Overview: Coordination of Poultry Genome Mapping during the initial phase of the National Animal Genome Research Program (NAGRP) has been a joint effort of the Michigan State University (MSU) Department of Microbiology and the USDA, ARS, Avian Disease and Oncology Laboratory (ADOL). Jerry Dodgson, Department of Microbiology, MSU, has been Coordinator since 10/01/94 with Lyman Crittenden having been Coordinator from 10/01/93-9/30/94, continuing to consult thereafter. Hans Cheng of ADOL is Co-Coordinator. Both ADOL and MSU provide facilities that support coordination efforts.

OBJECTIVES: The Coordinators have worked 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 TOWARD OBJECTIVE 1. POULTRY GENOME MAPS

The Reference Map(s). A panel of 52 backcross and parental DNAs has been shipped to numerous laboratories in the UK, the Netherlands, Israel, Australia, Canada, and the US where typing is done. At present, the East Lansing, (EL) panel has been typed for 954 markers of which 928 are resolved into 42 linkage groups (preliminary evidence suggests that at least 2 small linkage groups will eventually be linked to macrochromosomes; 40 linkage groups are expected from cytogenetic studies, 38 autosomes, Z and W). The map coverage within linkage groups is 3,376 cM which is about the estimated size of the chicken genome. There are 408 microsatellite markers which greatly enhance the utility of this map for genome-wide QTL searches. Also, 158 Type I genes have been mapped which aid in the development of a comparative map. In collaboration with Nat Bumstead (Compton, U.K.), a consensus map of the EL and Compton genetic maps has been developed and distributed by the Coordinators. An updated version of the consensus map presently is being prepared by Cheng, Bumstead, and Martien Groenen. Recently, for the first time, linkage groups have been assigned to all cytogenetically distinguishable chromosomes (macrochromosomes 1-8, sex chromosomes Z and W, and chromosome 16 containing the NOR). The latest available MapManager database continues to be available to users on the WWW Homepage.

PROGRESS TOWARD OBJECTIVE 2. DATABASE DEVELOPMENT

ChickGBASE: We previously supported Alan Hillyard on a consultant basis for the development of ChickGBASE (in parallel, the Swine Coordinator supported Hillyard for the development of PIGBASE). Dr. Hillyard was part of the initial development of Arkdb, the new, more inclusive version of animal databases released last summer. However, Arkdb was primarily constructed by Andy Law, Dave Burt, Alan Archibald, and others at the Roslin Institute. ChickGBASE is available in the Arkdb format at http://www.ri.bbsrc.ac.uk/chickmap/chickgbase/chickgbase.html.

WWW Homepage: We maintain a 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 our microsatellite kits, the latest cytogenetic map, and access to a host of other information. There is an extensive "About" section which includes annual Coordinator reports, the full NRSP-8 renewal proposal and publication list, a glossary, nomenclature rules, and a searchable address list, among other items. The homepage also contains copies of newsletters, access to the Crittenden reference database, and a large variety of links to other relevant Web sites. A new frames version of the Homepage was developed and installed last year. The Web page can be accessed at http://poultry.mph.msu.edu. Given the "democratic" nature of the Web, our homepage also serves an important function by informing the general public about progress in poultry genetics and genomics. (When we stopped counting a couple of years ago, homepage "hits" were already in the hundreds of thousands.)

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 laboratories throughout the world. Microsatellite Primer Kits: Five kits of microsatellite primer pairs are now available for free distribution. All of our primers are also fluorescent-labelled and can be used in either manual or ABI genotyping procedures. We've distributed a Population Tester Kit, containing 9 primer pairs which define microsatellites with high polymorphic information content (numerous alleles widely distributed in several populations). Four large Comprehensive Mapping Microsatellite Kits now containing a total of 575 primer pairs for markers covering most of the chicken genome are also available. The Homepage also has tables of the kit loci along with a larger table which includes information on all published microsatellite loci to date (and several unpublished ones from Hans Cheng and Martien Groenen). Approximately 40 laboratories have been provided one or more of these kits. (We recently had to replace kits #1 and #2 due to the heavy demand.) By the end of the year, we will be providing our first AFLP mapping primer kit and our first candidate gene PCR kit based on available chicken DNA sequence information.

Physical Mapping Resources: These potentially include large insert clone libraries (YACs, BACs), somatic hybrid cell panels, and radiation hybrid panels. Nat Bumstead and collaborators have developed a chicken YAC library that is available for screening through Dr. Hans Lehrach in Berlin. A chicken BAC library has been developed very recently by M. Groenen, in collaboration with the Texas A&M BAC Center. We have made arrangements with that BAC Center to develop a second BAC library using the Jungle Fowl source DNA for the EL reference map backcross to allow for screening it with JF-specific polymorphism markers. This should be ready by the end of this year. We hope to negotiate with the BAC Center to pay for filter sets and pooled DNA samples that will available to interested parties. Assuming Dr. Groenen agrees, we will also distribute filter sets for his BAC library. Other plans for new resource development are described in this application. At the last annual NAGRP meeting, the members of the Poultry Subcommittee were surveyed to determine the relative interest in various types of mapping resources.

Communication Resources. Newsletter: The Poultry Genome Newsletter was established and 13 editions distributed so far. The Newsletter is published quarterly and is distributed through our WWW Homepage, electronically on the angenmap email discussion group and via hard copy to scientists worldwide. Nomenclature: Nomenclature issues continue to be resolved, as led by Lyman Crittenden, Jim Bitgood and other interested parties. Meetings: The Poultry Coordinators have played an active role in supporting and coordinating several meetings, workshops and symposia over the past five years, including NAGRP meetings in Minneapolis and College Park. NRSP-8 Technical Committee and Species Subcommittee Chairs helped develop the joint Plant and Animal Genome annual meetings held for the first time in January, 1997, jointly with the annual NAGRP meeting. Approximately 1000 scientists attended PAG-VI last January. Coordination funds have supported travel for several Technical Committee members and students/postdocs. The Poultry Coordinator also chaired the writing committee that prepared the successful NRSP-8 renewal application, critical review, and reference list. In addition, Poultry Coordinators attended several meetings throughout their term to facilitate common NAGRP goals with other Coordinators, with representatives of CSREES and ARS, with industry representatives, and with other members of the public. The Poultry Coordinator was also a member of the Avian Genetic Resources Taskforce and helped to write and review their white paper on preservation of poultry germplasm resources.

PROGRESS TOWARD OBJECTIVE 4: RESEARCH PRIORITIES

The research priorities initially set by the Poultry Species Subcommittee were: (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 complete, although the map still needs to become more dense and a more realistic estimate is that at least 1000 microsatellites will be needed in order to have a reasonable number that are polymorphic in most populations of interest. Groenen and colleagues have also completed a genetic linkage map using the Wageningen resource population with average marker spacing of 7 cM. Microsatellites developed in the Groenen, Cheng and Burke labs, among others, were mapped. 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 still lag behind the genetic map. Work on comparative gene mapping of chicken loci using Type I markers continues at MSU, ADOL, and elsewhere. Type I markers on the EL map increased nearly 50% last year. With regard to Item 4, these resources have been and continue to be provided. As new technologies are developed (e.g., DNA chips), we have actively investigated providing these to our committee members and other interested scientists. 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 some labs. Progress on item 6 has been limited, probably due to lack of a critical mass of investigators working with these species. Dr. Smith at Tuskegee has developed and mapped a panel of turkey microsatellites on the BYU reference population.

Selected Relevant Publications of Coordinators:

1. Crittenden, L.B., L. Provencher, L. Santangelo, I. Levin, H. Abplanalp, R.W. Briles, W.E. Briles, and J. B. Dodgson. 1993. Characterization of a red jungle fowl by white leghorn backcross reference population for molecular mapping of the chicken genome. Poultry Science 72:334-348.

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

8. 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.

9. 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 74:1855-1874.

10. Crittenden, L.B., J.J. Bitgood, D.W. Burt, F.A. Ponce de Leon, and M. Tixier-Boichard. 1996. Nomenclature for naming loci, alleles, linkage groups and chromosomes to be used in poultry genome publications and databases. Genet. Sel. Evol. 28:289-297.

11. Smith, E.J., Cheng, H., and Vallejo, R. 1996. Mapping functional chicken genes: an alternative approach. Poultry Science 75:642-647.

12. Smith, E.J., Cheng, H.H., and Suchyta, S.P. 1997. Comparative mapping of the chicken genome using the East Lansing reference population. Poultry Science 76:743-747.

13. Dodgson, J.B., H.H. Cheng, and R. Okimoto. 1997. DNA marker technology: a revolution in animal genetics. Poultry Science 76:1108-1114.

14. 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.

15. Cheng, H.H. 1997. Mapping the chicken genome. Poultry Science 76:1101-1107.

16. Vallejo, R.L., G.T. Pharr, H.C. Liu, H.H. Cheng, R.L. Witter, and L.D. Bacon. 1997. Non-association between Rfp-Y major histocompatibility complex-like genes and susceptibility to Marek's disease virus-induced tumors in 6(3) x 7(2) intercross chickens. Animal Genetics 28:331-337.

17. Vallejo, R.L., L.D. Bacon, H.C. Liu, R.L. Witter, M.A. Groenen, J. Hillel, and H.H. Cheng. 1998. Genetic mapping of quantitative trait loci affecting susceptibility to Marek's disease virus induced tumors in intercross chickens. Genetics 148:349-360.

Recognition of coordinators and NAGRP:

1. Lyman Crittenden elected to U.S. Poultry Hall of Fame, 1998.

2. NAGRP coordinators receive USDA Honor Award, 1997.

3. Jerry Dodgson serves as Program Director for USDA-NRI Animal Genetic Mechanisms and Genome Mapping Panel, 1998.

4. Dodgson ('94) and Cheng ('95, '96) serve as members of USDA-NRI Animal Genetic Mechanisms and Genome Mapping Panel.

(Prepared 5/15/98)