Location:2008 Annual Report
1a. Objectives (from AD-416)
1. Develop germplasm and DNA/tissue collection coupled with measurement of diversity. 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.
3. Progress Report
Genetic security has improved as the collection has increased in size by more than 25% and there are now approximately one-half million samples in the repository. The number of breeds has also increased from 112 to 136. Significant strides were made in developing the second version of the animal database with Brazil and Canada joining the development effort. For six months an EMBRAPA (Brazil) database programmer has been detailed to this location to work with NAGP and Canadian programmers. Agriculture and Agri-Foods Canada periodically send their programmer for extended stays. This has resulted in harmonizing the development efforts and goals for the new version. Important work has been accomplished in the development of parameters for evaluating sperm quality. This CRIS has identified the optimal range of temperatures and pH for shipping fresh boar semen. Applying this result will improve the quality of germplasm cryopreserved by NAGP and can be used by the boar stud/pig breeding segments of the swine industry as they ship fresh semen to their customers. Very encouraging results have been obtained using computer assisted sperm analysis (CASA) in evaluating dairy bull semen and relating those results to fertility. Combining key CASA parameters and allowing for their compensatory effects upon each other appears to enable the identification of bulls with above average fertility. This effort will continue into the next fiscal year and be extended to boar sperm. Understanding the genetic relationships between US sheep breeds is useful in developing conservation strategies and actions. A broad sampling of individual sheep from 28 breeds was performed. DNA was extracted from the samples and genotyped. The following breeds were found to have relatively high inbreeding values: Columbia, Gulf Coast Native, Jacob, and Targhee suggesting genetic diversity is an issue for rare breeds and some commercially popular breeds. Genetic distances (which range from 0.0 to 1.0, with 0.0 being no genetic diffrence) were computed and ranged from 0.08 for Hampshire - Suffolk to 0.80 for the combinations of Blackbelly Barbados – Black Welsh Mountain, and Hog Island – Tunis. These data provide a baseline for determining the degree of genetic similarity between US sheep breeds. With this information germplasm collection activities can be refined, thereby ensuring that germplasm collections capture the genetic diversity needed to safely conserve sheep populations. This result is a component of the ARS National Program 101, Component I: Understanding, improving and effectively using animal genetic and genomic resources; and the National Program Action Plan Problem Statement: Preserve and curate livestock and poultry genetic resources.
1. Genetic security increased. Globally, genetic diversity is contracting across livestock species, development of comprehensive ex-situ-cryopreserved germplasm collections in genebanks offers a level of genetic security for the livestock industry and research community. During FY2008 the collection and preservation of animal genetic resources has increased by 29% and this includes fully securing the following types of populations: 10 breeds, seven commercial pig lines and 38 chicken strains. The number of populations that have exceeded 50% of the minimum collection requirement increased from 63 to 88. As a result of the collections growth there is ready access to various sources of germplasm should the livestock industry need it. This result is a component of the ARS National Program 101 component 1: Understanding, improving and effectively using animal genetic and genomic resources; and the National Program Action Plan Problem Statement c: Preserve and curate livestock and poultry genetic resources.
2. Determining germplasm collection requirements for chickens. Knowing the quantity of germplasm necessary to reconstitute a population is one requirement for genebanks to use in setting goals for germplasm collections. FAO has recommended that to secure a chicken breed, at 150% of reconstitution needs, genebanks have 2,454 straws (0.5 ml) of semen. In FY2007 this project evaluated inseminating hens intramagnally vs intravaginally and found the intramagnal procedure significantly better. In FY2008 econometric procedures were used to evaluate the maximum efficiency and duration by which fertile eggs could be obtained from a single insemination. These results showed that maximum efficiency occurred at day 8 and fertile eggs could be harvested until day 17. This finding significantly impacts the development of germplasm collections for chickens. By using intramagnal insemination, rather than intravaginal insemination the number of units of germplasm required to secure a breed can be reduced from 2,454 to 386. The impact of this finding is that collections of germplasm from chicken breeds can be secured more rapidly at a lower cost of collection and a lower storage cost. This result is a component of the ARS National Program 101, Component I: Understanding, improving and effectively using animal genetic and genomic resources; and the National Program Action Plan Problem Statement c: Preserve and curate livestock and poultry genetic resources.
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. These linkages support germplasm collection, interaction on research problems, and management of in-situ populations for genetic diversity. In certain instances these partners are leading conservation efforts for specific breeds (e.g., Spanish and Tennessee Stiff-legged goats).