Location: Agricultural Genetic Resources Preservation Research
2020 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 National Animal Germplasm Program (NAGP) collection has exceeded 1 million samples by adding eight new populations or breeds and filling collection gaps on 37 other breeds in fiscal year 2020 (Subobjective 1B and 1C). The second largest swine genetics company requested backup of their breeding populations because of the continuing threat of African Swine Flu and this is substantially finished. Germplasm samples from the sheep populations and tissues samples from cattle, swine, and sheep collections were sent to Fort Collins, Colorado, from ARS in Clay Center, Nebraska. In fiscal year 2020, 232 samples from 78 animals representing ten breeds exited the repository and were used for live animal regeneration (150), research (39), and DNA analysis (43).
We have previously shown cattle of the same breed raised in varying geographic regions have different gene frequencies for genes associated with environmental stress. This analysis evaluated how geographic, and thereby environmental differences, impact estimates of heritability for the intramuscular fat trait, using the statistical method of random regression. Data from 227,902 animals provided by the American Hereford Association were used. Results suggest in harsher environments heritability is decreased, which in turn can impact estimation of genetic merit. Furthermore, the differences in heritability confirm the presence of genetic by environmental interactions. Knowledge and quantification of these differences can be used by breed associations in their evaluation of an animal's genetic merit with improved accuracy. The NAGP will use the information to target collections from diverse environments.
Previously there has been no genetic diversity assessment for non-industrial chicken breeds in the U.S. (Subobjective 3A). Two important aspects in evaluating rare chicken breed genetic diversity are genetic differences among various breeds and within breed diversity among hatcheries producing the same breeds. Therefore, ARS scientists in Fort Collins, Colorado, evaluated ten non-industrial rare chicken breeds from nine hatcheries. Genetic analysis suggested that the New Hampshire is similar to the Rhode Island Red, its progenitor breed. Andalusian was found to be similar to both the Aseel and Phoenix breeds. For eight of the ten breeds, effective population size (a measure of genetic variability) ranged from 79 to 145 animals; which is greater than the 50 animals recommended by the United Nations Food and Agriculture Organization guidelines for livestock conservation. The Aseel and Crevecoeur breeds had effective population sizes of 44 and 47, respectively. While lower than the recommended minimum, the statistic still suggests the rate of inbreeding can be effectively managed. When ARS scientists evaluated hatchery differences within the breeds Crevecoeur, Aseel, and Buttercup, the hatcheries appear to be using a similar source of genetics for their breeding stock. This raises concerns about hatchery ability to maintain genetic variation in the identified populations. The remaining seven breeds were found to have genetic structure similar to other breeds of livestock, suggesting more genetic differences among hatcheries is present.
The NAGP collection of Wagyu cattle was evaluated for genetic diversity and how well the collection represented the breed by using the minimum variance clustering approach based upon the breed association’s pedigree records (Subobjective 3A). Several gaps in the collection were identified and will be filled in the next fiscal year. Fort Collins, Colorado scientists’ assessment of Wagyu showed the average level of inbreeding was 10% and the effective population size was 28 animals. The small effective population size suggests that breeders need to carefully plan their breeding programs. The Wagyu association recognized the need for better mating plans and has been working with ARS scientists in Fort Collins, Colorado, to incorporate the minimum variance clustering technique onto their website so producers can more fully use the information to plan future mating.
Laboratories assess livestock and human semen before and after freezing using computer assisted sperm analysis for quality control purposes (Subobjective 4A). However, no evaluations have been performed over time, which is crucial to gene banking. Over 300 beef and dairy bull semen samples from the NAGP germplasm collection in Fort Collins, Colorado, were evaluated to assess sample quality using computer assisted sperm analysis. This evaluation includes year cryopreserved, from 1950’s to 2010, and various industry sources. Over time, motility of the samples remained constant, ranging from 40 to 50 percent. It was noted that cell speed movement for dairy bulls was faster than beef bulls and it is unclear if faster speeds are indicative of increased or decreased fertilization. Companies freezing bull sperm use a wide variety of proprietary processes but in this analysis little difference between companies was found, suggesting an equivalence among sources when acquiring germplasm for the collection. Over time, laboratories update their equipment generally assuming the results between old and new machines are the same. Computer assisted sperm analysis machines purchased from the same manufacturer in 2000 and 2014 were compared using post-thawed boar semen. The same sample from each boar was evaluated on each machine. They differed between the old and new machine. However, using regression models each parameter measured from the old machine could be corrected to be comparable to the new machine which allows a number of future comparisons.
Freezing oocytes broadens the genetic diversity of the collection and provides alternative approaches for collection use (Subobjective 4B). However, the freezing process is technically challenging and time consuming because typically used devices are rate limited (designed to freeze one oocyte at a time). To increase the processing rate, a 3D printed device was developed that allows a technician to freeze larger quantities of oocytes simultaneously. Testing with both pig and cattle oocytes showed how the 3D printed device is more ergonomically friendly and should result in greater ease of use by a technician and increase the number of oocytes that can be processed per unit of time. Additional testing by other laboratories is needed to validate the devices’ utility.
Accomplishments
1. Time horizons in gene banking and cattle breeding, reaching a major milestone. Developing a comprehensive national collection of animal genetic resources requires substantial resources and long-term commitment. The livestock industry relies on the National Animal Germplasm Program (NAGP) collection to underpin its entire sector and increasingly utilizes the collection to address threats such as disease and shrinking genetic diversity. To meet this critical food security need, ARS scientists in Fort Collins, Colorado, increased the animal germplasm collection to more than 1 million samples and profoundly expanded its diversity. Recent high-profile uses include: 1) Brangus breeders found in their cattle a mutation, white eye disease. The NAGP collection contained the only sample of an important key ancestor (born 1982) that tested negative for the condition. Genomic testing can be used to eliminate such mutations, but comprehensive testing is cost-prohibitive. Thus, key ancestors are tested and if negative their offspring do not need testing. The NAGP sample of the key ancestor reduced the number of cattle tested by 150,000 animals and saved the industry about $1.5 million. 2) The nation’s largest seller of beef bulls (>3,900) needed to reintroduce 1980s-1990s genetics to advance their breeding program. This breeder accessed the NAGP collection for bulls born in 1987 and 1993 with the desired genetics. Samples from the collection produced approximately 70 embryos that were implanted in cows and will soon calve, thus advancing this critical breeding line. This approach is a paradigm shift, in that researchers and industry have viewed genetic improvement one dimensionally – only using the current population to find solutions. Both recent examples highlight the industry value of the NAGP with its diverse genetic collection to address current threats – enabling this paradigm shift and highlighting the critical need of the NAGP genetic resources collection.
2. Expanding genetic diversity in rare swine breeds. Rare breed producers generally fall within the USDA category of “underserved stakeholders”, and Large Black swine are one such breed. ARS scientists in Fort Collins, Colorado, in collaboration with researchers from Purdue University and the Livestock Conservancy leveraged ARS Innovation Funds to import Large Black semen from the United Kingdom, store the material in Fort Collins, Colorado, and then release it to mate Large Black sows maintained at Purdue University. This produced approximately 100 pigs that were transferred to breeders, as well as two Large Black boars that were added to a commercial operation’s stud line-up. The breeding of these Large Black pigs with genetics from United Kingdom empowered the breeders to use the new genetic resources for breed improvement. This advancement was critically important because underserved farmers often lack the technical expertise to perform artificial insemination and prepare females for mating, which reduces success of artificial insemination especially from semen originating from international sources.
Review Publications
Blackburn, H.D., Wilson, C.S., Krehbiel, B.C. 2019. Conservation and utilization of livestock genetic diversity in the United States of America through gene banking. Diversity. 11(12):244. https://doi.org/10.3390/d11120244.
Smyser, T.J., Tabak, M.A., Slootmaker, C., Robeson, M.S., Miller, R., Megens, H., Groenen, M., Paiva, S.R., Faria, D., Blackburn, H.D., Schmit, B., Piaggio, A.J. 2020. Mixed ancestry from wild and domestic lineages contributes to the rapid expansion of invasive feral swine. Molecular Ecology. 29(6):1103-1119. https://doi.org/10.1111/mec.15392.
Purdy, P.H., Spiller, S.F., McGuire, E., McGuire, K., Koepke, K., Lake, S., Blackburn, H.D. 2020. Critical factors for non-surgical artificial insemination in sheep. Small Ruminant Research. 191:106179. https://doi.org/10.1016/j.smallrumres.2020.106179.
Dechow, C.D., Liu, W.S., Specht, L.W., Blackburn, H.D. 2020. Reconstitution and modernization of lost Holstein male linages using samples from a gene bank. Journal of Dairy Science. https://doi.org/10.3168/jds.2019-17753.
Paim, T., Hay, E.A., Wilson, C.S., Thomas, M., Kuehn, L.A., Pavia, S.R., McManus, C., Blackburn, H.D. 2020. Genomic breed composition of selection signatures in Brangus beef cattle. Frontiers in Genetics. 11. Article e00710. https://doi.org/10.3389/fgene.2020.00710.
Paim, T.P., Faria, D.A., Hay, E.A., McManus, C., Lanari, M.R., Esquivel, L.C., Cascante, M.I., Alfaro, E.J., Mendez, A., Faco, O., Silva, K.D., Mezzadra, C., Mariante, A., Pavia, S.R., Blackburn, H.D. 2019. New world goat populations are a genetically diverse reservoir for future use. Scientific Reports. 9(1):1476. https://doi.org/10.1038/s41598-019-38812-3.
Delgadillo Liberona, J.S., Langdon, J.M., Herring, A.D., Blackburn, H.D., Speidel, S.E., Sanders, S., Riley, D.G. 2019. Random regression of Hereford percentage intramuscular fat on geographical coordinates. Journal of Animal Science. 98(1):skz359. https://doi.org//10.1093/jas/skz359.
Paim, T., Hay, E.A., Wilson, C.S., Thomas, M., Kuehn, L.A., Pavia, S.R., McManus, C., Blackburn, H.D. 2020. Dynamics of genomic architecture during composite breed development in cattle. Animal Genetics. 51(2):224-234. https://doi.org/10.1111/age.12907.
