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 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.

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, Genomics 13, 690-697, 1992), and the East Lansing population (Crittenden et al., Poultry Science 72, 334-348, 1993). Subsequently, the map has been enhanced by genotyping of a third cross, the Wageningen population, by Martien Groenen and colleagues (Groenen et al., Genomics 49, 265-274, 1998). A consensus map based on all three map populations has been published (Groenen et al., Genome Res. 10:137-147, 2000). Recent updates (Schmid et al., Cytogenet. & Cell Genet. 90:169-218, 2000) bring the number of markers on the consensus map to 1965, placed into 50 linkage groups, covering around 4000 cM. The East Lansing map has expanded to 1186 markers on 49 linkage groups. Of these, 512 are microsatellite markers. Nearly 300 genes have been mapped in the East Lansing map. Evidence continues to grow that gene order is conserved between the human and chicken genomes to a remarkable extent. Several studies have appeared (Burt et al., Nature 402:411-413, 1999; Groenen et al., op. cit.; Waddington et al., Genetics 154:323–332, 2000; Suchyta et al., An. Genet. 32:12-18, 2001) that estimate between 100 and 200 breakpoints in gene order separating the human and chicken genome, with some blocks of conserved synteny (not necessarily gene order) exceeding 100 cM. Most microchromosomes are now marked by hybridization tags and have been associated with the appropriate linkage group (Schmid et al., op. cit.).

PROGRESS TOWARD OBJECTIVE 2. Physical maps and map integration.

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 114 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 1680 scientists attended the joint Plant and Animal Genome IX meeting held last January, held jointly with the annual NAGRP meeting. Coordination funds helped support attendance at PAG-IX and will do so again for the upcoming PAG-X. A small amount of support was also provided for the Gordon Conference on Quantitative Genetics and Genomics last year.

PLANS FOR THE FUTURE.

OBJECTIVE 1. High resolution poultry genome maps.

Efforts will be made 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.

One or more full genome physical maps using BAC contig-building strategies and radiation hybrid panels should be available in FY 2003. Additional efforts will be made to fill gaps between contigs, improve map resolution and integrate these physical maps with existing linkage maps. EST and array approaches will continue to expand for both chicken and turkey in the U.S. and in Europe. Hopefully, full sequencing of the chicken genome will begin no later than FY 2003.

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 (library, clones, filter sets, PCR screening pools) and Type I gene-based primer panels. RH panel DNAs will be made available, pending agreement with INRA.

(Prepared 1/07/02)