PROJECT: NRSP-8 Horse Genome Coordinator

COOPERATING AGENCY AND PRINCIPAL LEADER:

University of Kentucky: Ernest Bailey

PROGRESS OF THE WORK AND PRICIPAL ACCOMPLISHMENTS:

Progress relative to Objective 1 (genome map development): The first generation map of the horse was realize with the publication of a linkage study involving 140 markers (Lindgren et al., 1998), a report of a 240 marker synteny map (Shiue et al, 1999) and a manuscript accepted for a 160 marker linkage map (Guerin et al., 1999). In addition, many additional markers have been mapped using fluorescence in situ hybridization bringing the total number of mapped genes to approximately 400 (reviewed in Bailey and Binns, 1998). The span of the two linkage maps was estimated at 679 cM with an average spacing of 12.6 cM and 936 cM with a spacing of 14.2 cM respectively (Lindgren et al., 1998; Guerein et al., 1999).

Progress relative to Objective 2 (database development): A database for the horse gene map was set up at Roslin Institute, Edinburgh, Scotland in the GBASE format used for other databases such as PIGBASE and CHICKBASE. A total of 78 gene mapping references and related information was added to the database. The European co-editor is Matthew Binns at Newmarket, United Kingdom. The database is accessible through the web address:http://www.ri.bbsrc.ac.uk/cgi-bin/arkdb/browsers/browser.sh?species=horseand can be updated by individual scientists followed by acceptance of the editors.

Progress relative to Objective 3 (Shared material and information):

Reference Family DNA: In connection with the International Equine Gene Mapping Workshop, the coordinator distributed DNA for a reference family for linkage mapping which consisted of 12 sires and their 448 offspring. DNA was aliquoted and shipped to 20 laboratories, worldwide, to construct the workshop linkage map. The families were tested for at least 5 DNA based markers and the results reported to Gerard Guerin at a duty laboratory in Jouy-en-Josas, France. The results were analyzed and discussed by the participants at workshop meetings in San Diego in January 1998 and Auckland, New Zealand in August 1998. The results were then prepared in a manuscript which was submitted to the journal, Animal Genetics, and accepted for publication (Guerin et al., 1999). In the Fall of 1998 reference family DNA was shipped to additional laboratories for continuation of the linkage map testing. Each laboratory receives 5 micrograms of DNA from each horse.

CATS Primers: Dr. Leslie Lyons provided this coordinator with CATS primers for distribution to scientists studying horse genetics (Lyons et al, 1997). During 1998 a full set was sent to one laboratory and a partial set sent to two other laboratories.

Communication: The coordinator has maintained an email list of scientists interested in the field of horse genomics research. The list includes 92 individuals, of whom, approximately 30 are actively contributing to development of the gene map. Through this list, individuals are regularly provided titles of manuscripts which have been accepted, notification of up coming meetings, messages broadcast regarding technical observations or requests for information pertaining to the horse. This communication is designed to keep scientists informed and to encourage scientists to become involved in collaborative activities.

Progress relative to Objective 4 (Research Priorities):

Research priorities are set by consensus during discussions at conferences. During 1998 there was a series of meetings concerning the development and application of the horse gene map. The email communication described above was used to share reports of meetings with those who could not attend and to solicit and share their points of view.

In January 1998, the workshop participants met to discuss the status of the linkage map at the Plant and Animal Genome Meeting in San Diego. At that time it was demonstrated that the international reference family was a valuable resource and the workshop linkage map effort was effective. At that time a goal was set to publish a 150 marker map in 1998 and a 300 marker map in 1999.

In March 1998 many of the workshop members participated in a conference at Banbury Center, Cold Spring Harbor, New York to discuss the application of the gene map to performance of horses. The meeting included geneticists working on horses, geneticists working on other species and horsemen. The meeting led to two major areas of agreement: First, horsemen are satisfied with their use of direct selection on performance traits but health related defects are perceived as a greater problem. Although the horseman can select for a competitive horse, too many are lost due to infectious diseases or physical breakdown. Research to solve these problems will probably require genomic information. Second, if the horse gene map is to be used effectively, it must be a high density map. Less than 500 microsatellite DNA markers are known for the horse and several thousand would be required. There is a great need for more funding and research at a greater pace than currently in practice.

The next major meeting was the Conference of the Animal Genetics Society in Auckland, New Zealand during August, 1998. At this meeting the final version of the workshop linkage map was approved. Scientists agreed to work towards the 300 marker linkage map. However, it was also apparent that other opportunities were available for the development of genome maps. Discussions began regarding the development and sharing of BAC libraries, radiation hybrid panels and scientists were strongly encouraged to continue development of genetic markers for the horse including EST, STS and especially microsatellite DNA markers.

PLANS FOR THE FUTURE

The NRSP-8 horse coordinator was not funded until renewal of the NRSP-8 project in October 1998. This funding provides increased opportunities for development of collaborative research.

Objective 1: The workshop linkage map will be tested for up to 300 markers during 1999. A workshop meeting is planned for June 1999 to discuss the data. The synteny mapping panel will be supported to test markers developed by any scientist in preparation for linkage mapping. As we add markers to the map we shall become increasingly aware of regions of the map which are underdeveloped. Use of the synteny panel will allow identification of the markers most valuable to add to the linkage map based on chromosome location. In late 1999 we anticipate making use of one of the radiation hybrid panels which are being developed. This will make it possible to create a linear map with markers regardless of the level of polymorphism and more economically.

Objective 2: The database should be fully updated with all gene mapping references. In additional, idiograms and images of FISH mapped markers should be added to the data base for easy reference. A mirror site should also be established at the Texas A&M computer site for the NRSP-8.

Objective 3: DNA for the reference families will continue to be shared. In addition the NRSP-8 may support development of BAC panel screening to facilitate physical map development and sharing of this resource at Texas A&M. Communication will continue to be promoted through the use of email. A horse gene mapping web site will be established to archive the most important information and to promote this research activity.

Objective 4: Two members of the horse NRSP-8 will participate in the Comparative Gene Mapping workshop to be help in Toulouse, France in May 2,3, 1999. In addition, the International Equine Gene Mapping Workshop is planning two meetings in Uppsala, Sweden. The first, on June 2, 1999 will entail discussion by the horse cytogeneticists to solve several problems concerning agreement on assignment of genes and linkage groups to chromosomes. Following that meeting, the workshop participants will meet in Uppsala from June 3-6 to discuss the linkage map and future development of the horse genome.

References

Bailey E. and Binns M.M. (1998) The Horse Gene Map. International Laboratory Animal Review 39: 171-176.

Guérin G, Bailey E, Bernoco D, Anderson I, Antczak DF, Bell K, Binns MM, Bowling AT, Brandon R, Cholewinski G, Cothran EG, Ellegren H, Förster M, Godard S, Horin P, Ketchum M, Lindgren G, McParlan H, Mériaux J-C, Mickelson JR, Millon LV, Murray J, Neau A, Røed K, Sandberg K, Shiue Y-L, Skow LC, Stott M, Swinburne J, Valberg J, Van Haeringen H, Van Haeringen WA, Zeigle J (1999). Report of the international equine gene mapping workshop: male linkage map. Animal Genetics (accepted).

Lindgren G, Sandberg K, Persson H., Marklund S, Breen M, Sandgren B, Carlstén J, Ellegren H (1998) A primary male autosomal linkage map of the horse genome. Genome Research 8: 951-966.

Lyons LA, Laughlin TF, Copeland NG, Jenkins NA, Womack JE, O'Brien SJ (1997). Comparative anchor tagged sequences (CATS) for integrative mapping of mammalian genomes. Nature Genetics 15: 47-56.

Shiue Y-L, Bickel LA, Caetano AR, Millon LV, Clark RS, Eggleston ML, Michelmore R, Bailey E, Guerin G, Godard S, Mickelson JR, Valberg SJ, Murray JD, Bowling AT. 1999. A synteny map of the horse genome comprised of 240 microsatellite and RAPD markers. Animal Genetics 30: 1-9.