Location: Agricultural Genetic Resources Preservation Research
2018 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
Germplasm inventory was increased for 42 breeds, and two new breeds were added to the collection during this reporting cycle. As a result, the collection has increased to 964,000 samples from 51,700 animals representing 166 breeds (Subobjective 1B). Significant progress in backing-up the research chicken lines at the Avian Disease and Oncology Laboratory in preparation for transferring the lines to ARS in Athens, Georgia took place (Subobjective 1C). It is anticipated that all lines will be fully conserved in FY19. Collaboration with Agri-Foods Canada and EMBRAPA in Brazil on developing and implementing the information system Animal-Genetic Resources Information Network (GRIN) continues (Objective 2). Breed census information has been updated in Animal-GRIN and the Food and Agriculture Organization of the United Nations database for 78 breeds, thereby providing long-term trends concerning the increase or decrease in registration numbers which are indicators of breed genetic diversity (Subobjective 1D). Generally, among rare cattle breeds there has been little change in the number of animals registered on an annual basis suggesting the genetic base should be relatively stable. In collaboration with the Department of State, a scientist working on this project represented the U.S. position at meetings on access and benefit sharing of animal genetic resources at the Intergovernmental Technical Working Group for Animal Genetic Resources at the Food and Agriculture Organization of the United Nations. 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).
Genetic diversity of goat breeds from the U.S., Brazil, Costa Rica, and Argentina were compared to each other and populations from Central Asia, Morocco, and South Africa. Western hemisphere meat goats raised in low input management systems had substantial genetic diversity, suggesting little if any variability has been lost in the 400 years since importation. Furthermore, the data suggest that for these types of goats the breed is not an important classifier for populations, unlike cattle or sheep. The U.S. Spanish goat was among the most genetically diverse populations evaluated. Using genome wide association studies, little evidence of selection among meat goat populations was found. Few genomic markers were identified among the highly selected Angora, which is peculiar since the breed has been highly selected for fiber characteristics for over 150 years (Objective 3).
Post-thaw assessment of cryopreserved semen entails using computer assisted sperm analysis and/or flow cytometry; both yield empirical results. But, by placing post-thawed sperm samples into solutions developed for routine in-vitro fertilization which allow sperm cells to mature, a robust indicator for fertilization capacity of the post-thawed sampled could be developed (Subobjective 4A). Comparison of two commercially available solutions with post-thawed semen indicated a statistically significant difference existed in the percentage of sperm in which the acrosome had reacted, and therefore suggest the activated cells were ready to start the fertilization process. In the next fiscal year, this effort will continue to evaluate the differences observed and work toward an evaluation protocol for post-thawed sperm.
Cryopreserving oocytes conserves genetic variability and provides another mechanism for reconstituting a population. Current industry based procedures call for freezing individual oocytes rather than groups of oocytes. A device for cryopreserving multiple oocytes has been constructed and oocytes have been frozen (1, 5, 10, 15, or 20 per freeze). Evaluation of this device showed that a higher percentage of the post-thawed oocytes were viable when compared to the current device used by industry (46.6% vs 23.5%, respectively). In the next fiscal year, the optimal number of oocytes to freeze at one time will be determined (Subobjective 4B).
Accomplishments
1. New Breed Evolution – Composite livestock breeds incorporate positive productive attributes of founding breeds. Brangus is an example of a composite breed and is comprised of 63% Angus and 37% Brahman. It has traditionally been assumed that proportions of the combined genome are uniformly distributed among the Brangus chromosomes and that this composition is consistent over time. ARS scientists in Fort Collins, Colorado explored this issue by genotyping Brangus from different generations and compared that data to Angus and Brahman genotypes. Results indicated that on average Brangus genomic composition has shifted to 70% Angus and 30% Brahman. A chromosome-by-chromosome analysis showed the proportion of Angus and Brahman were not uniformly distributed across chromosomes in the expected proportions. Rather, specific chromosomes tended to favor Brahman or Angus. When chromosomes for Brahman were further evaluated there was a significant association with traits associated with environmental stressors; while chromosomes with high proportions of Angus consisted of traits associated with growth and meat quality. These findings demonstrate at the genomic level how complementarity (the combining of breeds) may function. In addition, the results demonstrated how, over generations, a new breed becomes uniquely different from the founding breeds. For the scientific community this is the first time a breed’s formation has been quantified at the genomic level. The results confirm industry and research community suspicions that the genomic composition of Brangus is not consistent and that it is trending toward Angus. With this information industry will be able to better balance the breed’s composition through selection for both meat quality and environmental adaptability.
Review Publications
Blackburn, H.D. 2018. Biobanking genetic material for agricultural animal species. Annual Review of Animal Biosciences. 6:69-82. https://doi.org/10.1146/annurev-animal-030117-014603.
Cruz, V.V., Pantel, A., Ray, D.T., Niaura, W., Purdy, P.H., Dierig, D.A. 2017. Analysis of mode of reproduction of guayule (Parthenium argentatum A. Gray) using flow cytometry and identification of polyhaploids for breeding. Industrial Crops and Products. https://doi.org/10.1016/j.indcrop.2017.07.004.
Manter, D.K., Delgado, J.A., Blackburn, H.D., Harmel, R.D., Perez De Leon, A.A., Honeycutt, C.W. 2017. A new concept: national living soil repository. Proceedings of the National Academy of Sciences. 114:13587–13590. https://doi.org/10.1073/pnas.1720262115.
