1a. Objectives (from AD-416):
The ARS Project Plan has the objectives to generate genome-wide information on genetic variation that will enable genetic diversity studies in native goats of Africa, facilitate improved germplasm preservation decisions based on this data, and provide information necessary to initiate large scale genetic improvement programs in Africa. Using this approach, we intend to develop good scientifically based tools for animal improvement programs in Africa and to establish a cooperative network in such a way that the individual country breeding programs can leverage the efforts of one another and provide a nexus to enhance the cooperative efforts of advanced research institutions, such as ARS and ILRI. The Cooperator has: 1) continental expertise in locally adapted breeds and livestock animal improvement programs, 2) experienced personnel for identifying and sampling representative goat populations, and 3) facilities to host the inaugural workshop and for laboratory activities to aid sample preparation for genomic analysis. The facilities are located in a region of some relevant resource target populations, and the Cooperator’s locations can serve as hubs future scientific activities for this cooperative network of researchers studying genomics in ruminants of Africa.
1b. Approach (from AD-416):
ARS and the Cooperator will co-organize an inaugural workshop for a focused group of scientific and institutional research program experts that will attempt to determine the best approaches for developing genome-based tools and sampling current populations for animal improvement programs in Africa. The overall goal of this workshop will be to develop a mutually agreeable and actionable plan for all the research partners. From this time forward, the Cooperator will work with ARS in designing experimental plans for sample collection to generate the resource population of goats that will represent locally adapted breeds of importance. The overall goal of this cooperation is to provide a suitable environment to ensure reliable recording of phenotypes, and facilities, if needed, for temporary storage and/or extraction of genomic DNA from tissues that may not be importable into the U.S. ILRI locations may also provide training for ILRI and other collaborative scientists participating in this project as needed. ARS will serve initially as the genome characterization center for the resource population and the goat genome assembly and as a training facility to build genome analyses capacity with ILRI and other African scientists. Eventually, the results of characterizing the genomes of African goats will lead to the development and application of new breeding strategies to be implemented jointly by the Cooperator and ARS scientists with other African partners. These tools will be available to other global partners interested in application of goat genome results.
3. Progress Report:
The objective was to catalyze a cooperative effort to apply genomic tools to characterize the goat genomes of locally adapted, native breeds throughout sub-Saharan Africa. This information would help to develop genomic tools for animal improvement programs in Africa and provide a nexus to enhance the cooperative efforts of advanced research institutions, such as ARS and International Livestock Research Institute (ILRI). In the previous year, ILRI scientists aided ARS scientists in collecting more than 500 goat samples in Ethiopia, Kenya, and Cameroon. DNA from most of these samples was transferred to ARS for genetic analysis using the Caprine53K SNP beadchip (53,000 SNP). In addition, ILRI hosted a workshop to initiate collaboration and outreach to African partners in Uganda, Tanzania, and other Sub-Saharan countries. ARS paid and hosted a post-doctoral scientist from ILRI, who was trained in genomic methods of population genetics and bioinformatics of next-generation sequence analysis. This research supported all three objectives of an in-house project to develop biological resources and computational tools to enhance characterization of ruminant genomes, utilize genotypic data to enhance genetic improvement of food animals across a spectrum of ruminant production systems, and characterize functional genetic variation for environmental sustainability of ruminants.