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.

During the current year geneticists continued to add to the resolution of the gene map of the horse by the addition of genes, genetic markers and genomic information. There also were several key publications that deserve special mention. Milenkovic et al., (2002) reported localization of 136 additional genes to the cytogenetic map of the horse, increasing the number of cytogenetic localizations to 284. .Raudsepp et al. (2002) used a radiation hybrid map to determin the linear order of 34 genes on the X chromosome, demonstrating conservation of order when comparing human and horse X chromosomes. Chowdhary et al., (in press) is publishing the first comprehensive radiation hybrid map for the horse. This map comprises 730 loci including 258 type I loci and 472 type II loci. The map represents a significant improvement in the resolution of the linear map as well as a strong addition to the comparative gene map.

Work at the University of Georgia, Texas A&M University, University of Minnesota, University of California, Cornell University, Tufts University and University of Kentucky added EST markers to the Genbank Database for use in comparative mapping and microarray studies of gene expression.

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.

Work in press includes publication of the workshop linkage map (Guérin et al., in press) which includes 344 informative loci and, for the first time, linkage groups identified on all autosomes. This map is based on a half-sibling family and is comparable in size and coverage to the linkage map reported by Swinburne et al. (2000) based on a full sibling map. In addition, the resolution of the linear map was dramatically improved with the addition of the radiation hybrid map described above (Chowdhary et al., in press).

Genome scanning panels and the map were used to investigate simple genetic traits encoding coat color variation in horses. Three reports were published identifying ECA 25 as the location of the gray gene for the horse (Locke et al., 2002; Swinburne et al., 2002; Henner et al., 2002). The precise gene responsible for the trait is still under investigation. A SNP sssociated with Tobiano coat color was identified (Brooks et al., 2002). In addition a mutation responsible for junctional mechanobullous disease in Belgian horses was identified (Spirito et al., 2002) and a diagnostic test set up (Lee Millon, personal communication).

Progress relative to Objective 3:

1. Primers for a Genome Scanning Panel:

Currently there is a panel of 100 markers available. Development of additional markers for the panel remains a priority for the workshop.

2. Websites and Databases:

A 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://texas.thearkdb.org/

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 Domenico Bernoco of Stormont Laboratories, 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: An 11X BAC library has been created by Pieter DeJong, under the auspices of the USDA NRI program and copies were been distributed to Cornell University, University of California, University of Kentucky, Texas A&M University, Animal Health Trust/Newmarket,UK and INRA/Jouy-en-Josas, France. Filter sets distributed to these and additional 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. A first publication is described above.

Progress relative to Objective 4 (Research Priorities): Research priorities are set by consensus during discussions at the conferences. During 2002 priorities were established at PAG 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 radiation mapping panel, meeting support for the Gordon Conference on Quantitative Genetics and Biotechnology, meeting support for the North American Colloquium on Animal Cytogenetics and Gene Mapping, travel support for technical committee members to attend the PAGVIII meeting in San Diego, coordinator travel to support gene mapping work, travel support for technical committee members to attend meetings on topics directly related to NRSP8 interests, resources for development and distribution of the BAC library, use of the linkage family materials and support of marker development for linkage mapping.

References

Brooks, S.A., R.B. Terry and E. Bailey (2002) Association of PCR-RFLP for KIT with Tobiano coat colour in horses. Animal Genetics 33: 301-303.

Chowdhary BP, Raudsepp T, Kata SR, Goh G, Millon LV, Allan V, Piumi F, Guérin G, Swinburne J, Binns M, Lear TL, Mickelson J, Murray J, Antczak DF, Womack JE, Skow LC (2002). The first generation whole genome radiation hybrid map in the horse identifies conserved segments in human and mouse genomes. Genome Research (in press).

Henner, J., P-A. Poncet, G. Guérin, C. Hagger, G. Starnzinger, S. Rieder (2002) Genetic mapping of the (G)-locus responsible for the coat color phontype "progressive graying with age" in horses (Equus caballus). Manmmalian Genome 13: 535-537.

Locke, MM, MCT Penedo, SJ Bricker, LV Millon, JD Murray (2002) Linkage of the grey coat colour locus to microsatellites on horse chromosome 25. Animal Genetics 33: 329-337.

Milenkovic D, Oustry-Vaiman A, Lear TL, Billault A, Mariat D, Piumi F, Schibler L, Cribiu E, Guérin G (2002). Cytogenic localization of 136 genes in the horse: comparative mapping with the human genome. Mammalian Genome 13:524-534.

Pascual, I., A. K. D. Dhar, Y. Fan, M.R. Paradis, M.V. Arruga, A. Alcivar-Warren (2002) Isolation of expressed sequence tags from a Thoroughbred horse 5'-RACE cDNA library. Animal Genetics 33: 231-232.

Raudsepp T, Lear TL, Chowdhary BP (2002). Comparative mapping in equids: the asine X chromosome is rearranged compared to horse and Hartmann's mountain zebra. Cytogenetics and Genome Research 96:206-209.

Spirito, Flavia, A. Charlesworth, K. Linder, J-P Ortonne, J. Baird & G. Meneguzzi (2002) Animal models for skin blister conditions: Absence of laminin 5 causes hereditary junctional mechanobullous disease in the Belgian horse. Society for Investigative Dermatology 119: 684-691.

Swinburne, J., C Gerstenberg, M Breen, V Aldridge, L Lockhart, E Marti, D Antczak, M Egglestone-Stott, E Bailey, J Mickelson, K Röed, G Lindgren, W von Haeringen, G Guérin, J Bjornasson, W.R.Allen and M Binns (2000) First comprehensive low-density horse linkage map based on two, three-generation, full-sibling, cross-bred horse reference families. Genomics 66: 123-134.

Swinburne, JE, A Hopkins, MM Binns (2002) Assignment of the horse grey colt coulur gene to ECA25 using whole genome scanning. Animal Genetics 33: 338-342.