Biobanking genetic resources: challenges and implementation at the USDA National Animal Germplasm Program

Assessment of genetic diversity, inbreeding and collection completeness of Jersey bulls in the US National Animal Germplasm Program

Genomic selection and extensive use of a few elite bulls through artificial insemination are leading to reduced genetic diversity in Jersey cattle. Conservation of genetic diversity through gene banks can protect a breed's genetic diversity and genetic gain, ensuring continued genetic advancement in the future. The availability of genomic information in the US National Animal Germplasm Program (NAGP) facilitates characterization of Jersey bulls in the germplasm collection. Therefore, in this study, we compared the genetic diversity and inbreeding between Jersey bulls in the NAGP and the national cooperator database (NCD). The NCD is maintained and curated by the Council on Dairy Cattle Breeding (CDCB). We found the genetic diversity to be marginally higher in NAGP (Ho = 0.34 ± 0.17) relative to the NCD population (Ho = 0.33 ± 0.16). The average pedigree and genomic inbreeding (FPED, FGRM, FROH > 2Mb) were similar between the groups, with estimates of 7.6% with FPED, 11.07% with FGRM and 20.13% with FROH > 2Mb. An increasing trend in inbreeding was detected, and a significantly higher level of inbreeding was estimated among the older bulls in the NAGP collection, suggesting an overrepresentation of the genetics from elite bulls. Results from principal component analyses (PCA) provided evidence that the NAGP collection is representative of the genetic variation found in the NCD population and a broad majority of the loci segregating (98.2%) in the NCD population were also segregating in the NAGP. Ward's clustering was used to assess collection completeness of Jerseys in the NAGP by comparison with top 1000 sires of bulls, top 1000 sires of cow, and bulls with high Lifetime Net Merit (NM$). All the clusters were represented in the NAGP suggesting that most of the genetic diversity in the US Jersey population is represented in the NAGP and confirmed the PCA results. The decade of birth was the major driver grouping bulls into clusters, suggesting the importance of selection over time. Selection signature analysis between the historic bulls in the NAGP with the newer bulls, born in the decade after implementation of genomic selection, identified selection for milk production, fat and protein yield, fertility, health, and reproductive traits. Cluster analysis revealed that the NAGP has captured allele frequency changes over time associated with selection, validating the strategy of repeated sampling and suggests that the continuation of a repeated sampling policy is essential for the germplasm collection to maintain its future utility. While NAGP should continue to collect bulls that have large influence on the population due to selection, care should be taken to include the entire breadth of bulls, including low merit bulls.

The emerging role of open technologies for community-based improvement of cryopreservation and quality management for repository development in aquatic species

Genetic resources of aquatic species are of tremendous value, but worldwide these are maintained almost exclusively as live populations. This is extremely expensive and insecure, and largely results from a pervasive lack of production capability, quality management, and reproducibility in cryopreservation that are barriers in development of germplasm repositories. Community-based technology approaches are emerging that can stimulate research previously limited by a lack of affordable, customizable equipment. Open-access technologies can provide for custom design and fabrication not available through traditional manufacturing. This can assist repository development with robust sample production methods and strong quality management, and can greatly improve reproducibility and standardization. Open technologies can support establishment of new communities of users, makers, and developers that collectively strive to develop open hardware in a distributed (i.e., non-centralized) fashion that can yield aggregate throughput. This occurs through use of consumer-level tools, supplies, software, and equipment, free exchange of designs and modifications, and a shared sense of mission. For cryopreservation and repository development, we have identified 14 categories of open hardware for a processing pathway, and six categories for a quality management pathway. Open hardware offers economic incentives to develop repositories for aquatic species, something that has not occurred despite 70 years of research largely focused on protocol development rather than practical applications. Advanced development of custom scientific hardware enhancing open technologies will be facilitated by interdisciplinary collaboration across biological and engineering fields. This manuscript is a contribution to the Special Issue in memory of Dr. Duane Garner, a leader in the sperm biology.

3-D Printed Customizable Vitrification Devices for Preservation of Genetic Resources of Aquatic Species

Sperm vitrification as an alternative approach to conventional cryopreservation (equilibrium freezing) allows quick and low-cost sample preservation and is suitable for small-bodied aquatic species with miniscule testis, fieldwork at remote locations, and small-scale freezing for research purposes. The goal of this present study was to develop operational prototypes of 3-dimensional (3-D) printed vitrification devices with innovative components that can provide comprehensive functionalities for practical repository development for aquatic species. The design featured an elongated loop to suspend a thin film of sperm sample in cryoprotectant, a retractable sleeve to protect the vitrified samples and allow permanent labeling, a handle to facilitate processing and storage, and a shaft with annular grooves to guide positioning of the protective retractable sleeve. To span a wide range of sample capacities and configurations, a total of 39 different configurations (3 loop lengths ×13 loop heights) were fabricated by 3-D printing with the thermoplastics polylactic acid (PLA) and acrylonitrile butadiene styrene (ABS). A total of 86 devices were fabricated with ABS filament with a print failure rate of 9%, and 97 devices were fabricated with PLA filament with a failure rate of 20%. Major types of printing failures included disconnected loops, insufficient build surface adhesion, stringing, and inconsistent extrusion. The sample volume capacity ranged from 1-47 μL and had linear relationships to the loop lengths and layer numbers. Vitrified samples were observed in 10-mm and 15-mm loops fabricated with PLA and ABS but not in 20-mm loops. This study demonstrated the feasibility of development of standardized low-cost ($0.05 material cost) devices fabricated by 3-D printing with practical functions including vitrification, volume control, labeling, protection, and storage within conventional systems. These prototypes can be further developed, standardized, and used to assist development of germplasm repositories to protect the genetic resources of aquatic species by user groups such as breeders, hatcheries, aquariums, and researchers.

Reconstitution and modernization of lost Holstein male lineages using samples from a gene bank

More than 99% of all known Holstein artificial insemination (AI) bulls in the United States can be traced through their male lineage to just 2 bulls born in the 1950s, and all Holstein bulls can be traced back to 2 bulls born in the late 1800s. As the Y chromosome is passed exclusively from sire to son, this suggests that variation is limited for much of the Y chromosome. Two additional male lineages that are separate from modern lineages before 1890 were present at the start of the AI era and had semen available from the USDA National Animal Germplasm Program (Fort Collins, CO). Semen from representatives of those lineages were used for in vitro embryo production by mating to elite modern genetic females, resulting in the birth of 7 bulls and 8 heifers. Genomic evaluation of the bulls suggested that lineages from the beginning of the AI era could be reconstituted to breed average for total economic merit in 1 generation when mated to elite females due to high genetic merit for fertility, near-average genetic merit for fat and protein yield, and below-average genetic merit for udder and physical conformation. Semen from the bulls is commercially available to facilitate Y chromosome research and efforts to restore lost genetic diversity.

A Review of Living Collections with Special Emphasis on Sustainability and Its Impact on Research Across Multiple Disciplines

Formal living collections have unique characteristics that distinguish them from other types of biorepositories. Comprising diverse resources, microbe culture collections, crop and biodiversity plant germplasm collections, and animal germplasm repositories are commonly allied with specific research communities or stakeholder groups. Among living collections, microbial culture collections have very long and unique life histories, with some being older than 100 years. Regulatory, financial, and technical developments have impacted living collections in many ways. International treaty obligations and restrictions on release of genetically modified organisms complicate the activities of living collections. Funding for living collections is a continuing challenge and threatens to create a two-tier system where medically relevant collections are well funded and all other collections are underfunded and hence understaffed. Molecular, genetic, and whole genome sequence analysis of contents of microbes and other living resource collections bring additional value to living collections.

Effects of post-mortem storage conditions of bovine epididymides on sperm characteristics: investigating a tool for preservation of sperm from endangered species

The aim of this study was to establish and validate a reliable and efficient protocol for the recovery and cryopreservation of epididymal spermatozoa used for in vitro fertilization, using bulls of two different age classes. Testicles from 26 (37-51 weeks old, group 1) and 19 (52-115 weeks old, group 2) Danish Holstein bulls were collected after slaughter and stored at 5°C. After 0, 24 or 48 h, epididymides were isolated and spermatozoa collected. Assessments included spermatozoal motility, viability and morphology before and after cryopreservation and in vitro embryo production. Results showed that live spermatozoa can be collected from epididymides of bulls after their death. Storage of the testicles at 5°C for 24 h followed by cryopreservation of recovered epididymal spermatozoa resulted in 21% (group 1) and 31% (group 2) blastocysts produced in vitro. These results illustrate that epididymal spermatozoa recovered from testicles kept in specific conditions can be used to preserve genetic material from endangered and threatened species or populations in nature as well as in domestic and zoo animals.