2009 Annual Report
1a.Objectives (from AD-416)
1. Develop germplasm and DNA/tissue collection coupled with measurement of
o Continue to develop germplasm collections across species and associated information.
o Evaluate, refine and implement pedigree clustering approach for germplasm collection.
o Pursue approaches to compare collection to in-situ populations using quantitative and/or molecular approaches.
o Develop collections of DNA and/or tissues containing DNA and associated information.
2. Further develop the animal section of the GRIN network.
o Develop database information system that documents the germplasm/tissue collection (Version.
2)and has multi-location capacity.
o Expand descriptors for all species as defined by species committees, and substantially increase data collection efforts.
3. Develop methods for population regeneration.
o Computationally determine approaches for population regeneration and their management.
4. Improve cryopreservation methods for tissues.
o Development of predictors/evaluation of post-thaw semen viability.
o Procedures for collection and freezing of small ruminant and/or beef oocytes.
o Determination of optimal semen cryopreservation diluents and freezing methodologies.
1b.Approach (from AD-416)
The over-arching goal of the National Animal Germplasm Program (NAGP) is to increase the security of U.S. livestock genetic resources by the development of a repository containing diverse livestock genetic resources. The proposed objectives of this plan are important because they will: strengthen the genetic diversity contained in the collection; improve the ability and efficiency of reconstituting populations through improved cryopreservation procedures and reconstitution strategies; and provide potential collection users with a more comprehensive understanding of what is contained in the collection through the GRIN database. Executing these objectives will require the utilization of quantitative and molecular genetics, reproductive biology, cryopreservation, and information systems science. The beneficiaries of this effort cover a wide spectrum including: livestock breeders; researchers reconstituting populations and performing various types of molecular studies; and the American public at large which benefits from the increased food security the program provides.
Genetic security of livestock populations has been improved as the total collection increased beyond 540,000 samples an 18% increase from the previous year. Significant efforts were made to achieve collection growth for Hog Island and Black Welsh Mountain sheep and seven poultry research lines held by the University of Arkansas. Importantly, the collection has not only grown but during this fiscal year 1,194 samples from 263 animals left the repository for animal generation, germplasm evaluation, or DNA studies.
Database development has been advanced with programmers from Brazil and Canada working at their home institutions or working at our laboratory. The database itself has been completed and work initiated on the necessary forms to enter data into the database.
The genetic distancing study involving US sheep breeds was extended to include five breeds from Kazakhstan. In general the Kazakh breeds were clustered and separate from US breeds, with the exception of the Karakul breed. While the Kazakh breeds tend to be unique, in terms of overall diversity the US breeds appear to have a much greater range of genetic diversity.
In an unfunded cooperative agreement with Louisiana State University, two important question are starting to be resolved. While semen has been cryopreserved since the 1950’s there has never been a controlled experiment documenting the viability of samples that have been stored for long periods of time. Therefore, beef cattle samples frozen from 1969 to 2004 have been used to breed approximately 200 cows. Preliminary results indicate that storage time has not affected fertility. The fertility results and the motility characteristics of each bull will be extended to address objective 4A.
Improving the efficiency of mating procedures with cryopreserved germplasm can insure collection material is effectively used and potentially reduce minimum collection goals. To this end experiments have been performed to evaluate a non-surgical procedure for artificially inseminating sheep. The procedure has been shown effective with fresh ram semen (55% fertility) however, cryopreserved semen is significantly lower and therefore requires additional exploration for methods (e.g., better estrus detection) to overcome this limitation.
Utilization of animal germplasm collection. A genetically diverse germplasm and tissue collection was developed that is available for use by industry and researchers for animal generation or genomic research was developed. A wide array of unique germplasm has been collected and stored in the repository. The collection of germplasm has been used by genomic researchers in the development of genomic tools and analytical tools that enable dairy producers to make more informed choices about the bulls they use to breed their cows. Private industry has used samples from the collection to reintroduce genetic variation and desirable gene combinations.
Genetic security increased. U. S. livestock and poultry genetic resources are contracting while consumer demand is starting to favor the utilization of different genetic resources. The ARS animal germplasm collection grew in quantity and diversity to unprecedented numbers across all livestock species. As a result the livestock industry can access the collection to meet new production challenges and consumer demand. This increase also will enable livestock producers to more quickly establish their populations in the event of a significant outbreak of contagious diseases.
5.Significant Activities that Support Special Target Populations
Many rare breeds are owned by small scale farmers. To capture this diversity for the repository we perform field collections on small farms. Such action provides us with an opportunity to provide small scale producers with information about the breeding soundness of their animals and management of genetic diversity. Significant collaborations exist with a number of historically black colleges and universities in the collection of germplasm. Substantial collaboration and dialog exists between the primary non-governmental organization working in the area of conservation of animal genetic resources. These linkages support germplasm collection, interaction on research problems, and management of in-situ populations for genetic diversity.
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