2007 Annual Report 1a.Objectives (from AD-416) The objective of this cooperative research project is to identify quantitative trait loci (QTL) corresponding to gastro-intestinal (GI) parasite infection and disease phenotypes measured from a sheep research population (Dorper x Red Masaii) developed and maintained by the International Research Livestock Institute (ILRI) in Nairobi, Kenya. The results of this study will be used to identify new QTL and validate results for similar disease-related QTL identified using the Beltsville Agricultural Research Center (BRC) Angus population. 1b.Approach (from AD-416) Sheep genomic DAN (N=35) from grandparents, F1 sires, and backcross progeny was imported from Animal Genetic Resources at ILRI to the Bovine Functional Genomics Laboratory (BFGL) at BARC with the guidance of APHIS. Using the international sheep linkage map (v.3), more than 40 DNA markers with utility in both cattle and sheep were selected from 6 sheep chromosomes that corresponded to cattle chromosomes containing potential QTL for parasite indicator traits. Genotypes from these markers will be generated and scored to tract the inheritance of chromosomal segments from grandparents to test progeny with phenotypic data for parasite disease and infection. QTL mapping analyses will be done to identify which, if any, of these six chromosomes contain QTL comparable to this found in the BARC Angus herd. 3.Progress Report This report documents research conducted under Specific Cooperative Agreement between ARS and the International Livestock Research Institute (ILRI) in Nairobi, Kenya. Additional details of the research can be found in the report for the parent in-house project 1265-31000-081-00D, “Identification, validation and fine-mapping of quantitative trait loci in dairy cattle.” Efforts were focused on improving the QTL analysis of this sheep backcross populations as previous preliminary analyses had failed to develop the appropriate statistical models for QTL detection and ignored unlikely genotypic marker scores denoting double recombination events which inflated map distance and affected marker order. Our laboratory has genotyped another 21 microsatellite markers from this population to fill in gaps in genome coverage, and started QTL detection using transformed phenotypes and a more sophisticated analysis package, QxPak. This project will end in December, 2007 with a publication comparing QTL derived from three different statistical analyses. Monitoring activities with this project include monthly teleconference calls with the other collaborating institutions. This research continues to support the objective of in-house project to characterize conserved genome elements and identify functional genetic variation (objective #3).