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) During the current year, progress was made in development of radiation hybrid panels for comparative map development (one at Texas A&M and one at Cambridge, United Kingdom) as well as continued publication of genes mapped to chromosomes using FISH. One report described the use of a radiation hybrid panel from Cambridge to map genes to chromosomes 1 and 10 of the horse (Kiguwa et al., 2000). Other studies, submitted or published this year identify other genes that increase the resolution of comparative maps (Lear et al., 2000; Lindgren et al., 2000a; Lindgren et al., 2000b; Mariat et al., 2000; Godard et al., 2000). Several laboratories sequenced cDNA clones for development of ESTs however those works have not yet been published.

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.

During the current year, the horse gene map was significantly advanced with the publication of a linkage map based on a full-sibling horse family and tests of 353 markers (Swinburne et al., 2000a). This work described 37 linkage groups assigned to all 31 autosomes plus the X chromosome; the average interval between markers was 10.5 cM with a collective span of 1780 cM. This study corroborated information from previous linkage map studies and expanded the map by addition of markers. Previous contributions described two maps with a span of 679 cM and 936 cM and with an average spacing of 12.6 cM and 14.2 cM respectively (Lindgren et al., 1998; Guérin et al., 1999). Overlap of markers between the three maps is significant but not complete. During 2000-2001 a second generation linkage map is being developed based on approximately 330 markers tested on the International Horse Reference Family Panel (500 half-sibs). With achievement of this level of coverage, it becomes possible to apply these maps for investigation of economically important traits in horses. The physical, comparative and linkage maps are being integrated by corroborative mapping of genes and microsatellites on the somatic cell hybrid panel, by FISH or by testing on the radiation hybrid map. Other studies greatly added to the number of microsatellite loci available for future linkage mapping (Bailey et al., 2000; Tozaki et al., 2000a,b,c; Swinburne et al., 2000b; Roberts et al., 2000; Caetano et al., 2000; Lindgren, 2000; Kakoi et al., 2000; Bjørnstad et al., 2000). At this time, approximately 506 polymorphic genetic markers have been tested and 495 localized to the horse gene map. An additional 100 polymorphic markers have been reported but not yet mapped.

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:
For application of the gene map information developed by the workshop, 102 pairs of primers were synthesized with support of the Dorothy Russell Havemeyer Foundation and Applied Biosystems, Incorporated (ABI). These primers are specific for 102 microsatellite DNA markers and were selected based on their polymorphism and their distribution on the horse map. One primer of each pair is labeled with a fluorescent dye suitable for analysis with the ABI fragment analyzers. These primer sets are available to participants in the International Equine Gene Mapping Workshop for research purposes. A total of 32 sets were ordered and 5 have been distributed.

2. Websites and Databases:
A new website was added 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 Gérard Guérin 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. CATS Primers: Dr. Leslie Lyons provided this coordinator with CATS primers for distribution to scientists studying horse genetics (Lyons et al, 1997). By 1998-1999 the set was completely distributed.

6. Bacterial Artificial Chromosome (BAC) Libraries: BAC libraries have been developed at INRA, Jouy-en-Josas, France and at Texas A&M University. Contacts for use of those resources are Dr. Gérard Guérin and Dr. Loren Skow, respectively. Both libraries have approximately 3X coverage of the genome. The libraries can be screened for genes of interest as a collaborative activity with scientists at those institutions. NRSP-8 funds were provided to the laboratory at Texas A&M for development of the BAC panel.

7. Synteny Mapping Panel: A somatic cell hybrid panel is available for synteny mapping markers. This resource has been used to create a framework map, map non-polymorphic genes to chromosomes and verify the chromosomal location of genes mapped using other techniques. To use the panel scientists may provide oligonucleotide primers suitable for PCR amplification of the gene to Dr. Jim Murray of the University of California, Davis. NRSP-8 funds have been used to develop this resource in previous years.

8. Radiation Hybrid Panel: Two radiation hybrid panels have been developed and are planned for use by the workshop. At present only the radiation hybrid panel at Texas A&M is subject of collaborative work. To contribute or use this resouce, 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 2000 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 panel for linear mapping of both polymorphic and EST markers.
3. Increase the density of markers on the linkage maps.
4. Develop and use the BAC libraries.
5. Development of marker sets for distribution and use in genome scanning studies.

Funds from the horse species coordinator were used during 2000 to support development of the equine database, the synteny mapping panel, the BAC library at Texas A&M University, meeting support for the Animal Genetics Society in Minnesota during July 2000, Gordon Conference on Quantitative Genetics and Biotechnology during February 2001 and the Northa American Colloquium on Gene Mapping and Cytogenetics of Domestic Animals, travel support for technical committee members to attend the PAGVII meeting in San Diego, coordinator travel to support gene mapping work, and support of marker development for linkage mapping.

References

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