U.S. Poultry Species Coordination Activities

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 & Molecular Genetics, 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 1160 markers which are resolved into 40 linkage groups. Included are over 460 microsatellite markers which greatly enhance the utility of this map for genome-wide QTL searches. Recent progress has focused on locating specific genes on the EL map that aid in comparative mapping (see below), with approximately 260 genes now on the map. The map coverage within linkage groups is over 3,900 cM which is about the estimated size of the chicken genome. A second generation consensus map based on all three map populations has been published (Groenen et al. 2000) and an updated version of this is in press (Schmid et al. 2001). The latter contains 1965 markers, placed into 50 linkage groups. 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. 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. 2000, Suchyta et al. 2001, Waddington et al. 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, Suchyta et al. 2001).

PROGRESS TOWARD OBJECTIVE 2. Physical maps and map integration.

Vignal and colleagues at INRA (Fillon et al. 1998, Morisson et al. 1998, Schmid et al. 2001) have made major progress over the past year in integrating the linkage map with specific microchromosomes, as identified by FISH mapping. Linkage groups have been assigned to specific microchromosomes 9-19, and 21-31, leaving only microchromosomes 20 and 32-38 yet to be assigned. 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 et al. 2000, and see objective 3 below), have recently been constructed. The Groenen lab has made extensive progress in linking the physical map to the linkage map in selected locations, especially on chromosome 10. Efforts are underway by Crooijmans, Groenen and colleagues; Zhang, Dodgson and colleagues; and INRA to construct BAC-based contig maps across the full chicken genome.

PROGRESS TOWARD OBJECTIVE 3: Database and other map resources.

Reference Panel DNA: DNA from the East Lansing international reference population has been sent to laboratories throughout the world.

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. Kits #1 and #2 were replaced this year with a newly made, select group of markers as Kit #1/2. One or more kits have now been provided to 100 different labs, worldwide. 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.

Table 1. Chicken (Jungle Fowl UCD001) BAC libraries

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 1500 scientists attended the joint Plant and Animal Genome VIII meeting held last January, held jointly with the annual NAGRP meeting. Coordination funds helped support attendance at PAG-VIII and will do so again for the upcoming PAG-IX. A small amount of support was also provided for the ISAG 2000 meeting held in Minneapolis last year and the upcoming Gordon Conference on Quantitative Genetics and Genomics.

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. Crooijmans R.P.M.A., Vrebalov J., Dijkhof R.J.M., van der Poel J.J., Groenen M.A.M: Two-dimensional screening of the Wageningen chicken BAC library. Mammalian Genome 11:360–363 (2000).

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.; 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.

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. 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.

11. 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.

12. Schmid, M.; Nanda, I.; Guttenbach, M.; Steinlein, C.; Hoehn, H.; Schartl, M.; Haaf, T.; Weigend, S.; Fries, R.; Buerstedde, J-M.; Wimmers, K.; Burt, D.W.; Smith, J.; A’Hara, S.; Law, A.; Griffin, D.K.; Bumstead, N.; Kaufman, J.; Thomson, P.A.; Burke, T.A.; Groenen, M.A.M.; Crooijmans, R.P.M.A.; Vignal, A.; Fillon, V.; Morisson, M.; Pitel, F.; Tixier-Boichard, M.; Ladjali-Mohammedi, K.; Hillel, J.; Mäki-Tanila, A.; Cheng, H.H.; Delany, M.E.; Burnside, J.; Mizuno, S. 2001. First report on chicken genes and chromosomes. Cytogenet. Cell Genet., in press.

13. Suchyta, S.P.; Cheng, H.H.; Burnside, J.; Dodgson, J.B. 2001. Comparative mapping of chicken anchor loci orthologous to genes on human chromosomes 1, 4 and 9, Animal Genetics, in press.

14. 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.

15. Waddington D.; Springbett A.J.; Burt D.W. (2000) A chromosome based model to estimate the number of conserved segments between pairs of species from comparative genetic maps. Genetics 154:323–332.

16. 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 and to improve overall map marker density. Comparative chicken/human map development will also continue and QTL analysis should expand.

OBJECTIVE 2. Physical maps and map integration.

Physical map contig assembly will continue in several labs, focused on regions of special interest based on QTL analysis or cytogenetic interest. Efforts to expand our existing BAC library are underway, and work will continue on full genome physical maps using a BAC contig-building strategy. Parallel efforts will occur at Wageningen and INRA. Arrangements have been made to have the initial BAC library pooled for 3-dimensional PCR screening and DNA pools made, purified, and aliquotted by Research Genetics, Inc. DNA pool arrays will be made available at a reasonable cost to those who prefer PCR screening approaches. EST and array approaches will continue to expand by Burnside and colleagues, Cheng, and others in the U.S. and by collaborators in Europe.

OBJECTIVE 3: Database and other map resources.

The chicken ChickGBASE database will continue to be updated and improved at the Roslin Institute and the Iowa State mirror site. Newsletter and homepage information will be distributed and enhanced. We will continue to distribute reference panel DNAs, expanded microsatellite primer panels, BAC library resources and Type I gene-based primer panels. Groenen and colleagues expect to make a ChickAce (Acedb format) database available by the end of the year.

(Prepared 12/15/00)