Development and Application of Genomic Breeding Values
in the Katahdin Breed
Katahdin Hair Sheep International
1. Activities Performed:
Since Katahdin Hair Sheep International (KHSI) was awarded funding through this grant, the organization has been busy working with its industry partners in educating the industry on the use of genomically-enhanced breeding values (GEBV’s), preparing to launch GEBV’s for the Katahdin breed, and collaborating with producers to ensure success.
The project began with preparation for educating producers about GEBV’s. This was done through several methods, primarily through educational documentation, Internet promotion, and webinars.
A webpage was built and launched on NSIP’s website to serve as a central location for the industry to receive information about GEBV’s (Genomic-enhanced EBVs – National Sheep Improvement Program (nsip.org)). The first educational document published was “Genomic-Enhanced Estimated Breeding Values (GEBV) for the American Sheep Industry” (Weaver, Weeks, and Bielek, 2021). Next, KHSI collaborated with Dr. Andrew Weaver of North Carolina State University to host a webinar series about GEBV’s. Links to those webinars are stored on the GEBV website link above. A logo generic to all breeds was also developed, which has been used to promote GEBV’s throughout the industry.
The second phase was to prepare producers about the process of collecting and submitting data. This was done through webinar education as well as the development of several documents:
● “NSIP Genotyping Strategies: guidelines for on-farm DNA sampling to generate Genomic-enhanced Estimated Breeding Values” (Hodgman and Lewis, 2021).
● “Framework for Obtaining Genomic-enhanced EBVs” (2021).
● “NSIP Genomics Check List” (2021).
● “NSIP Genomics Sheep Submission Form” (2021).
These documents facilitated producers in strategically sampling over 2000 animals during the summer of 2021. This is twice the number of sheep that were expected to be sampled, a further testament to the enthusiasm in the industry for GEBV’s.
The next phase of the project was calculating, processing and producing GEBV’s, and preparing materials to assist other organizations with developing GEBV’s for their breeds. Sample collection and submission for genomic testing for GEBV’s began in the spring of 2021. This allowed KHSI an opportunity to work with NSIP to determine the process and equipment necessary to make GEBV sample collection scalable for the whole industry. GEBV’s for Katahdins were officially launched on the October 1st data run with NSIP. Additionally, a document was developed by the NSIP Technical Committee, in collaboration with this project, to give a framework within which other breeds can begin to implement GEBV’s into their genetic selection tools. “Guidelines for sheep genotyping strategies: building the basis for successful implementation of genomic selection in U.S. sheep populations” (Lewis and Brito, 2021).
The current phase of the project is educating producers on the new GEBVs, the incremental changes to GEBVs, and the remaining work to be done. Two more webinars were held in October, taught by Dr. Ron Lewis, to highlight and explain the biggest changes and next steps in the program.
Everything done to date with this grant will be available for the researchers who received the USDA-NIFA grant for “Improving Robustness and Climatic Resilience in U.S. Sheep Populations Through Genomics.” This NIFA grant is a multi-breed grant that will involve the genomic sampling of thousands of animals. As that grant starts to generate GEBV’s the researchers can use the documents developed, thanks to this Sheep Center grant to educate breeders in other breeds about GEBV’s.
As of the October 1st data run with the National Sheep Improvement program, the U.S. sheep industry received its first GEBV’s for the Katahdin breed. The education provided in advance of the launch of GEBVs, in large part thanks to this grant, helped producers sample the appropriate sheep which helped to maximize the impact of the GEBV’s, encouraged broad participation from a large number of NSIP-enrolled Katahdin flocks, and helped to provide the industry with information about how this could impact their operations.
The project is estimated to be 70% complete.
1 Pre-launch Educational campaign: Dec-March Prepare industry for what’s coming: why GEBVs benefit us, how they work, and logistics of sample collection and submission, strategies for choosing which animals to sample, participation fees.
2 Website creation - January A central storage site for guidance documents, links to webinars, etc.
3 Process development and documentation Define the process for sample collection, submission to NSIP, collation and submission to NeoGen, and data transmission to LambPlan. Gain stakeholder agreement on end-to-end process between NSIP, NeoGen and LambPlan. Create instruction documents and educational material around this.
4 Test run using Reference Population Data- March Initial genomics run was done using existing Reference Population data, to dry-run the process end-to-end: parentage testing, DNA testing, and GEBV calculation. Process issues were resolved here before doing 1st run using producer submitted samples/data.
5 Update Katahdin EBV parameters, validate GEBV calculations Long overdue step to update “standard” EBV parameters and calculations, to bring EBV + GEBV calculations up to date with best known modeling data to-date. Final validation of GEBVs and underlying algorithmic data.
6 First and second runs on producer-submitted samples and data: July and September Samples collected and collated by Rusty Burgett, forwarded on to NeoGen. Parentage and DNA results sent back to producers.
7 GEBV and EBV updates: educational sessions Sept-Oct Further sessions held to explain how EBV models were updated, and what to expect once GEBVs are received in October.
8 “Flip the switch” to turn on GEBVs for all Katahdins in NSIP - October 1st Strategic decision to wait until after spring/summer show/sale season, two sets of DNA submission, and most lambing crops submitted. Updated GEBVs received in time for fall breeding decisions.
Challenges and Developments
1 As the GEBV model was being evaluated for introduction, it became clear that updates were needed to the base EBV modeling as well, and were long overdue. It made sense to do them at the same time. Added this to the scope of the project, and completed the work summer 2021.
2 The “USA HAIR” Katahdin index needs to be updated; it is no longer relevant/accurate based on updated models. This will require significant effort. For the short term, stopped reporting the index. Will remodel it and re-publish spring 2022.
3 Sample handling, collation and organization is still a very manual process. Some producers needed a lot of help in preparing their submissions, which was provided by Rusty Burgett; but took a significant amount of his time. This is not scalable or sustainable without further improvements. Grant money may be used to compensate NSIP for Rusty Burgett’s time in this regard. Hold a retrospective to identify key parts of the process which could be better explained and documented in education materials. Analyze what portions could be automated, what other livestock industries do, and what other process improvements could be made before GEBVs are taken to scale across the industry.
4 Delays experienced with dependencies on process steps needed from AGBU, LambPlan, NeoGen. Hold weekly meetings with AGBU and NeoGen stakeholders, track action items and commitment dates. Discuss blocking issues and resolution strategies. Invest in the partnership while also holding our partners accountable for their contractual commitments.
Outcome and Indicator Results to Date
1 Producer participation Producer engagement and participation far exceeded expectations. This is a key indicator that our industry is ready for GEBVs, that producers see value in them, and are willing to invest time and money in this technological development.
2 Research community support This project would not have been possible without the tremendous support and contribution from Dr. Ron Lewis, Dr. Joan Burke and many others in the research community. They contributed many hours in preparing and delivering education, as well as updating and validating the models and developing and honing the process for sample processing and data relay between NSIP, NeoGen and LambPlan.
3 GEBVs are live! The most significant portion of this project is complete, and that is that GEBVs have permanently “gone live” for the Katahdin breed. This sets a path forward for other breeds to follow suit, using the infrastructure created from this project: Reference Population, educational materials, process for sample submission and processing, and resultant GEBV calculations.
1 Final sample submission deadline late 2021/ early 2022 for this round. Develop regular sample submission schedule/ cadence for subsequent years March 2022
2 Continued education- repeat 2021 webinars and/or host new ones for Q&A and continued discussion on producer experience with GEBVs as well as the process for and costs of participation. Strive to expand participation beyond “early adopters”. Continue to listen to, evaluate and respond to feedback from producer experience. August 2022
3 Complete update of the “USA HAIR” Katahdin index June 2022
4 Identify and implement needed process improvements for sample submission, handling, collation and forwarding on to NeoGen. June 2022
5 Create a “handbook” for other breeds to follow to implement GEBVs in their own breeds October 2022