Location: Agricultural Genetic Resources Preservation Research
2024 Annual Report
Objectives
Objective 1: Build, secure, manage, and facilitate the use of the animal genetic resource collection.
Subobjective 1A. Operate species committees to advise NAGP on collection development and use.
Subobjective 1B. Build, secure and manage genetic resource collections using quantitative and molecular analyses to further enhance the germplasm collection.
Sub-objective 1C. Engagement and representation in the United Nation’s Food and Agriculture Organization’s (FAO) Intergovernmental Technical Working Group on Animal Genetic Resources (ITWG-AnGR).
Objective 2: Development, maintenance, and implementation of the publicly accessible Animal-GRIN database Version 2.
Subobjective 2A. Redesign and/or necessary software upgrades to database and public webpages.
Objective 3: Characterize genetic diversity to guide collection development and increase its utility.
Subobjective 3A. Quantify genetic differences within and among breeds across different environmental zones.
Subobjective 3B. Quantify genetic diversity of minor, rare, or heritage chicken breeds.
Objective 4: Rejuvenate poultry research lines from cryopreserved semen using both surgical and non-surgical approaches.
Objective 5: Develop and refine assisted reproductive technologies that enable the efficient and effective collection, evaluation, and utilization of germplasm.
Subobjective 5A. Visualization of computer aided sperm analysis (CASA) results.
Subobjective 5B: Develop improved preservation and utilization methodologies for sperm.
Sub-objective 5C. Adapt and improve chicken primordial germ cell collection, preservation, utilization, and quality evaluation methods for use by gene banks and industry.
Approach
The United States is the epicenter of improved livestock genetics. American poultry breeding companies distribute genetic stocks to more than 110 countries, and the Holstein is the premier genetic package used globally for milk production and to a level that more dairy bull semen is exported than used domestically. The breeding complex, using genetic diversity of our breeds, fuels increased animal productivity and economic activity on a global scale and underpins the global food supply of animal protein. However, there has been a contraction of genetic variability and the number of farm enterprises engaged in livestock breeding. This draws into question the stability of the breeding complex and access to the full complement of genetic resources and thereby hindering the U.S. competitive position, and our ability to reintroduce lost genetic variability and address challenges such as climate change. Therefore, this project’s primary goal is to secure genetic resources and make the collected material and information accessible in national emergencies, for research purposes, or industry’s desire to utilize the USDA National Animal Germplasm Program (NAGP) collection for genetic improvement programs. Developing robust collections requires quantification of genetic variability, publicly accessible information, and cryopreservation of tissues used to reconstitute animals of interest. The project and its framework is established and operational. We will use this framework to acquire germplasm/tissue from targeted animals within a breed or commercial line, evaluate various attributes of genetic diversity, and document the collection in the Animal-Genetic Resources Information Network (Animal-GRIN) information system. As demonstrated, there have been short-term research activities (by the project or stakeholders accessing the collection) that transformed the livestock sector, and long-term the project can facilitate corrective mating or reintroduction of genetics absent from populations. The proposed project plan will provide tools to stakeholders and will continue developing the collection, thus providing the U.S. with greater security for its animal genetic resources.
Progress Report
The USDA National Animal Germplasm Program (NAGP) collection now represents 198 breeds and holds 1.28 million samples, from 65,598 animals (Subobjective 1B). Species committees met and held substantive discussions on the status of the collection and future directions of collection growth (Subobjective 1A). The Aquatic species committee work on inter agency (Fish and Wildlife Service and National Oceanic and Atmospheric Administration) collaboration continued with a symposium held at the Aquaculture America meeting in San Antonio, Texas, on the interaction between aquatic genetic resources and climate change. Genomic comparison of the Jersey dairy cattle collection vs industry population using genotypes from 40,000 animals showed the germplasm collection to be highly representative of live population. It also demonstrated that breed collections need to be refreshed over time due to genetic changes caused by selection in the in-situ population (Subobjective 1B). Collection use is key for robust collection development, but there has been no documentation on the performance levels of progeny from collection sires. For Holstein, daughters (generation 1) from collection 1970 era bulls performed at levels equal to or above contemporary herd mates for milk production. Second generation daughters have been produced and will start lactating in 2025. Contemporary animals have higher inbreeding levels perhaps depressing performance. Runs of homozygosity, calculated from single nucleotide polymorphisms, can be used to measure inbreeding among first- and second-generation collection progeny and compare to contemporary Holstein. We demonstrated that by using 1970 era collection bulls runs of homozygosity were reduced from contemporary progeny by 76% in generation 1 and 41% in generation 2. A second collection use is underway with 1958 and 1990 era Angus sires that were mated to a producer’s cows. Using adjusted birth and weaning weights we found the progeny of the older bulls was slightly higher than contemporary bred progeny. Using over 40,000 single nucleotide polymorphisms from 28,900 animals it was determined that old bull progeny runs of homozygosity were 66% different than the top 10% and bottom 10% of contemporary bulls. For both Holstein and Angus, it appears use of older collection bulls break apart existing runs of homozygosity (inbreeding) which raises the progeny’s phenotypic performance.
With continued outbreaks of avian influenza collection efforts using primordial germ cells were successfully executed for Coq de Leon, research lines at Iowa State University and University of Arkansas (Subobjective 1B). Necessary upgrades and features for Animal-Genetic Resources Information Network were performed (Objective 2) and the information system is the major avenue for gene bank managers and the public to know which animals and breeds are in the collection. Computer assisted sperm analysis on dairy cattle was performed and published (Subobjective 5A). Findings supported a novel method of evaluation where various sperm motility and physiological factors are viewed in combination with each other instead of as independent measures. This is a departure in the dogma previously assumed appropriate for computer assisted sperm analysis.
The effects of genotype and cryopreservation diluent on rooster sperm physiology and motility were investigated (Subobjective 5B). The analyses revealed that the genotype/chicken line and the cryoprotectant had a strong influence on post-thaw rooster sperm motility and function. Moreover, inferior cryoprotectants were identified which helps to narrow the scope of future investigations. Next steps will include testing the fertility of the cryoprotectant treatments that resulted in acceptable post-thaw quality to determine if they are viable alternatives to glycerol. Doing so will enable development of a more secure collection of chicken germplasm and provide the poultry industry with a powerful technology for preserving and utilizing genetic resources. Also, the effect of chicken line on primordial (embryonic) germ cell quantity and quality were analyzed (Subobjective 5C). There is a definitive line effect which is imperative to know when modeling collection goals for populations via this technology. Knowledge of these differences will empower ARS researchers in Fort Collins, Colorado, to expand collection of chicken genetic resources.
Accomplishments
1. Shifting dogma improves sperm analysis. Cattle and swine breeding industries use computer-assisted sperm analysis to evaluate sperm quality for artificial insemination, a major breeding tool in animal agriculture. Unfortunately, the individual sperm traits measured do not effectively predict fertility. To overcome this deficiency, ARS researchers in Fort Collins, Colorado, advanced a new hypothesis and tests that combine measured traits into groups with specific ranges for each trait, thus substantially increasing the predictive power of computer assisted sperm analysis. Furthermore, the approach can be incorporated into the software suite already present on computer assisted sperm analysis equipment in operation in commercial operations across the county. This will benefit the U.S. beef and dairy cattle and swine industries by increasing the accuracy of their sperm assessments leading to enhanced utility of evaluation results and increased profitability of artificial insemination companies.
2. 1960 to 1990s bulls reduce inbreeding while raising performance. Inbreeding and loss of genetic diversity are widely recognized as important issues confronting the U.S. livestock industry; however, the USDA National Animal Germplasm Program collection contains as much or more diversity than observed in live animal populations. Numerous samples in the collection are from bulls from previous generations - some born as early as 1958 - which are thought to have lower productivity than contemporary animals from the same breed. ARS researchers in Fort Collins, Colorado, demonstrated that by utilizing older gene banked Holstein and Angus bulls, inbreeding can be reduced while maintaining or improving performance for milk production, weaning weights, and weight gain. This is a significant advancement opening countless avenues for industry and research communities to use collection samples to address problems in the animal agriculture industry that threaten food security.
Review Publications
Haagen, I.W., Blackburn, H.D. 2024. Efforts to cryopreserve shrimp (Penaeid) genetic resources and the potential for a shrimp germplasm bank in the United States. Aquaculture. 580. Article e740298. https://doi.org/10.1016/j.aquaculture.2023.740298.
Blackburn, H.D., Azevedo, H.C., Purdy, P.H. 2023. Incorporation of biotechnologies into gene banking strategies to facilitate rapid reconstitution of populations. Animals. 13(20). Article e3169. https://doi.org/10.3390/ani13203169.
Blackburn, H.D., Lozada-Soto, E.A., Paiva, S. 2023. Biobanking animal genetic resources: Critical infrastructure and growth opportunities. Trends in Genetics. 40(2):115-117. https://doi.org/10.1016/j.tig.2023.11.004.
Purdy, P.H. 2024. Germplasm preservation for rare domestic animal breeds. In: Skinner, M.K. editor. Encyclopedia of Reproduction. 3rd edition. New York, NY: Elsevier Inc. p. 1-8.
Molina, J.C., Santos da Silva, R., Bidegain, F., Souza, Y., Purdy, P.H., Blackburn, H.D., Azevedo, H. 2023. Bioclimatic thermal stress indices and their relationships with andrological characteristics in hair rams. International Journal of Biometeorology. 68:253-261. https://doi.org/10.1007/s00484-023-02587-0.