OVERVIEW: Coordination of Poultry Genome Mapping under the National Animal Genome Research Program (NAGRP) is a joint effort of Michigan State University (MSU) and the USDA, ARS, Avian Disease and Oncology Laboratory (ADOL). CSREES support is allocated via a National Research Service Program, NRSP-8. The NAGRP is made up of the membership of the Animal Genome Technical Committee, including the Poultry Species Subcommittee. MSU and ADOL were chosen by competitive review in June of 1998 to continue in the coordination role after the renewal of NRSP-8, starting 10/01/98.

FACILITIES AND PERSONNEL: Jerry Dodgson, Department of Microbiology, MSU, serves as Coordinator with Hans Cheng of ADOL as Co-Coordinator. Both MSU and ADOL provide facilities and support to the Poultry Coordination effort.

OBJECTIVES:

1. Develop high resolution comparative genome maps aligned across species that link agricultural animal maps to those of the human and mouse genomes,

2. Increase the marker density of existing linkage maps used in QTL mapping and integrate them with physical maps of animal chromosomes, and

3. Expand and enhance internationally shared species genome databases and provide other common resources that facilitate genome mapping.

Numerous labs have cooperated in mapping DNA-based polymorphic markers by genotyping samples from the same two international reference crosses, the Compton population (Bumstead and Palyga, 1992), and the East Lansing population (Crittenden et al. 1993). Subsequently, the map has been enhanced by genotyping of a third cross, the Wageningen population, by Martien Groenen and colleagues (Groenen et al. 1998). At present, the East Lansing (EL) panel has been typed for over 1000 markers which are resolved into 42 linkage groups (preliminary evidence suggests that at least 2 small linkage groups will eventually be linked to macrochromosomes). Included are over 400 microsatellite markers which greatly enhance the utility of this map for genome-wide QTL searches. Also, 180 Type I genes have been mapped which aid in the development of a comparative map. The map has been expanded substantially this year via the addition of about 200 AFLP markers. The map coverage within linkage groups is over 3,500 cM which is about the estimated size of the chicken genome. A second generation consensus map based on all three map populations will soon be available (Groenen et al., in preparation). It will contain approximately 2000 markers, placed into 50 linkage groups, covering around 3400 cM. The number of linkage groups exceeds the number of chromosomes in part because not all linkage groups found in different populations have been unified, but also because some microchromosomes may contain recombination hotspots that divide them into more than one meiotic linkage group. The most recent EL MapManager database continues to be available to users on the WWW Homepage. While this map remains incomplete, it has sufficed for QTL analysis and map-based cloning in several instances (e.g., Ruyter-Spira et al., 1998; Vallejo et al., 1998). With regard to comparative mapping, evidence continues to accumulate that gene order is conserved between the human and chicken genomes to a remarkable extent, perhaps even more than is true between human and rodent genomes (Burt et al. 1997, Cheng et al. 1998, Smith et al. 1997). However, recent results confirm the earlier hypothesis that avian sex chromosomes evolved independently from those of mammals (Fridolfsson et al. 1998). Furthermore, McQueen et al. (1996, 1998) have presented evidence that gene density is higher on chicken microchromosomes than on macrochromosomes. These studies suggest that many differences between the human and chicken genome remain to be resolved through fine structure comparative mapping.

Vignal and colleagues (Fillon et al. 1998; Morrison et al. 1998) have made a good beginning in corresponding some of the microchromosomes to genetic linkage groups. Smith and Burt (1998) report a chromosome by chromosome comparison of genetic versus physical length with an average ratio of about 0.4 million base pairs per cM. Physical mapping resources, such as chicken large insert recombinant DNA libraries (cosmid, Buitkamp et al. 1998; YAC, Toye et al. 1997; BAC, Zoorob et al. 1996 and Crooijmans and Groenen, personal communication, also see objective 3 below), have recently been constructed, along with initial attempts at radiation hybrid mapping panels (Kwok et al. 1998).

Reference Panel DNA: 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. 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). 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. For those with access to ABI sequencers, they are also fluorescent and can be multiplexed. A fifth kit will soon be available with at least 37 more labeled primer pairs. This year a new Chicken Gene Primer Pair kit has been made available containing 200 primer pairs to sequenced chicken genes for use in EST mapping and expression analysis.

Physical Mapping Resources: At least two public BAC libraries have been made or are under construction. One, has been made by Crooijmans and Groenen at the Texas A&M BAC Center, and filters can be obtained through them. Coordination funds are presently being used to generate a second library (using a different DNA source and restriction enzyme cleavage) through this Center that should be available by early in 1999.

Newsletter: The Poultry Genome 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. Meetings: Over 1000 scientists attended the joint Plant and Animal Genome VI meeting held last January, jointly with the annual NAGRP meeting. Coordination funds helped support several Technical Committee members and students/postdocs who wish to attend and will do so again for the upcoming PAG-VII. Other meetings attended included the ISAG meeting in Auckland, NZ and the associated Poultry Gene Mapping Workshop, Poultry Breeders' Roundtable, and the World Conference on Animal Production in Seoul, Korea. A small amount of support was also provided for the upcoming Genetic Visions Symposium "From Jay Lush to Genomics: Visions for Animal Breeding and Genetics" at Iowa State U.

Relevant Publications :

1. Buitkamp, J.; Ewald, D.; Schalkwyk, L.; Weiher, M.; Masabanda, J.; Sazanov, A.; Lehrach, H.; Fries, R. (1998) Construction and characterization of a gridded chicken cosmid library with four-fold genomic coverage. Animal Genetics 29, 295-301.

2. Bumstead, N.; Palyga, J. (1992) A preliminary linkage map of the chicken genome. Genomics 13, 690-697.

3. Burt, D.W.; Bumstead, N.; Burke, T.; Fries, R.; Groenen, M.; Tixier-Boichard, M.; Vignal, A. (1997) Current status of poultry genome mapping - June 1997. In: Proceedings of the 12th AVIAGEN Symposium: Current Problems in Avian Genetics, Prague, Czech Republic, pp. 33-45.

4. Cheng, H.H.; Burt, D.W.; Dodgson, J.B. (1998) Recent advances in poultry genome mapping. In: Proceedings of the 8^th World Conference on Animal Production, Seoul, South Korea, pp. 168-178.

5. Crittenden, L.B.; Provencher, L.; Santangelo, L.; Levin, I.; Abplanalp, H.; Briles, R.W.; Briles, W.E.; Dodgson, J.B. (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.

6. Fillon, V.; Morisson, M.; Zoorob, R.; Auffray, C.; Douaire, M.; Gellin, J.; Vignal, A. (1998) Identification of 16 chicken microchromosomes by molecular markers using two-colour fluorescence in situ hybridization (FISH). Chromosome Research 6, 307-313.

7. Fridolfsson, A.-K.; Cheng, H.; Copeland, N.G.; Jenkins, N.A.; Liu, H.-C.; Raudsepp, T.; Woodage, T.; Chowdhary, B.; Halverson, J.; Ellegren, H. (1998) Evolution of the avian sex chromosomes from an ancestral pair of autosomes. Proceedings of the National Academy of Sciences USA 95, 8147-8152.

8. Groenen, M.A.M.; Crooijmans, R.P.M.A.; Veenendaal, A.; Cheng, H.H.; Siwek, M.; van der Poel, J.J. (1998) A comprehensive microsatellite linkage map of the chicken genome. Genomics 49, 265-274.

9. Kwok, C.; Korn, R.M.; Davis, M.E.; Burt, D.W.; Critcher, R.; McCarthy, L.; Paw, B.H.; Zon, L.I.; Goodfellow, P.N.; Schmitt, K. (1998) Characterization of whole genome radiation hybrid mapping resources for non-mammalian vertebrates. Nucleic Acids Research 26, 3562-3566.

10. McQueen, H.A.; Siriaco, G.; Bird, A.P. (1998) Chicken microchromosomes are hyperacetylated, early replicating, and gene rich. Genome Research 8, 621-630.

11. McQueen, H.A.; Fantes, J.; Cross, S.H.; Clark, V.H.; Archibald, A.L.; Bird, A.P. (1996) CpG islands of chicken are concentrated on microchromosomes. Nature Genetics 12, 321-324.

12. Morisson, M.; Pitel, F.; Fillon, V.; Pouzadoux, A.; Bergé, R.; Vit, J.P.; Zoorob, R.; Auffray, C.; Gellin, J.; Vignal, A. (1998) Integration of chicken cytogenetic and genetic maps: 18 new polymorphic markers isolated from BAC and PAC clones. Animal Genetics 29, 348-355.

13. Ruyter-Spira, C.P.; de Groof, A.J.C.; van der Poel, J.J.; Herbergs, J.; Groenen, M.A.M. (1998) The HMGI-C gene is a likely candidate for the autosomal dwarf locus in the chicken. Journal of Heredity 89, 295-300.

14. Smith, E.J.; Lyons, L.A.; Cheng, H.H.; Suchyta, S.P. (1997) Comparative mapping of the chicken genome using the East Lansing reference population. Poultry Science 76, 743-747.

15. Smith, J.; Burt, D.W. (1998) Parameters of the chicken genome (Gallus gallus). Animal Genetics 29, 290-294.

16. Toye, A.A.; Schalkwyk, L.; Lehrach, H.; Bumstead, N. (1997) A yeast artificial chromosome (YAC) library containing 10 haploid chicken genome equivalents. Mammalian Genome 8, 274-276.

17. Vallejo, R.L.; Bacon, L.D.; Liu, H.-C.; Witter, R.L.; Groenen, M.A.M.; Hillel, J.; Cheng, H.H. (1998) Genetic mapping of quantitative trait loci affecting susceptibility to Marek's disease virus induced tumors in F₂ intercross chickens. Genetics 148, 349-360.

18. Zoorob, R.; Billaut, A.; Severac, V.; Fillon, V.; Vignal, A.; Auffray, C. (1996) Two chicken genomic libraries in the PAC and BAC cloning systems: organization and characterization. Animal Genetics 27, 69.

Efforts will be made to generate and map more microsatellite markers and to improve overall map marker density using AFLP markers. Another goal is completion and publication of the second, updated version of the consensus map. Comparative chicken/human map development will also continue in East Lansing and elsewhere.

Research will continue in several labs to "tag" all the microchromosomes definitively and connect them with the appropriate linkage group. The second public BAC library should be available by early next year. It will need to be characterized and made readily accessible. Physical map contig assembly hopefully will occur in several labs, focused on regions of special interest based on QTL analysis or cytogenetic interest.

The chicken Arkdb database will continue to be updated and improved at the Roslin Institute and the Iowa State mirror site should soon be fully implemented. Newsletter and homepage information will continue to be distributed and enhanced. We will continue to distribute reference panel DNAs, expanded microsatellite primer panels and Type I gene-based primer panels. At least one additional gene primer panel and two more microsatellite primer panels hopefully will be made available next year. The second BAC library will also be made available (see Objective 2). Negotiations with Keygene, N.V., continue regarding the possible availability of an AFLP primer panel.

(Prepared 12/1/98)