U.S. Poultry Species Coordination Activities

U.S. Poultry Species Coordination Activities

Supported by Allotments of Regional Research Funds, Hatch Act

For the Period 1/1/99-12/31/99

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.

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.

PROGRESS TOWARD OBJECTIVE 1. High resolution poultry genome maps.

The Reference Map(s). 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 1100 markers which are resolved into 42 linkage groups (E34 may actually be a part of chromosome 5, however). Included are over 460 microsatellite markers which greatly enhance the utility of this map for genome-wide QTL searches. Also, 202 Type I genes have been mapped which aid in the development of a comparative map. The map has been expanded substantially via the addition of about 200 AFLP markers (Knorr et al., 1999). The map coverage within linkage groups is over 3,700 cM which is about the estimated size of the chicken genome. A second generation consensus map based on all three map populations is now available (Groenen et al., 2000). It contains 1889 markers, placed into 50 linkage groups, covering around 3800 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 the current 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. 1999, Groenen et al., 1999 and 2000, Suchyta and Dodgson, 2000). However, recent results confirm the earlier hypothesis that avian sex chromosomes evolved independently from those of mammals (Fridolfsson et al. 1998, Nanda et al., 1999). 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.

PROGRESS TOWARD OBJECTIVE 2. Physical maps and map integration.

Vignal and colleagues (Fillon et al. 1998; Morisson et al. 1998) have made a good beginning in corresponding some of the microchromosomes to genetic linkage groups. 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.

PROGRESS TOWARD OBJECTIVE 3: Database and other map resources.

ChickGBASE: The latest version of ChickGBASE is constructed in the comparative mapping Arkdb format. Arkdb was primarily developed 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. As per the NRSP-8 renewal proposal, a mirror site for the poultry database is being mounted at the Iowa State database site, http://www.genome.iastate.edu/

WWW Homepage: 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 our microsatellite kits, the latest cytogenetic map, and access to a host of other information. It can be accessed at http://poultry.mph.msu.edu.

Reference Panel DNA: DNA from the East Lansing international reference population has been sent to laboratories throughout the world. Microsatellite Primer Kits: Seven kits of microsatellite primer pairs have been made 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). Six large Comprehensive Mapping Microsatellite Kits containing a total of 647 primer pairs for markers covering most of the chicken genome have also been available. For those with access to ABI sequencers, they are also fluorescent and can be multiplexed. (At present, we are out of kits #1 and #2. Plans are being made to partially replace that resource with a re-synthesized kit of selected marker primers. Two Chicken Gene Primer Pair kits have been made available containing a total of 300 primer pairs to sequenced chicken genes for use in EST mapping and expression analysis.

Physical Mapping Resources: At least two public BAC libraries are now available. One has been made by Crooijmans and Groenen at the Texas A&M BAC Center, and filters or the full library can be obtained through the latter (http://hbz.tamu.edu). This library employed HindIII partial digest fragments, the average insert size is about 130 kb, and nearly 50,000 clones have been made (ca. 5X coverage). Coordination funds were used to generate a second library (using a UCD 001 bird as the DNA source). This library presently contains about 38,000 clones with an average insert size of 150 kb (also ca. 5X). Inserts are BamHI partial digest fragments cloned into the corresponding site of pBeloBAC11. Work is underway (using non-NAGRP funds) to expand this library to around 80,000 clones using both EcoRI and HindIII partial digests of UCD 001 DNA. The initial 38,000 clone library is available from the BAC Center (http://hbz.tamu.edu). Several filter sets of the first 30,000 clones of this library have been purchased using NAGRP support, and those filter sets have been made available for free while they last. Once a clone(s) of interest has been identified, it (they) can be obtained at nominal cost from the Texas A&M BAC Center.

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 1300 scientists attended the joint Plant and Animal Genome VII meeting held last January, held jointly with the annual NAGRP meeting. Coordination funds helped support several Technical Committee members and students/postdocs who wished to attend and will do so again for the upcoming PAG-VIII. A small amount of support was also provided for the Genetic Visions Symposium "From Jay Lush to Genomics: Visions for Animal Breeding and Genetics" held at Iowa State U and for the ISAG 2000 meeting to be held in Minneapolis next year.

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.; Bruley, C.; Dunn, I.C.; Jones, C.T.; Ramage, A.; Law, A.S.; Morrice, D.R.; Paton, I.R.; Smith, J.; Windsor, D.; Sazanov, A.; Fries, R.; Waddington, D. (1999) The dynamics of chromosome evolution in birds and mammals. Nature 402, 411-413.

4. 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.

5. 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.

6. 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.

7. Groenen, M.A.M.; Cheng, H.H.; Bumstead, N.; Benkel, B.; Briles, E.; Burt, D.W.; Burke, T.; Crittenden, L.B.; Dodgson, J.; Hillel, J.; Lamont, S.; Ponce de Leon, F.A.; Soller, M.; Takahashi, H.; Vignal, A. (2000) A consensus linkage map of the chicken genome. Genome Research, in press.

8. Groenen, M.A.M.; Crooijmans, R.P.M.A.; Dijkhof, R.J.M.; Acar, R.; van der Poel, J.J. (1999) Extending the chicken-human comparative map by placing 15 genes on the chicken linkage map. Animal Genetics 30, 418-422.

9. 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.

10. Knorr, C.; Cheng, H.H.; Dodgson, J.B. (1999). Application of AFLP markers to genome mapping in poultry. Animal Genetics 30, 28-35.

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

12. 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.

13. 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.

14. Nanda, I.; Shan, Z.; Schartl, M.; Burt, D.W.; Koehler, M.; Nothwang, H.-G.; Grüntzer, F.; Paton, I.R.; Windsor, D.; Dunn, I.; Engel, W.; Staeheli, P.; Mizuno, S.; Haaf, T.; Schmid, M. (1999) 300 million years of conserved synteny between chicken Z and human chromosome 9. Nature Genetics 21, 258-259.

15. 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.

16. Suchyta, S.P.; Dodgson, J.B. (2000) Remarkable similarity of chicken and human genome maps. Abstract. Plant and Animal Genome VIII.

17. 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.

18. 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.

19. 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.

PLANS FOR THE FUTURE.

OBJECTIVE 1. High resolution poultry genome maps.

Efforts will be made to generate and map more microsatellite markers. Comparative chicken/human map development will also continue in East Lansing and elsewhere.

OBJECTIVE 2. Physical maps and map integration.

Research will continue in several labs to "tag" all the microchromosomes definitively and connect them with the appropriate linkage group. Physical map contig assembly hopefully will occur in several labs, focused on regions of special interest based on QTL analysis or cytogenetic interest. Further expansion and improvement of existing BAC libraries will continue. Generation of a complete genome BAC contig map will begin.

OBJECTIVE 3: Database and other map resources.

The chicken Arkdb database will continue to be updated and improved at the Roslin Institute and the Iowa State mirror site. Newsletter and homepage information will continue to be distributed and enhanced. We will continue to distribute reference panel DNAs, BAC library filters, microsatellite primer panels and Type I gene-based primer panels. A replacement microsatellite primer panel for early kits that are now out of stock or of poor quality will be generated and distributed.

(Prepared 12/21/99)