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

In previous years, a low resolution human-horse comparative map was established based on a Zoo-FISH map for the horse using human chromosome paints (Raudsepp et al., 1996), a synteny map based on somatic cell hybrid panel (Shiue et al, 1999) as well as other studies in which genes were mapped to chromosomes using FISH, synteny mapping or chromosome specific paints, (for example, Lear et al., 1999; Raudsepp et al., 1999a; Raudsepp et al., 1999b; Chaudhary et al., 1999; Senese et al., 1999, Caetano et al., 1999a, Caetano et al., 1999b, Lear et al., 2000; Lindgren et al., 2000a; Lindgren et al., 2000b; Mariat et al., 2000; Godard et al., 2000) and use of a radiation hybrid mapping approach (Kiguwa et al., 2000; Chowdhary et al., submitted).

During the current year the workshop group met in Brisbane Australia, under the auspices of the Dorothy Russell Havemeyer Foundation to evaluate progress and consider future priorities. A compilation of published and unpublished data showed that the number of mapped markers exceeded 1000 (workshop, unpublished data) of which 875 appear in the horse genemapping database at Jouy-en-Josas. A need was identified for additional markers and several groups have been working on development of ESTs (Cornell, Kentucky, Georgia, Texas, California, France and Tufts) as well as microsatellite markers (Minnesota, Japan, New Market). Genes continue to be added to the half-sib (354) and full sib linkage maps (587).

Progress relative to Objective 2: Increase the marker density of existing linkage maps used in QTL mapping and integrate them with physical maps of animal chromosomes.

As noted above, the density of markers on the gene map has increased significantly. Over 1000 genes have been mapped as of July 2001. A high priority was placed on development of a radiation hybrid map using a resource developed at Texas A&M by Bhanu Chowdhary and Loren Skow. Preliminary work is being completed on that map based on a framework of 800 markers. In addition the workshop linkage maps have increased to 354 for the half-sibling map and 587 for the full-sibling map. A genome scanning panel of 100 markers has been developed by the workshop group and freely provided to participants. The panel has been distributed to 12 labs and investigations are underway to identify genes responsible for traits of health or economic interest in horses. Several publications are submitted.

Progress relative to Objective 3: Expand and enhance internationally shared species genome databases and provide other common resources that facilitate genome mapping.

1. Primers for a Genome Scanning Panel:

Currently there is a panel of 100 markers available. The workshop group has investigated alternative means for developing such panels and anticipate development of a 300 marker panel in 2002.

2. Websites and Databases:

A new website is maintained with information describing the workshop efforts and significant developments for the horse gene map. The address of that website is:

http://www.uky.edu/Ag/Horsemap/

Two databases exist for the horse:

http://www.ri.bbsrc.ac.uk/cgi-bin/arkdb/browsers/browser.sh?species=horse

This database is situated in Edinburgh, Scotland, with a mirror site at Texas A&M University.

http://bos.cvm.tamu.edu/cgi-bin/arkdb/browsers/browser.sh?species=horse

The species coordinator for the horse, Dr. Ernest Bailey, shares curator duties with the technical staff at Roslin Institute, Edinburgh.

The second database is located at:

http://locus.jouy.inra.fr/cgi-bin/lgbc/mapping/common/intro2.pl?BASE=horse

This database is curated by Dr. Gérard Guérin at INRA at Jouy-en-Josas.

3. Reference Family DNA: In connection with the International Equine Gene Mapping Workshop, the coordinator distributed DNA for a reference family for linkage mapping that consisted of 13 sires and their 500 offspring. DNA aliquots are available in 5 microgram amounts for shipment to laboratories, worldwide for work on the linkage map. The results must be reported in a standard format to Gerard Gue¦rin of Jouy-en-Josas, France, for analysis.

4. Full-sibling Family for Linkage Mapping: A family based on full siblings has been described and used for creation of a linkage map for the horse (Swinburne et al., 2000). To expand the map, workshop participants are strongly encouraged to contact the laboratory at the Animal Health Trust about adding new markers to this map. Scientists will be provided parental DNA to determine the level of polymorphism of the markers in this family. If the markers appear useful, then they will be further tested with DNA samples of the offspring at the Animal Health Trust in Newmarket.

5. Bacterial Artificial Chromosome (BAC) Libraries: A 10X BAC library has been created by Pieter DeJong, under the auspices of the USDA NRI program and a copy has been distributed to Cornell University and Texas A&M University. Filter sets are being distributed to interested laboratories.

6. Radiation Hybrid Panel: A radiation hybrid panel at Texas A&M is subject of collaborative work. To contribute or use this resource, scientists contact Dr. Loren Skow or Dr. Bhanu Chowdhary at Texas A&M University.

Progress relative to Objective 4 (Research Priorities):

Research priorities are set by consensus during discussions at the conferences. During 2001 priorities were established at PAGVIII to:

1. Develop more markers for mapping, including microsatellite DNA markers and expressed sequence tags (EST).

2. Development of a radiation hybrid map.

3. Increase the density of markers on the linkage maps.

4. Develop and use the BAC libraries, especially with application to contig construction in anticipation of genome sequencing.

5. Development of larger marker sets for distribution and use in genome scanning studies.

6. Develop tools for use in functional genomics.

Funds from the horse species coordinator were used during 2000 to support the synteny mapping panel, the BAC library at Texas A&M University, meeting support for the Gordon Conference on Quantitative Genetics and Biotechnology during February 2001 travel support for technical committee members to attend the PAGVII meeting in San Diego, coordinator travel to support gene mapping work, resources for development and distribution of the BAC library, use of the linkage family materials and support of marker development for linkage mapping