Location: Agricultural Genetic Resources Preservation Research
2021 Annual Report
Objectives
Objective 1: Build, secure, manage, and facilitate the use of the animal genetic resource collection.
Sub-objective 1A: Operate species committees to advise NAGP on collection development and use.
Sub-objective 1B: Targeted acquisition of animals for breeds already in the collection based upon quantitative or molecular genetic analysis, number of animals and germplasm in the collection.
Sub-objective 1C: Acquire samples from breeds not presently in the collection or with limited numbers of animals and samples and minor species (yak, water buffalo or bison).
Sub-objective 1D: Engagement with other countries through the United Nation’s Food and Agriculture Organization (FAO) Intergovernmental Technical Working Group on Animal Genetic Resources.
Objective 2: Development and implementation of the publicly accessible Animal-GRIN V2 database.
Sub-objective 2A: Redesign and develop public facing webpages, perform necessary software upgrades and increase user friendliness of the genomic component of Animal-GRIN.
Sub-objective 2B: Design GIS interface with Animal-GRIN.
Objective 3: Characterize genetic diversity to guide collection development and increase its utility.
Sub-objective 3A: Use quantitative and/or molecular approaches to evaluate and compare genetic variability within and among livestock populations and the collection. Specifically focusing upon: using Yorkshire and Duroc compare in-situ vs. collection genetic diversity; extend molecular characterization of goat breeds; and initiate molecular characterization of water buffalo.
Sub-objective 3B: Combine genomic and production system parameters into a GIS format to assist in making collection decisions as they relate to production systems and climate change.
a. Evaluate genetic diversity of oysters in relation to environmental factors.
b. Gradients of allele frequency for loci associated with geographic regions.
Objective 4: Develop and refine cryopreservation technologies enabling efficient germplasm collection, evaluation, and utilization by gene banks and stakeholders.
Sub-objective 4A: Establish assays using flow cytometry and CASA to evaluate sperm quality.
Sub-objective 4B: Create an inexpensive device and accompanying methods for vitrification of oocytes in bulk.
Sub-objective 4C: Develop quality control standards and best practices for germplasm repositories.
Approach
Genetic resources underpin the livestock sectors ability to improve productivity and contribute to global food security and economic well-being of rural America. Despite the importance of genetic resources there continues to be a contraction of genetic variability nationally and internationally. Furthermore, genetic resources will likely become more contentious under the Convention on Biological Diversity and its Nagoya Protocol. Developing secure collections of germplasm and tissue from U.S. livestock breeds and associated populations is a mechanism to safeguard and promote US interests. To date substantial amounts of genetic resources and information have been curated. Importantly, large numbers of animals in the collection have been used by industry and researchers for a variety of purposes. However, more work is needed to curate germplasm from livestock populations, understand their genetic diversity, enhance effective mechanisms for cryopreservation, and to make the collection available to a wide array of stakeholders and customers via a robust user friendly information system. Steps to achieve such goals are detailed in this project plan. At the end of this project cycle it is anticipated that the germplasm collection will be more robust, better methods and tools will have been developed for collecting, analyzing and utilizing genetic resources.
Progress Report
The USDA National Animal Germplasm Program’s Dairy Species Committee (Subobjective 1A) has raised a red flag for dairy cattle breeders. In their view, the rate of inbreeding for dairy cattle is increasing at rates that may lead to significant losses of genetic variation for major breeds like Holstein and Jersey, which are the world’s two most prominent dairy breeds. This increased inbreeding has been fueled by growth of using genomic breeding values without employing approaches to correct for potential mating among cattle within the breeds mentioned. Accordingly, the committee has developed a white paper articulating the problem and recommending how the National Animal Germplasm Program (NAGP) may alter collection strategies. They have further initiated steps to make the industry aware of this issue by teaming up with the American Dairy Science Association which will support sponsoring a Discover Conference in April of 2022. At this meeting breeders, the artificial insemination industry, and breed associations will engage in a dialog to explore potential solutions and future research directions. This action is not only important for the dairy industry but also underscores the importance of such groups providing informal input to ARS.
The NAGP collection has exceeded 1.1 million samples by adding six new populations or breeds in fiscal year 2021 (Subobjective 1B and 1C). The requested backup of the breeding populations from the second largest swine genetics company, due to the continuing threat of African Swine Flu, is near completion. Germplasm samples from sheep populations were sent to Fort Collins, Colorado, from ARS in Clay Center, Nebraska, to ensure the population is backed up. In fiscal year 2020, 321 samples from 53 animals representing ten breeds exited the repository and were used for live animal regeneration (254), research (65), and DNA analysis (2).
ARS scientists in Fort Collins, Colorado, evaluated genetic diversity for Guernsey (dairy cattle), Charolais (beef cattle), Wagyu (beef cattle), Dorper (sheep), and White Dorper (sheep) breeds to determine long-term inbreeding trends and to categorize the breed into genetic clusters to guide germplasm collection (Subobjective 1B). These breeds were evaluated because they play different roles in the livestock industry; for example, Wagyu are increasing in popularity due to their healthy meat qualities, and Dorper are transforming sheep production in Texas. Inbreeding for the current generations ranged from 5.6% to 10.0%, which are moderate levels. An often-used genetic diversity statistic is effective population size. Charolais had the lowest level of inbreeding and highest effective population size (74). All other breeds had effective population sizes of less than 50, which falls below the Food and Agriculture Organization of the United Nations recommendation that breeders strive to maintain an effective population size of 50. These results suggest the sheep breeds and Wagyu need heightened genetic management as they continue to increase in popularity so that inbreeding does not limit options for selection.
Initiating efforts to use genomic selection requires breeding groups such as the National Sheep Improvement Program to understand the genetic diversity of their breed(s) so that well represented training populations can be constructed. To achieve this goal, ARS scientists in Fort Collins, Colorado, worked with the National Sheep Improvement Program to evaluate genetic diversity of the Suffolk sheep breed, as part of a technology transfer award (Objective 3). We determined the United States Suffolk population is distinct from those in Australia and Ireland, due to genetic drift and selection. Using clustering analyses we determined breeders enrolled in the National Sheep Improvement Program could be placed into distinct breeding groups. We also determined that genetic linkages among these groups was sufficiently large to enable cross flock evaluations to occur, which is necessary in developing genomic selection procedures.
Computer Automated Semen Analysis (CASA) is commonly used across species by the commercial semen industry to objectively evaluate sperm motility and quality, but the results from those analyses are not well understood; this limits the application of that technology for identifying sperm with high or low fertilizing potential. ARS scientists in Fort Collins, Colorado demonstrated that genotype influences the total percentages of motile boar sperm and the quality of motion of those cells when analyzed using CASA. To expand those results, we performed post-thaw CASA analyses using sperm from Jersey and Holstein bulls of known fertility (Subobjective 4A). The data from those analyses will be used to develop models, like the boar models, to identify the sperm motion characteristics that have the most influence on fertilizing potential. In addition, this data will also be used to develop software and tools that will enable CASA users to identify males with sufficient fertilizing potential to use on a wide scale. Refinement of the approach will continue to improve their accuracy and precision. The anticipated product will provide the commercial semen, artificial insemination, and gene banking industries with a new and innovative software tool.
Freezing mammalian eggs (oocytes) is an inefficient and challenging process because of the fragility of the eggs, non-optimized protocols, and the limitations of current methods which are designed to preserve single, rather than batches, of eggs. Those challenges limit the ability of gene banks or assisted reproduction companies to preserve and utilize the genetics of valuable animals effectively and efficiently. ARS researchers in Fort Collins, Colorado, developed a prototype device to rapid freeze large quantities of oocytes, but its structure was too large, generated significant quantities of heat during the freezing process, and was detrimental to oocyte quality and fertilizing ability (Subobjective 4B). Redesign of the device, and subsequent development and comparison of three distinctly different versions, has enabled us to identify the design and materials that provide promising post-warming oocyte quality when vitrifying large quantities of oocytes concurrently. Additional analyses to determine the fertilizing potential of oocytes vitrified with this device and creation of an improved device design that is smaller and more ergonomically friendly are planned.
Establishing quality control standards and best practices is essential to ensure that germplasm can be collected, preserved, evaluated, and utilized, and results in the production of live animals and high-quality samples for the national repository and customers in the assisted reproduction and gene banking industries. To that end, ARS scientists in Fort Collins, Colorado, have established, and are documenting, standards and practices in text and graphic formats (Subobjective 4C). When completed, the final product will provide our customers and collaborators with guidelines to properly preserve germplasm, across species and types of germplasm, and successfully utilize the samples for research, assisted reproduction techniques, and evaluation for quality. Completion of this handbook will enable other gene banks and commercial entities in the animal assisted reproduction industry to enact standards and protocols, while simultaneously establishing a continuity of operations plan for germplasm preservation, evaluation, and use for the National Animal Germplasm Program.
Accomplishments
1. Mapping genetics and heat stress tolerance benefits beef cattle breeding programs. Differences in beef cattle genetics may confer resistance/resilience to environmental stressors like heat, and these genetic differences become more apparent when a population is exposed to environmental conditions over time. Determining how well the USDA National Animal Germplasm Program collection represents genetics capable of adapting to climate stressors is key to future collection development. To start assessing the beef cattle collection, ARS scientists in Fort Collins, Colorado, blended the geographic origin of animals contributing samples to the collection with the average thermal heat index on a county-by-county basis for the 48 contiguous states using geographic information systems. A national map was created where five different thermo-heat index zones were identified and combined with locations that provided samples to the USDA national collection. This allowed the determination of which cattle types in the collection were represented in each thermal heat index zone. The collection’s Brahman type cattle were highly represented in the zone with the highest heat stress (in part, the Gulf Coast region), along with some breeds originating from the United Kingdom and southern Europe. Continental breeds (e.g., Limousin, Salers) and the majority of breeds (e.g., Hereford, Angus, Shorthorn) in the collection came from areas with lower thermal heat index zones. By mapping the beef cattle collection against locations of different heat stress, the geographic gaps in the collection became apparent and can be targeted in future germplasm collection efforts. For the first time, a national map has been created differentiating thermo-heat index zones to assist industry in better matching cattle genotypes to specific environments. The map also indicates that the germplasm collection is broad and diverse among varying thermo-heat zones. Furthermore, the map can be used to identify specific environmental pockets where germplasm from cattle should be collected.
Review Publications
Thorne, J.W., Murdoch, B.M., Freking, B.A., Redden, R.R., Murphy Jr, T.W., Taylor, J.B., Blackburn, H.D. 2021. Evolution of the sheep industry and genetic research in the United States: Opportunities for convergence in the 21st century. Animal Genetics. 52(4):395-408. https://doi.org/10.1111/age.13067.
Oppenheimer, J., Rosen, B.D., Heaton, M.P., Vander Ley, B.L., Shafer, W.R., Schuetze, F.T., Stroud, B., Kuehn, L.A., McClure, J.C., Barfield, J.P., Blackburn, H.D., Kalbfleisch, T.S., Bickhart, D.M., Davenport, K.M., Kuhn, K.L., Green, R.E., Shapiro, B., Smith, T.P.L. 2021. A reference genome assembly of American bison, Bison bison bison. Journal of Heredity. 112(2):174-183. https://doi.org/10.1093/jhered/esab003.
Heaton, M.P., Smith, T.P.L., Bickhart, D.M., Vander Ley, B.L., Kuehn, L.A., Oppenheimer, J., Shafer, W.R., Schuetze, F.T., Stroud, B., McClure, J.C., Barfield, J.P., Blackburn, H.D., Kalbfleisch, T.S., Davenport, K.M., Kuhn, K.L., Green, R.E., Shapiro, B., Rosen, B.D. 2021. A reference genome assembly of Simmental cattle, Bos taurus taurus. Journal of Heredity. 112(2):184-191. https://doi.org/10.1093/jhered/esab002.
