Progress 01/01/06 to 08/31/07
Outputs
OUTPUTS: The objective of the specific project was to augment the density of polymorphic markers in the linkage map to improve upon its efficiency to identify hereditary traits in the horse. Three hundred new microsatellites markers were screened of which 214 were found to be polymorphic. The 214 markers were genotyped in the consortium resources - the International Horse Reference Family Panel and the two full-sib families developed at the Animal Health Trust. Linkage analysis assigned 170 markers to 30 of 31 autosomes and 8 markers to the X chromosome, with 83 markers being added to the linear order and 93 given approximate locations within chromosomes. In addition, targeted map expansion was done using BAC-end sequences or the horse whole genome sequence to increase marker density in four chromosomal regions in order to refine the location of four traits - coat colors Dun, Roan and Splash White, and the neurological defect cerebellar abiotrophy in Arabian horses. For the targeted development, a total of 55 polymorphic microsatellites and 14 single nucleotide polymorphisms (SNPs) were developed and mapped in the trait-specific mapping resources that we assembled. Outputs from the consortium linkage map were shared with other members of the group at workshops and conferences. The linkage map produced in this project was one of the resources used by The Broad Institute to assist in the assembly of the whole genome sequence of the horse, first released in January 2007. The map was also used for integration with the high-density physical and comparative map produced by other consortium members. Outputs from the targeted map expansion were used to implement linked-marker genetic tests for cerebellar abiotrophy, Dun and Roan, available to owners through the Veterinary Genetics Laboratory, U.C. Davis. PARTICIPANTS: Maria Cecilia T. Penedo, PI/PD. Conceived experimental design, collected genotype data, performed linkage analysis and map construction. Conceived intelectual content and experimental design for targeted map development for fine-mapping of traits. James D. Murray, Co-investigator. Contributed intelectual content and provided critical input to fine-mapping experiments and results. Thea Ward, staff. Performed genotyping procedures of microsatellite markers on international reference mapping families. Teruaki Tozaki, Department of Molecular Genetics, Laboratory for Racing Chemistry, Japan. Contributed the majority of microsatellite markers used for linkage map expansion usign international reference families. Stephanie Pedroni, part-time staff and graduate student. Performed genotyping procedures, DNA sequencing, marker development, map building analysis related to mapping of Dun trait. Leah Brault, part-time staff and graduate student. Performed genotyping procedures, DNA sequencing, marker development, map building analyses related to mapping of the Cerebellar Abiotrophy trait. Diane Kerr, graduate student. Performed genotyping procedures, DNA sequencing, marker development, map building analyses related to mapping of Splash White trait. Stephanie Jones, graduate student. Carried out genotyping procedures of microsatellite markers, DNA sequencing, marker development, haplotype analyses related to the Roan trait. Dave Adelson, collaborator, Texas A&M University. Provided BAC clones for marker development on horse chromosome 8. Terje Raudsepp and Bhanu Chowdhary, collaborators, Texas A&M University. Provided RH panel and integrated data for development of physical/comparative map. The project provided opportunities for training of two MSc (Kerr, Jones) and two PhD students (Pedroni, Brault). TARGET AUDIENCES: A target audience for the effort of expanding the linkage map of the horse is the international community of geneticists investigating the genetic basis of inherited traits in the horse. The critical target audience for outcomes related to the linked-marker tests developed as an outcome of the project are horse owners and breeders, and veterinarians who benefit from the applications of these tests. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.
Impacts
The increase of marker density and chromosome coverage to improve the utility of the horse linkage map for mapping genetic traits was attained. While the project was initially conceived to create a "stand-alone" linkage map, the focus was redirected to support the horse whole genome sequencing project approved by the National Human Genome Research Institute in 2005. The map developed using the Consortium mapping families was one of the resources used by The Broad Institute to assist in the assembly of the whole genome sequence of the horse, publicly available to the scientific community since January 2007. A manuscript titled "Genome sequence, comparative analysis and population genetics of the domestic horse (Equus caballus)" is in preparation by The Broad Institute scientists and consortium collaborators. The targeted map expansion in four horse chromosomes allowed the fine-mapping of four traits and identification of conserved haplotypes segregating with Cerebellar Abiotrophy, and with coat colors Dun and Roan. While identification of specific genes and mutations responsible for these traits are the focus of continuing research, the linked-marker tests already impact the horse breeding industry. Arabian horse breeders can manage a genetic health problem (cerebellar abiotrophy) through identification of disease-carrier animals, and selection of breeding pairs to eliminate the risk of producing affected foals. Veterinary practitioners have a genetic tool to assist with differential diagnosis of neurological problems in Arabians. Since the test was made available in February 2008, over 300 animals from lineages at risk have been tested. Selection for phenotypic traits such as coat color is an integral part of horse breeding industry. The linked-marker tests for Dun and Roan add to the catalogue of assays for coat color genes. Horse breeders at large use these tests to determine the genetic status regarding coat color traits to implement breeding strategies to produce foals with attractive colors that increase the market value of animals.
Publications
- Brault, L.S., M. C. T. Penedo. Refinement Of The Equine Cerebellar Abiotrophy Locus On ECA2 By Haplotype Analysis. Electronic conference proceedings (abstract). Plant and Animal Genomes Conference XII. January 2009.
- Raudsepp T, Gustafson-Seabury A, Durkin K, Wagner ML, Goh G, Seabury CM, Brinkmeyer-Langford C, Lee EJ, Agarwala R, Stallknecht-Rice E, Schaffer AA, Skow LC, Tozaki T, Yasue H, Penedo MCT, Lyons LA, Khazanehdari KA, Binns MM, MacLeod JN, Distl O, Guerin G, Leeb T, Mickelson JR, Chowdhary BP. A 4,103 marker integrated physical and comparative map of the horse genome. Cytogenetics and Genome Research 2008, 122(1): 28-36.
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