Genomics can deliver great benefits to agricultural breeding programs, including efficient management of diversity and inbreeding, accurate parentage assignment, optimal mating designs, improved breeding value prediction, selection decisions, and breeding strategies. Using the appropriate platform for the population of interest is critical. It is often expected that optimal results require a customized tool with a higher level of initial investment and larger ongoing costs. However, it is possible to keep costs reasonable with optimal outcomes through the creation or use of a collaboratively designed universal genotyping platform.
Collaborative genotyping solutions for specific species are created using diverse populations to ensure a design that contains a core set of markers with broad utility among all populations along with markers that capture specific population characteristics. The design also provides the ability to capture published markers associated with key traits. Many industry parties can benefit through using such platforms, creating a sample volume to keep costs reasonable and enabling results and outcomes that are easily compared and evaluated. As the platform is updated and improved, the benefit flows to all users.
A successful example of this approach is in the livestock domain, where the widely used Illumina BovineSNP50 BeadChip array was developed in collaboration with the USDA-ARS, the University of Missouri, and the University of Alberta. The array allows for high-throughput, cost-effective genetic screening using 53,000 markers validated across 18 common beef and dairy breeds. The platform supports many genomic applications, including genomic selection, across both the dairy and beef industries, where its widespread use creates high demand and keeps costs per sample low. More recent extensions of this concept have been deployed as GeneSeek Genomic Profiler (GGPs) arrays. The updated content over time can leverage the continuously developing knowledge base about the genomic structure of a species as new tools and resources become available.
This approach is also proving extremely beneficial for aquaculture species, as exemplified by the creation of a collaborative genotyping platform for L. vannamei shrimp designed using samples from eleven populations. This talk will discuss the design of the array, validating the array’s results, how to achieve maximal benefit from the array, and the economic impacts of creating and using such genotyping platforms for aquaculture species.