Location: Agricultural Genetic Resources Preservation Research
2019 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 publically 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 US 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 collection of germplasm has exceeded one million samples (1,044,709) this fiscal year (Subobjective 1B). No other national gene bank has afforded its livestock and aquaculture sectors (and the public at large) this level of protection. The threat of African Swine Fever led to a request from a large swine genetics company to collect and preserve germplasm from their elite populations; and this important effort was completed. Efforts to protect ARS populations were also taken for the East Lansing, Michigan chicken lines and the Miles City, Montana cattle lines. In total, samples from 33 breeds were acquired for the collection (Subobjectives 1B and 1C). In collaboration with the U.S. Department of State, a scientist working on this project represented the U.S. at the Food and Agriculture Organization of the United Nations meetings. Due to U.S. participation in the meetings, working documents developed incorporated U.S. positions and reflect an interest in promoting the international flow of genetic resources (Subobjective 1D).
Repository semen samples from Duroc pigs collected and cryopreserved in 2004 and 2014 were used to artificially inseminate sows maintained by Purdue University to evaluate sample fertilization capacity. Samples collected across both time frames had acceptable fertility. This finding suggests the repository can be used to reconstitute pig populations as needed. An additional study using the progeny to evaluate genetic differences that may have occurred between 2004 and 2016 growth, muscling, and fat composition. Results suggest that during the time interval barrow and gilt average daily gain were significantly changed and the growth curves differed by sex, suggesting that Durocs had sufficient genetic variability to alter growth patterns to meet industry expectations. The results also indicate that the germplasm collection has captured the genetic change created by industry.
Work incorporating lost Y chromosomes in Holstein dairy cattle continues with Pennsylvania State University, and this work continues to attract extensive industry attention. Bull progeny, whose sires were born in the early 1980’s from repository samples had genomic breeding values equal with the current live Holstein population. A second generation is planned using the bull progeny as sires which should yield calves with substantially higher genomic breeding values.
The Animal – Genetic Resources Information System (Animal-GRIN), a collaboration among ARS, Agri-Foods Canada, and EMBRAPA in Brazil, successfully implemented initial capacities to interactively map where animals with samples in the collection were derived (Objective 2). The advancement will increase our ability to identify gaps in the collection and provide users with an additional tool by which they can survey the collection and potentially choose germplasm to use for a variety of purposes. In addition, the genomics component of the database was completed and made publicly available.
The germplasm collection and live populations of Duroc (n = 62) and Yorkshire (n = 102) were compared to determine how well the germplasm collection represented the genetic diversity of the breed when pedigree and molecular information were used (Subobjective 3A). Based upon pedigrees the Duroc germplasm collection had all but one subpopulation represented, while all Yorkshire subpopulations were represented in the collection. Using a panel of 60,000 genetic markers, 99% of the alleles were present in both the germplasm collection and the samples from the live population. Additional genetic analyses, such as principal components, suggested no differences between the two groups within their respective breed were present. These results indicate sampling procedures were robust and capable of capturing a wide array of within breed genetic diversity. Molecular evaluation of oysters from different locations along the Louisiana coast indicated no subpopulation structure (Subobjective 3B).
Tools providing meaningful information about frozen-thawed semen and that enable an end-user to differentiate between samples based on quality, is in great demand by industry. Furthermore, that ability to select a sample based on quality will add value to national germplasm collections. In the previous fiscal year, we were able to identify some methodologies that have the potential to accomplish this differentiation. Consequently, our research over the last fiscal year explored the application of these methods using in vitro flow cytometry analyses that approximate sperm maturation conditions (Subobjective 4A). In the next fiscal year, the sperm maturation experiments will conclude, and the results will be correlated with fertility achieved via in vitro fertilization experiments.
Oocyte cryopreservation is essential for preserving the genetics of mammalian species and enables creation of a more robust national germplasm collection. Currently, oocytes are preserved as single cells rather than in groups which is inefficient for both the industry and the repository. To address this, we compared the use of a device commonly used in industry with one developed by our program (Subobjective 4B). Our evaluations resulted in two significant findings. First, use of the device that we developed results in the recovery of significantly more viable oocytes following freezing compared with the device traditionally used by industry. Secondly, the device that we developed can be used to freeze 1, 5, 10 or 15 oocytes simultaneously, and results in greater post-thaw viability compared with the other device. In the next fiscal year, our efforts will be directed at understanding how the different devices affect oocyte quality and physiology during cryopreservation, as well as refinement of the oocyte cryopreservation process.
Accomplishments
1. Answered a critical question for animal genebanks: How complete are breed collections. A persistent question for animal gene banks is how well collections contain the genetic variability of living populations? ARS scientists in Fort Collins, Colorado, performed comprehensive analyses on two important swine breeds (Duroc and Yorkshire) comparing gene bank collections to each breed’s living population. For 15 years the National Animal Germplasm Program has collected samples from these two breeds using pedigree information and computed genetic relationships as a basis for selecting animals to sample. The germplasm collection consists of 64 Duroc and 102 Yorkshire pigs meant to represent thousands of living animals. The current evaluation utilized pedigree data from the National Swine Registry, plus molecular data from the same organization, land grant universities, and ARS in Clay Center, Nebraska. Based upon pedigree records all but one small group of Durocs was represented in the collection. Within Duroc or Yorkshire the molecular genetic analysis, using 60,000 single nucleotide polymorphisms, revealed that the germplasm collections and living populations had 98% of the alleles in common with each other. Results showed that only minor differences exist between the gene bank collection and the living populations, which is a critical result that provides the swine industry confidence that a genetically robust collection of germplasm has been acquired; therefore, critical genetic variability to protect the U.S. swine industry is securely protected.
2. Developed genetic and reproductive technologies for under-served pig and sheep producers. Rare breeds of livestock are typically raised by producers who are often under-served and minorities. The nexus of producer expertise, appropriateness of technology, and potentially biological differences limit ARS capacity to collect germplasm and employ genetic techniques needed to maintain genetic diversity. To assist producers and this important segment of the animal industry, ARS scientists in Fort Collins, Colorado, sponsored workshops for sheep and Large Black pig producers. Sheep workshops focused on transferring basic information on reproduction and in particular the implementation of non-surgical artificial insemination. The Large Black workshop, supported by ARS Innovation Funds, addressed reproductive technologies and breeding plans to enhance the breed’s genetic diversity. In preparation for this workshop, collaborative research with Purdue University evaluated artificial insemination. This research showed insignificant differences in ovulation time in Large Black pigs demonstrating to Large Black pig producers the feasibility of artificial insemination. Our research also suggests the breed has sufficient genetic diversity so as not to be an impediment to production. To transfer this knowledge, a blueprint for breeders was developed cooperatively with stakeholders and distributed to this under-served producer group.
Review Publications
Krehbiel, B.C., Thomas, M.G., Wilson, C.S., Speidel, S.D., Enns, M.R., Paiva, S.R., Blackburn, H.D. 2019. Evaluation of genetic structure across U.S. climate zones using prominent AI sires of Red Angus cattle. Livestock Science. 225:26-31. https://doi.org/10.1016/j.livsci.2019.04.012.
Paim, T.P., Hay, E.A., McManus, C., Faria, D.A., Cascante, M.I., Mezzadra, C., Mariante, A., Pavia, S.R., Blackburn, H.D. 2019. New world goat populations: a genetically diverse reservoir for future use. Scientific Reports. 9:1476. https://doi.org/10.1038/s41598-019-38812-3.
Rexroad III, C.E., Vallet, J.L., Matukumalli, L.K., Ernst, C., Van Tassell, C.P., Cheng, H.H., Reecy, J., Fulton, J., Taylor, J., Lunney, J.K., Liu, J., Cockett, N., Smith, T.P., Van Eenennaam, A., Clutter, A., Telugu, B., Purcell, C., Bickhart, D.M., Blackburn, H.D., Neibergs, H., Wells, K., Boggess, M.V., Sonstegard, T. 2019. Genome to phenome: improving animal health, production, and well-being: a new USDA blueprint for animal genome research 2018–2027. Frontiers in Genetics. 10:327. https://doi.org/10.3389/fgene.2019.00327.
Faria, D., Pavia, S., Wilson, C.S., Blackburn, H.D. 2019. Assessing Sus scrofa diversity among continental United States, and Pacific Islands populations using molecular markers from a gene banks collection. Scientific Reports. 9:3173. https://doi.org/10.1038/s41598-019-39309-9.
