Hatch Act, as Amended August 11, 1955
January 1 to December 31, 1999
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: Develop high resolution comparative genome maps aligned across species that link agricultural animal maps to those of the human and mouse genomes.
The first generation comparative map for the horse was realized with the publication of a Zoo-FISH map for the horse based on the use of human chromosome paints (Raudsepp et al., 1996). The comparative map was expanded with the mapping of 14 genes using fluorescence in situ hybridization (FISH) (reviewed in Bailey and Binns, 1998). During the current year a 240 marker synteny map was reported (Shiue et al, 1999) including genes as well as polymorphic microsatellite DNA markers. Other studies were reported in which genes were mapped to chromosomes using FISH, synteny mapping or used chromosome specific paints, (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).
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.
Prior to this year a linkage map was published based on 140 markers (Lindgren et al., 1998) This year a manuscript for a 161 marker linkage map (Guerin et al., 1999) expanded the level of gene mapping for the horse. 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; Guerin et al., 1999). Overlap of markers between the two maps was approximately 30%. During 1999 and 2000 two second generation linkage maps are being developed based on a total of 300 markers tested on the International Horse Reference Family Panel (500 half-sibs) and with approximately 350 markers tested on a full sib family. With achievement of this level of coverage, it will be 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 or by FISH.
Progress relative to Objective 3: Expand and enhance internationally shared species genome databases and provide other common resources that facilitate genome mapping.
Databases: 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, although a mirror site is scheduled to be set up at Texas A&M University. 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.
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 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 to Gérard Guérin for analysis.
CATS Primers: Dr. Leslie Lyons provided this coordinator with CATS primers for distribution to scientists studying horse genetics (Lyons et al, 1997). During 1998-1999 the complete set was distributed.
Bacterial Artificial Chromosome (BAC) Libraries: BAC libraries have been developed at INRA, Jouy-en-Josas, France and at Texas A&M University. Both libraries have approximately 1.5X coverage of the genome. The libraries can be screened for genes of interest as a collaborative activity with scientists at those institutions.
Progress relative to Objective 4 (Research Priorities):
Research priorities are set by consensus during discussions at conferences. During 1999 priorities were established to:
1. Develop more markers for mapping, including polymorphic microsatellite DNA markers and gene sequences, commonly known as 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 to 500 markers.
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 1999 to support development of the equine database, the synteny mapping panel, the BAC library at Texas A&M University, 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
Bailey, E.; Binns M.M. (1998) The Horse Gene Map. International Laboratory Animal Review 39: 171-176.
Caetano A.R., Lyons L.A., Laughlin T.F., O'Brien S.J. , Murray J.D. and Bowling A.T. . (1999a) Equine synteny mapping of comparative anchor tagged sequences (CATS) from human chromosome 5. Mammalian Genome 10: 1082-1084.
Caetano A.R., Pomp D., Murray J.D. and Bowling AT. (1999b). Comparative mapping of 18 equine Type I genes assigned by somatic cell hybrid analysis. Mammalian Genome 10: 271-176.
Chaudhary, R., T. Raudsepp, X.Y. Guan, H. Zhang, B.P. Chowdhary (1999) Zo-FISH with micordissected arm specific paints for HSA2, 5, 6, 16 and 19 refines known homology with pig and horse chromosomes. Mammalian Genome 9:44-49.
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).
Lear TL, Brandon R, Masel A, Bell K, Bailey E (1999) Horse alpha-1-antitrypsin (AAT), beta-lactoglobulin 1 and 2 (BLG1, BLG2) and transferrin (TF) map to positions 24q15-q16, 28q18-qter, 28q18-qter and 16q23. Chromosome Research 7, 667.
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.
Raudsepp, T., B.P. Chowdhary (1999) Construction of chromosome specific paints for meta and sub-metacentric autosomes and the sec chromosomes in the horse and their use to detect homologous chromosomal segments in the donkey. Chromosome Research 6:103-114.
Raudsepp, T., J. Kijas, S. Godard, G. Guerin, L. Andersson, B.P. Chowdhary (1999) Comparison of horse chromosome 3 with donkey and human chromosomes by cross-species painting and heterologous FISH mapping. Mammalian Genome 10: 211-282.
Raudsepp, T.; Fronicke, L.; Scherthan, H.; Gustavsson, I.; Chowdhary, B.P. (1996). Zoo-FISH delineates conserved chromosomal segments in horse and man. Chromosome Research 4: 1-8.
Senese, C., MCT Penedo, Y.L. Shiue, AT Bowling, LV Millon (1999) A HaeIII PCR-RFLP in the ZFY/ZFX genes of horses. Animal Genetics 30: 382-405.
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.
