Location: Agricultural Genetic Resources Preservation Research
2023 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 collection now represents 198 breeds and holds 1.27 million samples, from 64,670 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 expressed interest in exploring the interaction between aquatic genetic resources and climate change. As a result, inter-agency meetings were conducted with a goal of determining how Federal agencies (United States Department of Agriculture, National Oceanic and Atmospheric Administration, United States Fish and Wildlife Service) might team together to address the topic. A series of meetings were held with scientists (Fargo, North Dakota and Baton Rouge, Louisiana) and industry on further development of the honeybee collection. A broad range of analyses were conducted exploring the collection completeness for Jersey cattle; diversity of genotypes for genes associated with fat synthesis using Angus, Wagyu, Jersey, and Brahman; and an evaluation of Sanga breeds to other Bos taurus and Bos indicus composite breeds. The Jersey analysis suggests that the germplasm collection has captured most if not all the genetic diversity for this breed. Sanga cattle breeds are Bos indicus and Bos taurus composites formed centuries ago in southern Africa and of interest to beef producers in the U.S. We have quantified the diversity of Sanga breeds in the U.S. and are exploring the stabilized components of Bos indicus and Bos taurus. Collection utility was demonstrated by working with a major breeder of Angus cattle. In this instance collection bulls born before 1998 were used by the breeder to incorporate genetic attributes which they deemed to be missing from their current population. Results, as evidenced by the bulls’ progeny, were that the newly created animals were as productive or more so than contemporary animals. Necessary upgrades and features for Animal-Genetic Resources Information Network (GRIN) 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. Data needed for Subobjective 3A, quantification of genetic diversity across ecozones, was generated via genotyping animals in the germplasm collection from various ecozones identified in the previous project plan. Quantification of genetic diversity among non-commercial chicken breeds was performed and published (Subobjective 3B). It was determined that the U.S. developed breeds were unique when compared to breeds that were originally imported into the U.S. in the 1800’s. Effective population size ranged from 47 to approximately 150 animals suggesting ample genetic diversity was present among these breeds. While the in-situ population sizes of the breeds evaluated were small, it was determined that among these populations there is ample genetic diversity for producers to utilize as they determine best – even though some breeds tested have been classified as being rare and in need of special management. The collection was the source of the samples used in this analysis therefore the results suggest the collection contains a broad sampling of genetic resources for these breeds. For mammalian species computer assisted sperm analysis is widely used to assess sperm parameters (Subobjective 5A). However, the large amounts of data from these analyses are rarely used and predictive capacity is poor. To improve the utility of computer assisted sperm analysis, semen samples from over 250 Holstein and Jersey bulls currently in the collection have been analyzed via this method and those data are ready for analyses in future years of this project plan. Work on analytical approaches for Sub-objective 5B have been performed. The ability to collect and cryopreserve primordial germ cells from chickens is an important development (Sub-objective 5C) which will substantially change how avian populations can be preserved. With training completed, we advanced the technique by freezing gonads from day 9.5 embryonic gonads for isolation and culture of embryonic germ cells. Using this technology enabled USDA to securely preserve the genetics of 13 important university research lines and rare and unique feather lines used for tying flies or ornamental feather applications. Of the feather line varieties, 26 lines were preserved via embryonic germ cells and 38 lines were preserved through collecting and freezing of gonads from day old chicks (Subobjective 1B).
Accomplishments
1. USDA collection mirrors Jersey population. ARS researchers in Fort Collins, Colorado, and Beltsville, Maryland, compared genotypes from all of USDA’s Jersey collection (760 animals) to over 40,000 industry animals. This monumental task - the largest evaluation of any animal gene bank’s holdings - determined that all major genes in the population have been captured in the collection. In addition, it appears all alleles with a frequency of greater than 2% have been captured. This important analysis of the collection tells Jersey breeders that their genetics are secure and that their population can be reconstituted or modified in the event of lost genetic resources, which provides the industry confidence in their contribution to food security.
2. New technology secures feather industry – not just chicken feed. Feathers used to tie flies for fishing are worth approximately $10 – 12 million per year. Additionally, the chicken breeds and lines used to produce these feathers are some of the most unique in terms of their source of origin, multifunctionality (feathers, meat, and egg production) and potentially genes that may harbor resistance to disease. Using a state-of-the-art approach to harvest and conserve embryonic germ cells, ARS researchers in Fort Collins, Colorado, securely preserved the genetics of 26 unique feather lines used for fly fishing lures and ornamental fashion. In addition, another 38 lines were preserved through collecting and freezing of gonads from day old chicks. With potential outbreaks of avian influenza, this genetic preservation effort has protected the industry's genetic resources but more importantly their entire businesses.
3. Germplasm collection bulls show value in industry. Industry utilization of the USDA National Animal Germplasm Program (NAGP) collection further exemplifies its value to U.S. agriculture. A prominent Angus breeder recently accessed the NAGP collection for five bulls born between 1958 and 1997 to reintroduce those genetics into their herd. Their goal was to increase maternal performance of the herd. The resulting progeny’s performance either matched or exceeded current levels of performance, which was a surprising but beneficial outcome. These Angus progeny are now in high market demand with sale prices that are two to six times higher than the average price of $7,400.
Review Publications
McManus, C., Pimentel, F., Pimentel, D., Sejian, V., Blackburn, H.D. 2023. Bibliographic mapping of heat tolerance in farm animals. Livestock Science. 269. Article e105163. https://doi.org/10.1016/j.livsci.2023.105163.
Blackburn, H.D., Krehbiel, B.C. 2023. A gene bank’s collection of genetic diversity among minor chicken breeds. Poultry Science. 102(8). Article e102827. https://doi.org/10.1016/j.psj.2023.102827.
McManus, C., Pimentel, F., Pimentel, D., Sejian, V., Blackburn, H.D. 2023. Bibliographic mapping for heat tolerance in pigs and poultry. Tropical Animal Health and Production. 55. Article e256. https://doi.org/10.1007/s11250-023-03655-8.
Rodrigues, C.S., Faria, D.A., Lacerda, T.S., Pavia, S.R., Caetano, A.R., Blackburn, H.D., McManus, C. 2022. Lentivirus susceptibility in Brazilian and US sheep with TMEM154 mutations. Genes. 14(1). Article e70. https://doi.org/10.3390/genes14010070.
De Oliveira, M.B., Molina, J.C., Santos Da Silva, R., Ramos, A.F., Purdy, P.H., Azevedo, H.C. 2022. Effects of cell concentration during cryopreservation on the post-thaw quality of Santa Inês ram sperm. CryoLetters. 43(6):357-367. https://doi.org/10.54680/fr22610110812.
Blesbois, E., Purdy, P.H., Santiago Moreno, J., Liptói, K., Rajamohan, A., De Souza-Fabjan, J., Somfai, T., Parnpai, R., McGrew, M.J., Mermillod, P., Bailey, J. 2023. Section 6: Collection and cryopreservation of germplasm and tissues. In: Boes, J., Boettcher, P., Honkatukia, M., editors. Innovations in Cryoconservation of Animal Genetic Resources - Practical Guide. FAO Animal and Health Guidelines, No. 33. Rome, Italy. p. 105-157. https://doi.org/10.4060/cc3078en.
Purdy, P.H., Blesbois, E., Santiago Moreno, J., Parnpai, R., Smits, K., Somfai, T., Liptói, K., Rajamohan, A., McGrew, M.J., Roelen, B., Várkonyi, E.P., Loi, P., Paiva, S.R., Lessard, C., Zhao, X., Blackburn, H.D., Woelders, H., Bailey, J. 2023. Section 3: Choice of biological material to be preserved. In: Boes, J., Boettcher, P., Honkatukia, M., editors. Innovations in Cryoconservation of Animal Genetic Resources - Practical Guide. FAO Animal and Health Guidelines, No. 33. Rome, Italy. p. 41-68. https://doi.org/10.4060/cc3078en.
Guo, Y., Sharp, K., Blackburn, H.D., Richert, B., Stewart, K., Zuelly, S. 2022. Processed meat characteristics between commercial Duroc-sired and heritage breed Large Black pigs. Foods. 11(15). Article e2310. https://doi.org/10.3390/foods11152310.
Wilson, C.S., Petersen, J.L., Blackburn, H.D., Lewis, R.M. 2022. Assessing population structure and genetic diversity in U.S. Suffolk sheep to define a framework for genomic selection. Journal of Heredity. 113(4):431-443. https://doi.org/10.1093/jhered/esac026.
Blackburn, H.D., Tixier-Boichard, M., Hiemstra, S., Boettcher, P. 2022. Section 1: Building a gene banking strategy. In: Boes, J., Honkatukia, M., editors. Innovations in Cryoconservation of Animal Genetic Resources. Rome, Italy: Food and Agriculture Organization of the United Nations. p. 1-24.
