Overview: Coordination of Poultry Genome Mapping under the National Animal Genome Research Program (NAGRP) is a joint effort of the Michigan State University (MSU), Department of Microbiology and the USDA, ARS, Avian Disease and Oncology Laboratory (ADOL). It is supported financially by ADOL, CSRS, and MSU. CSRS support is allocated via a National Research Service Program, NRSP-8. The NAGRP is supported by the membership of the Animal Genome Technical Committee (AGTC). That membership is divided up into Species Subcommittees.

FACILITIES AND PERSONNEL:

U.S. aspects of the coordination effort are housed at ADOL and MSU. Lyman Crittenden, Research Professor, MSU served as Coordinator through 9/30/94. Jerry Dodgson, Department of Microbiology, MSU has been a collaborator on the project and assumed the Coordinator role as of 10/01/94 with Lyman Crittenden remaining a collaborator. Hans Cheng of ADOL has been and will remain a Co-Coordinator. Both ADOL and MSU provide facilities that support coordination efforts. ARS, through ADOL, provides a technician, Lenny Provencher, laboratory and office space, freezers, support of copying, mailing, shipping and some other office services. Scott Eisensmith is the Database Curator for the project and is located at MSU along with most of the computer facilities.

OBJECTIVES:

The Coordinator works with the Poultry Species Committee to achieve the following objectives: (1) Serve as custodian of poultry maps. (2) Serve as coordinator of species databases. (3) Serve coordinator of shared material and information. (4) Serve as coordinator for developing research priorities.

PROGRESS:

PROGRESS TOWARD OBJECTIVE 1. POULTRY GENOME MAPS

The Reference Map(s). A panel of 52 backcross and parental DNAs has been shipped to 11 laboratories in the UK, the Netherlands, Israel, Australia, Canada, and the US where typing is done as well as at the two laboratories in East Lansing. This panel is a subset of a BC population of 400 individuals. As mapping techniques become more routine, the full panel or at least a larger subset will be available to improve the resolution and usefulness of the overall map. At present, our (East Lansing) panel has been typed for over 500 markers. Data are returned to East Lansing and entered into Map Manager, a MAC program that can accomodate F2 and recombinant inbred line data as well as backcross data. The typing data from Map Manager can also be moved directly to MapMaker, a multipoint linkage program. Most of these laboratories also have a panel of DNA from a backcross population developed by Nat Bumstead at the Compton Laboratory (U.K.). Preliminary maps on both reference populations have been published (1,2). A map of the chicken Z chromosome has also been published mostly using RAPD markers (3). A revised map based on highly informative microsatellite markers has recently been developed (10). We have now typed enough common markers in these two international reference populations to associate the largest linkage groups and develop a preliminary consensus molecular genetic map (Crittenden and Bumstead, manuscript in preparation, see also reference 9 for a review and attached map update from Crittenden).

PROGRESS TOWARD OBJECTIVE 2. DATABASE DEVELOPMENT

Overview: Our database efforts are aimed at (at least) two levels of data. 1. An online international public database of published mapping data or data released to the public by individual investigators. This would include data, references, maps, and other relevant data in a convenient relational format. 2. An online international working database restricted to collaborators in the International Poultry Genome Workshop. This would include published data and data released by individual investigators for collaborative purposes. It would focus on linkage data that could be accessed, reviewed, updated and discussed by the whole mapping workshop community. A public database is now on-line through the World Wide Web (WWW) from Roslin, UK, and a version is also maintained at the National Agriculture Library (NAL) in Beltsville. This is called ChickGBASE and is based on the shell developed at The Jackson Laboratory for GBASE, which is the widely accepted mouse genomic database. Efforts are on-going to improve both versions.

ChickGBASE: We have supported Alan Hillyard of Jackson Labs on a consultant basis for the development of ChickGBASE (in parallel, the Swine Coordinator has supported Hillyard for the development of PIGBASE). Dr. Hillyard has also worked with Andy Law, Dave Burt, Alan Archibald, and others at the Roslin Institute to develop a totally new, more inclusive version of animal databases that should be available within the coming year. Details on the use of ChickGBASE have been outlined in the Newsletters and have also been demonstrated at the NAGRP meetings.

WWW Homepage: We have developed a WWW homepage for the Poultry Genome which links to ChickGBASE, the Roslin Institute homepage, the National Agricultural Library and a variety of other genome mapping resources. The Homepage provides the recently developed microsatellite map (10), a list of published microsatellites, descriptions of our microsatellite kits, the latest cytogenetic map, and access to a host of other information. Mechanisms for discussion groups and other electronic communication are also provided.

PROGRESS TOWARD OBJECTIVE 3: SHARED MATERIAL AND INFORMATION

Reference Panel DNA: As noted above, DNA from the East Lansing international reference population has been sent to nine laboratories throughout the world. Linkage analysis is performed at East Lansing and results returned to the collaborators. Informal reports are being distributed. RFLP probes are made available from the originating laboratory, but no central repository for these probes is planned at this time.

Microsatellite Primer Kits: Two kits of microsatellite primer pairs are now available for free distribution. The first of these is the Population Tester Kit. This contains 9 primer pairs which define microsatellites with high polymorphic information content (numerous alleles widely distributed in several populations). For those with access to ABI sequencers, they are also fluorescent and can be multiplexed. This kit is available to those who wish to test just a few loci to characterize a strain or genetically fingerprint chickens. The relevant sequences are listed along with collateral information on our WWW homepage at http://poultry.mph.msu.edu.

A larger microsatellite kit containing 120 primer pairs that define markers covering most of the chicken genome, called the Comprehensive Mapping Kit 1, is also available. These are also fluorescently labeled sets that can be used with either automated or manual mapping techniques. The Comprehensive Mapping Kit 1 will be provided free to any public scientists who are involved in major mapping efforts. The Homepage also has a table of these 120 loci along with a larger table which includes information on all published microsatellite loci to date (and a few unpublished ones from Hans Cheng). Tables are provided as attachments to this report. We welcome information from everyone on useful microsatellite (or other) primers for posting on the WWW and for inclusion in free primer packages for distribution. As more data becomes available, we plan to synthesize further primer kits containing additional informative loci. Further microsatellite sequence information will be required to generate enough markers to adequately map in a variety of populations. Once tested, the microsatellite primers will be made available to collaborators who can use them in major mapping projects. The goal is to develop a set of about 200-400 evenly spaced, highly polymorphic markers that will allow us to form a kit for international use in QTL mapping. While the ideal marker set will continue to evolve as more is learned about the chicken gene map and about assay technologies, we hope to reach this goal sometime in 1995-96.

Newsletter: The Poultry Genome Newsletter has been established and the first 3 editions are attached. The Newsletter is published quarterly and is distributed through our WWW Homepage, electronically on the angenmap electronic discussion group and via hard copy to scientists throughout the world. Copies are also distributed to the Poultry Breeders of America.

A wild turkey by domestic turkey backcross been developed at Brigham Young University by Stephen Estes and Cory Teuscher. Another turkey mapping population has been developed by Israeli workers collaborating with BUTA. (A third population has been developed commercially, but will probably not become publicly available.) Details concerning distribution of DNA, analysis of data, and publication have not been completely worked out.

Physical Mapping Resources: These potentially include large insert clone libraries (YACs, BACs), somatic hybrid cell panels, and radiation hybrid panels. Most of these resources are not yet available. Nat Bumstead and collaborators have developed a chicken YAC library. Negotiations are on-going about using Coordination funds to provide and distribute sets of filters of YAC clones that can be sent (free of charge) to investigators who wish to screen such panels. If successful, the original YAC clone would be obtained from Dr. Bumstead. At least two BAC libraries are presently under construction and, once completed, we hope to be able to distribute these as well. Other possibilities remain to be worked out.

Nomenclature: Gene and Allele: Three drafts of a proposal to adopt the human gene nomenclature with modifications for anonymous loci were prepared and discussed at an open meeting of the Poultry Genome Committee at the 1993 Poultry Science Meetings (East Lansing, MI). The draft presented at the Second International Poultry Genome Workshop (ISAG 94) was approved by that group. An International Nomenclature Committee, and a resource panel of consultants for different types of classical genes to help convert the Somes, 1980 nomenclature to the new system, has been formed and is returning suggested changes. An initial description of nomenclature has recently been published as a supplement to Trends in Genetics (8). Nomenclature determinations should eventually become routinely done via entry into the ChickGBASE system. Andy Law, Dave Burt, Lyman Crittenden and others are working out a system for this.

Meetings: The second annual NAGRP meeting was held in College Park, MD this October with support from Coordination funds. Coordinators are also supporting representation of animal gene mapping discussion at the HUGO Conference in Australia this December. Plans are underway to join the annual NAGRP meetings with the Plant Genome meetings held in San Diego early each year. This is expected to provide the NAGRP meetings with higher attendance and greater international impact.

PROGRESS TOWARD OBJECTIVE 4: RESEARCH PRIORITIES

The research priorities discussed at the September, 1994 NAGRP meeting include: (1) Develop a consensus map of at least 200 microsatellite markers embedded in a dense map of other markers. (2) Develop resource populations designed to use that map to identify QTL for major economic traits. (3) Integrate the genetic, physical, and classical maps. (4) Develop resources for joint use such as primer sets and large insert DNA libraries. (5) Develop rapid mapping techniques and protocols that will allow economic and efficient use of genetic markers for a variety of purposes. (6) As resources permit, extend the map to other species of poultry in the following priority: turkeys, ducks, and Coturnix quail as a model.

Progress: Item 1 is nearly complete, although the map needs to become more dense and a more realistic estimate is that 400 microsatellites (or more) will be needed in order to have a reasonable number that are polymorphic in most populations of interest. Item 2 is well underway at several locations in the U.S. and elsewhere. Considerable progress has been made on Item 3, although physical and classical maps are lagging behind the genetic map. Work on comparative gene mapping of chicken loci using Type I markers is under way at the USDA-ADOL. With regard to Item 4, primer sets are already available and more will be made soon. Large insert libraries are under construction. The major problem with Item 5 involves resources. Rapid mapping using existing microsatellite primers is best done using automated equipment, which are presently too expensive for most labs. Progress on item 6 has been limited, probably due to lack of a critical mass of investigators working with these species. Some progress has been made with turkeys and reports that many chicken microsatellite primer pairs can work in turkeys (11) provides hope for the future. However, it remains unproven to what extent polymorphic loci in turkeys are strictly homologous to those in chickens. Research is underway to answer this question.

REFERENCES:

1. Bumstead, N. and J. Palyga. 1992. A preliminary linkage map of the chicken genome. Genomics 13: 690-697.

2. Levin, I., L. Santangelo,H. Cheng, L.B. Crittenden, and J.B. Dodgson. 1994. An autosomal genetic linkage map of the chicken. J. Hered. 85: 79-85.

3. Levin, I., L.B. Crittenden, and J.B. Dodgson. 1993. Genetic map of the chicken Z chromosome using random amplified polymorphic DNA (RAPD) markers. Genomics 16: 224-230.

4. Cheng, H.H., and L.B. Crittenden. 1994. Microsatellite markers for genetic mapping in the chicken. Poultry Sci. 73: 539-546.

5. Crittenden, L.B. 1994. Genome mapping and animal improvement-An introduction. Proc. 5th World Cong. on Genetics Appl. to Livestock Prod. 21: 3-4.

6. Burt, D.W., N. Bumstead, and L.B. Crittenden. 1994. The international poultry genome mapping project. Proc. 5th World Cong. on Genetics Appl. to Livestock Prod. 21: 45-47.

7. Burt, D.W., N. Bumstead, and L.B. Crittenden. 1994. The international poultry genome mapping project. Proc. XXIV International Conf. on Animal Genetics, page 109.

8. Crittenden, L., J. Bitgood, and D. Burt. 1995. Chick. in "Genetic Nomenclature Guide", Trends in Genetics, pp. 33-34.

9. Burt, D.W., N. Bumstead, J.J. Bitgood, F.A. Ponce de Leon, and L.B. Crittenden. 1995. Chicken genome mapping: a new era in avian genetics. Trends in Genetics 11: 190-194.

10. Cheng, H.H., I. Levin, R.L. Vallejo, H. Khatib, J.B. Dodgson, L.B. Crittenden, and J. Hillel. 1995. Development of a genetic map of the chicken with markers of high utility. Poultry Science, in press.

11. Levin, I., H.H. Cheng, C. Baxter-Jones, and J. Hillel. 1995. Turkey microsatellite DNA loci amplified by chicken specific primers. Animal Genetics 26:107-110.

PLANS FOR THE FUTURE.

OBJECTIVE 1. POULTRY GENOME MAPS

Continued progress on the reference genome map will be encouraged by distribution of reference panel DNAs, microsatellite primers and shared data. We will continue to work with international collaborators to enhance the usefulness of the reference map and to consolidate data and map distances between the two accepted reference populations.

Mapping efforts will move increasingly towards resource populations. We will use this data and develop methods to consolidate this data, where possible, to improve the consensus map. We will encourage sharing of resource mapping data through our efforts in data collection and distribution (see objective 2.) We will examine the possibility of distributing DNA panels from selected resource populations.

Efforts will be made to develop and use a reference genome map for turkeys and to compare that map to the existing chicken map. Reference panels for other species will be under consideration.

OBJECTIVE 2. DATABASE DEVELOPMENT

Continued improvements of ChickGBASE will be made and the information made available on-line will be expanded and improved. Efforts will focus on expanding the number of database users by public education on the utility of the database and assistance in accessing it. Further efforts will be made to integrate different types of genome data in a relational mode (the new ChickGBASE). We hope to begin to include physical map data based on cloned DNA contigs.

OBJECTIVE 3: SHARED MATERIAL AND INFORMATION

Shared information has been discussed in Objective 2 above. As noted under Objective 1, we will continue to distribute chicken reference mapping population DNAs and hope to develop resource chicken DNA panels and turkey reference DNA panels for distribution.

Further kits will be developed containing microsatellite primer pairs for the key, highly polymorphic reference markers, and these will also be distributed to interested scientists. During FY96 it is hoped that microsatellite or other polymorphic markers will have been identified for each chicken chromosome. Primers for anchor loci will be distributed as part of the above process to allow rapid localization of new genetic loci. Efforts will be made to encourage a better integration of physical, genetic and classical maps. Two to three large insert cloned DNA libraries should also become available by the end of FY96. We will coordinate distribution of library stocks for rapid screening purposes.

Development of consensus on nomenclature issues should have considerably progressed by FY96. It is hoped that remaining issues can be resolved at the Third International Genome Mapping Workshop at the ISAG meeting in Tours, France in summer of 1996 and at the annual meeting of the NAGRP Technical Committee.

OBJECTIVE 4: RESEARCH PRIORITIES

Research priorities will continue to be developed by consensus of the Poultry Technical Subcommittee. That Subcommittee and the whole NAGRP Technical Committee met in October of 95 in College Park, MD to further coordinate and consolidate progress. NAGRP Coordinators participated in the organization of the meeting and the coordination activities at the meeting. Coordination activities with industry representatives at such gatherings as the Poultry Breeders' Roundtable will continue.

Attachments:

1. Poultry Genome Newsletters

2. Tables of available microsatellite kits

3. Update on consensus map development

(Prepared 10/20/95, revised 11/2/95)