database site, http://www.genome.iastate.edu/. We maintain a WWW homepage for the Poultry Genome at http://poultry.mph.msu.edu. A new version of a framework primer kit (with 147 well-spaced microsatellite marker primer pairs) called the Comprehensive Mapping Kit #7 was made available this year. Filter arrays of robot-spotted BAC clones are being distributed for both the Texas A&M and CHORI-261 chicken BAC libraries.

Impacts
Our efforts will help form the basis for full genome sequence analysis of the chicken next year. This information will enhance poultry breeding and research for decades to come.

Publications

• Romanov, M.N., S. Suchyta, E. Peters, F. Sizemore, and J.B. Dodgson. 2002. Alignment of the chicken linkage map with BAC contigs Proceedings, Plant, Animal & Microbe Genome X. p. 225 (abstract).
• Lee, M.-K., C. Ren, B. Yan, B. Cox, J.B. Dodgson, and H.-B. Zhang. 2002. Development of a whole genome, BAC-based integrated physical/genetic map of the chicken genome: 1. Construction and characterization of source BAC libraries. Proceedings, Plant, Animal & Microbe Genome X. p. 225 (abstract).
• Ren, C., M.-K. Lee, B. Yan, P. Ling, K. Ding, B. Cox, J.B. Dodgson, and H.-B. Zhang. 2002. Development of a whole genome, BAC-based integrated physical/genetic map of the chicken genome: 2. BAC fingerprinting and physical map contig assembly. Proceedings, Plant, Animal & Microbe Genome X. p. 225 (abstract).
• Swanberg, S.E., H.D. Hunt, W.S. Payne, J.B. Dodgson, and M.E. Delany. 2002. Characterization and comparison of telomerase activity in transformed and non-transformed chicken cells in vitro. Proceedings, Plant, Animal & Microbe Genome X. p. 227 (abstract).

Progress 01/01/01 to 12/31/01

Outputs
A consensus map based on all three map populations has been published (Groenen et al., Genome Res. 10:137-147, 2000). Recent updates (Schmid et al., Cytogenet. & Cell Genet. 90:169-218, 2000) bring the number of markers on the consensus map to 1965, placed into 50 linkage groups, covering around 4000 cM. The East Lansing map has expanded to 1186 markers on 49 linkage groups. Of these, 512 are microsatellite markers. Nearly 300 genes have been mapped in the East Lansing map. Evidence continues to accumulate that gene order is conserved between the human and chicken genomes to a remarkable extent. Several studies have appeared (Burt et al., Nature 402:411-413, 1999; Groenen et al., op. cit.; Waddington et al., Genetics 154:323-332, 2000; Suchyta et al., An. Genet. 32:12-18, 2001) that estimate between 100 and 200 breakpoints in gene order separating the human and chicken genome, with some blocks of conserved synteny (not necessarily gene order) exceeding 100 cM. Most microchromosomes are now marked by hybridization tags and have been associated with the appropriate linkage group (Schmid et al., op. cit.). Physical mapping resources, such as chicken large insert bacterial artificial chromosome (BAC) libraries, have been expanded. Zhang, Dodgson and colleagues now have generated a library of over 115,000 BACs (15X) and have fingerprinted 60,000 of these. Negotiations are underway in hopes of fingerprinting the full BAC library at the Wash. U. Genome Center. Crooijmans and Groenen are also fingerprinting their BAC library (Crooijmans et al., Mamm. Genome 11:360-363, 2000) and building contig maps. Burnside, Cogburn, Morgan, Cheng, Reed and Neiman in the U.S. and several European groups are generating EST collections (Tirunagaru et al., Genomics 66:144-151, 2000) and beginning to apply them for microarray analysis. We maintain the Poultry Genome Mapping Homepage, http://poultry.mph.msu.edu, which links to ChickGBASE and a variety of other genome mapping resources. DNA from the East Lansing international reference population has been sent to many laboratories throughout the world. Six Comprehensive Mapping Microsatellite Kits now containing a total of 647 primer pairs for markers covering most of the chicken genome have been made available. Last year's new framework kit 1/2 with 166 selected microsatellite primer pairs is nearly gone and a replacement will soon be ordered. A total of 114 labs, worldwide, have received one or more microsatellite kit. Two Chicken Gene Primer Pair Kits containing a total of 300 primer pairs also have been made available. The BAC library described under objective 2. has been completed, and filter sets of robot-spotted BAC clones are being distributed (so far, 26 requests have been filled with more filters on order). PCR-screenable BAC DNA pools have been prepared and are now available. The Poultry Genome Newsletter is published quarterly and is distributed through our Homepage, electronically on the angenmap email discussion group, and via hard copy to scientists worldwide.

Impacts
Resources and data (via web databases) have been provided worldwide to hundreds of poultry geneticists. The genetic linkage map has advanced to the stage where many searches for heritable traits of agricultural significance are going on using resources and information we have developed and/or provided.

Publications

• Romanov, M.N., Ellegren, H. and Dodgson, J.B. 2001. Polymerase chain reaction amplified markers for bird sexing. Proceedings, Plant and Animal Genome IX. p. 118 (abstract).
• Suchyta, S.P., Cheng, H.H., Burnside, J. and Dodgson, J.B. 2001. Comparative mapping of chicken anchor loci orthologous to genes on human chromosomes 1, 4 and 9. Animal Genetics 32:12-18.

Progress 01/01/00 to 12/31/00

Outputs
PROGRESS TOWARD OBJECTIVE 1. High resolution poultry genome maps. A consensus map based on all three map populations has been published (Groenen et al., Genome Res. 10:137-147, 2000). Recent updates (Schmid et al., Cytogenet. & Cell Genet., in press) bring the number of markers on the consensus map to 1965, placed into 50 linkage groups, covering around 4000 cM. The East Lansing map has expanded to 1162 markers covering 3944 cM on 40 linkage groups. Of these, 465 are microsatellite markers. Over 200 genes have been mapped in the consensus map. Evidence continues to accumulate that gene order is conserved between the human and chicken genomes to a remarkable extent. PROGRESS TOWARD OBJECTIVE 2. Physical maps and map integration. Physical mapping resources, such as chicken large insert recombinant DNA libraries have been constructed. We have fingerprinted 20,000 BAC clones; Crooijmans and Groenen are also beginning fingerprinting and contig building efforts. PROGRESS TOWARD OBJECTIVE 3: Database and other map resources. The chicken genome mapping searchable database, ChickGBASE, is available at http://www.ri.bbsrc.ac.uk/chickmap/chickgbase/chickgbase.html. It is in the Arkdb format, developed primarily by Archibald, Law, Burt, and colleagues at the Roslin Institute. As per the NRSP-8 renewal proposal, a mirror site for the poultry database is maintained at the Iowa State site, http://www.genome.iastate.edu/. We maintain the Poultry Genome Mapping Homepage, http://poultry.mph.msu.edu, which links to ChickGBASE and a variety of other genome mapping resources. DNA from the East Lansing international reference population has been sent to many laboratories throughout the world. Six Comprehensive Mapping Microsatellite Kits now containing a total of 647 primer pairs for markers covering most of the chicken genome have been made available. Kits 1 to 3 have been used up or are no longer functional, so we recently generated a replacement kit with 166 selected highly polymorphic microsatellite primer pairs. Two Chicken Gene Primer Pair Kits have been made available, now containing a total of 300 primer pairs to sequenced chicken genes for use in EST mapping and expression analysis. A BAC library has been prepared in collaboration with the Texas A&M BAC Center using BamHI partial digest inserts of UCD001 line DNA (the inbred Red Jungle Fowl parent line of the EL map population). It presently contains about 38,000 clones with inserts averaging 150 kb, about 5X coverage, and filter sets of robot-spotted BAC clones are being distributed (so far, 17 requests have been filled with more filters on order). The Poultry Genome Newsletter is published quarterly and is distributed through our Homepage, electronically on the angenmap email discussion group and via hard copy to scientists worldwide.

Impacts
Resources and data (via web databases) have been provided worldwide to hundreds of poultry geneticists. The genetic linkage map has advanced to the stage where many searches for heritable traits of agricultural significance are going on using resources and information we have developed and/or provided.

Publications

• Groenen, M.A.M., H.H. Cheng, N. Bumstead, B.F. Benkel, W.E. Briles, T. Burke, D.W. Burt, L.B. Crittenden, J. Dodgson, J. Hillel, S. Lamont, F.A. Ponce de Leon, M. Soller, H. Takahashi, and A. Vignal. 2000. A consensus linkage map of the chicken genome. Genome Research 10:137-147.
• Dodgson, J.B., H.H. Cheng, and J. Burnside. 2000. Integrating quantitative and molecular techniques in selection for disease resistance. Poultry Science, in press.
• Suchyta, S.P., H.H. Cheng, J. Burnside and J.B. Dodgson. 2001. Comparative mapping of chicken anchor loci orthologous to genes on human chromosomes 1, 4 and 9, Animal Genetics, in press

Progress 01/01/99 to 12/31/99

Outputs
Over 1100 markers have now been typed on our linkage mapping panel of DNAs, including common markers to both international mapping reference populations, and a second generation consensus molecular genetic map with 1889 markers has been developed. Several important advances were made in comparative mapping, demonstrating remarkable conservation of gene order between human and chicken genomes. Database resources continue be available out of the Iowa State node and through the MSU Poultry Homepage. New microsatellite mapping kits were again developed this year and kits have been sent to over 40 labs world-wide. Almost 650 primer pairs have been made and distributed. In addition two gene mapping and RT-PCR kits with 300 primer pairs are now available. A new chicken BAC library (5X coverage) has been made and BAC filter sets are being distributed to several laboratories free of charge. It is expected that the BAC library will be doubled in size shortly.

Impacts
Molecular techniques have provided a far more detailed map of the chicken genome than previously available for use by chicken breeders. Physical and comparative map data will allow for a much more thorough understanding of the ontogeny of selected traits in poultry.

Publications

• Knorr, C., Cheng, H.H., Dodgson, J.B. 1999. Application of AFLP markers to genome mapping in poultry. Animal Genetics 30:28-35.
• Dodgson, J.B. and H.H. Cheng. 1999. Poultry genomics: An alien perspective. AgBiotechNet 1:1-5.

Progress 01/01/98 to 12/31/98

Outputs
Over 1000 markers have now been typed on our linkage mapping panel of DNAs, including common markers to both international mapping reference populations, and a second generation consensus molecular genetic map is being developed. Several comprehensive QTL searches are beginning to yield promising results. In the area of database development, the new Arkdb version of ChickGBASE is now available both from the Roslin Institute and from the Iowa State node. Our Poultry Genome Homepage and newsletter continue to be widely used. Two new microsatellite mapping kit were developed this year and kits have been sent to over 40 labs world-wide. Over 500 primer pairs are now available. In addition a new gene mapping and RT-PCR kit with 200 primer pairs is now available. A new chicken BAC library is nearing completion and should soon be available. The next annual NAGRP meeting will occur jointly with Plant and Animal Genome VII, to be held in Jan. 1999.

Impacts
(N/A)

Publications

• Cheng, H.H., Burt, D.W., Dodgson, J.B. 1998. Recent advances in poultry genome mapping. Proceedings, World Conference on Animal Production, Seoul, Korea. 168-178pp.
• Knorr, C., Cheng, H.H., Dodgson, J.B. 1999. Application of AFLP markers to genome mapping in poultry. Animal Genetics 30:28-35.
• Dodgson, J.B., Cheng, H.H. 1999. Poultry genomics: An alien perspective. AgBiotech News and Information, in press.

Progress 01/01/97 to 12/31/97

Outputs
Over 800 markers have now been typed on our linkage mapping panel of DNAs, including common markers to both international mapping reference populations, and a preliminary consensus molecular genetic map has been developed. Several comprehensive QTL searches are beginning to yield promising results. In the area of database development, the new Arkdb version of ChickGBASE is now available on-line. Our Poultry Genome Homepage continues to be regularly updated. A third microsatellite mapping kit was developed this year and kits have been sent to over 40 labs world-wide. Over 500 primer pairs are now available. The poultry genome mapping newsletter continues to be circulated widely. The next annual NAGRP meeting will occur jointly with Plant and Animal Genome VI, to be held in Jan. 1998 with assistance from coordination funds.

Impacts
(N/A)

Publications

• Dodgson, J.B., H.H. Cheng, and R. Okimoto. 1997. DNA marker technology: a revolution in animal genetics. Poultry Science 76:1108-1114.
• Okimoto, R., H.H. Cheng and J.B. Dodgson. 1997. Characterization of CR1 repeat random PCR markers for mapping the chicken genome. Animal Genetics 28:139-145.

Progress 01/01/96 to 12/30/96

Outputs
Over 600 markers have now been typed on our linkage mapping panel of DNAs, including common markers to both international mapping reference populations, and a preliminary consensus molecular genetic map has been developed. Several comprehensive QTL searches have begun. In the area of database development, an advanced version of ChickGBASE continues to be available on-line, as is our Poultry Genome Homepage which is regularly updated. A second microsatellite mapping kit was developed this year and kits have been sent to over 32 labs world-wide. A poultry genome mapping newsletter has been developed and circulated widely. The next annual NAGRP meeting will occur jointly with Plant and Animal Genome V, to be held in Jan. 1997 with assistance from coordination funds.

Impacts
(N/A)

Publications

• CRITTENDEN, L. B., ET AL. 1996. Nomenclature for naming loci, alleles, linkage groups and chromosomes to be used in poultry genome publications & databases. Genet. Sel. Evol. 28:289-297.
• DODGSON, J.B., CHENG, H. H., OKIMOTO, R. 1997. DNA marker technology: a revolution in animal genetics, Poultry Science, in press.

Progress 01/01/95 to 12/30/95

Outputs
Almost 500 markers have now been typed on our linkage mapping panel of DNAs, including common markers to both reference populations, such that we can begin to develop a preliminary consensus molecular genetic map. An advanced map has been published based heavily on the use of microsatellite markers, with a large number having been developed through the use of an enriched library developed by collaborators, Drs. Cheng and Levin. In the area of database development, an advanced version of ChickGBASE is now available on-line, as is our Poultry Genome Homepage. Reviews of chicken gene mapping and nomenclature were published this year. Microsatellite mapping kits are now being distributed in addition to the reference population DNA panels. A poultry genome mapping newsletter has been developed and circulated widely. The poultry species coordinator participated in the development of the first two annual NAGRP meetings, with plans being made for an even larger meeting in the future.

Impacts
(N/A)

Publications

• CHENG, H.H., LEVIN, I., VALLEJO, R.L., KHATIB, H. DODGSON, J.B., CRITTENDEN, L.B., HILLEL, J. 1995. Development of a genetic map of the chicken with markers of high utility. Poultry Sci. 74:1855-1874.
• CRITTENDEN,L., BITGOOD, J., BURT, D. 1995. Chick. In: Genetic nomenclature guide. Trends in Genetics pp. 33-34.
• BURT, D.W., BUMSTEAD, N., BITGOOD, J.J., PONCE DE LEON, F.A., CRITTENDEN, L.B. 1995. Chicken genome mapping: a new ear in avian genetics. Trends in Genetics 11:190-194.
• LEVIN, I., CHENG, H.H., BAXTER-JONES, C., HILLEL, J. 1995. Turkey microsatellite DNA loci amplified by chicken specific primers. Anim. Genetics 26:107-110.

Progress 01/01/94 to 12/30/94

Outputs
Almost 300 markers have now been typed on our linkage mapping panel of DNAs, including common markers to both international reference populations, such that we can begin to develop a preliminary consensus molecular genetic map. Initial efforts have also begun in the development of an on-line, World Wide Web chicken genome mapping database. Database development occurs in close coordination with Dave Burt of The Roslin Institute, Edinburgh. Microsatellite primer pairs will soon be available, supported by the combined resources of the Coordinator and USDA-ARS. Coordination efforts also included the organization of the annual NAGRP meeting and the on-going development of a usable standard nomenclature for gene maps.

Impacts
(N/A)

Publications

• LEVIN, I., SANTANGELO, L., CHENG, H., CRITTENDEN, L.B., DODGSON, J.B. 1994. An autosomal genetic linkage map of the chicken. J. Hered. 85:79-85.
• CHENG, H.H., CRITTENDEN, L.B. 1994. Microsatellite markers for genetic mapping in the chicken. Poultry Sci. 73:539-546.
• CRITTENDEN, L.B. 1994. Genome mapping and animal improvement-An introduction. Proc. 5th World Cong. Genet. Appl. Livestock Prod. 21:3-4.
• BURT, D.W., BUMSTEAD, N., CRITTENDEN, L.B. 1994. The international poultry genome mapping project. Proc. 5th World Cong. Genet. Appl. Livestock Prod. 21:45-47.
• BURT, D.W., BUMSTEAD, N., CRITTENDEN, L.B. 1994. The international poultry genome mapping project. Proc. XXIV Int. Conf. An. Genet. page 109.