INTERBULL EXECUTIVE SUMMARY NO. 2024-3: JULY-SEPTEMBER 2024
This executive summary reports the latest information about the Interbull Centre and important decisions taken by the Interbull Technical Committee (ITC) in their meeting of 16 September 2024, and by the Interbull Steering Committee (SC) in their meetings on 17 July and 16 September 2024.
Governance – Interbull Steering Committee
New Steering Committee Vice Chair
At the Interbull Steering Committee meeting on 16 September 2024, the SC members elected Urs Schnyder, representative of Germany, Austria and Switzerland, as Vice Chair of the Steering Committee. Urs replaces the previous Vice Chair, Brian Van Doormaal, who stepped down from the Steering Committee earlier this year.
Interbull SC Working Groups
During the SC meeting of 17 July 2024, the SC decided to disband two Working Groups,: The mandate for the ”New Traits Pipeline Working Group” is considered to be fulfilled: a pipeline is in place, and has in fact led to the current call for 9 new traits (for more info, see “New Traits” under “Research & Development”, below). We would like to thank Gerben de Jong, Ezequiel Nicolazzi, Valentina Palucci and Toine Roozen for their contributions.
During the same meeting it was decided to disband the InterGenomics-Holstein (”IgHOL”) Working Group, and establish an IgHOL Management Group. The SC thanks IgHOL members Brian Van Doormaal, Marija Klopčič, Toine Roozen for being instrumental in establishing the IgHOL service. The IgHOL Management Group will consist of representatives of the IgHOL member countries (Ireland, Slovenia, South Korea and Israel) to ensure a continuous delivery of the service. Interbull Centre is represented by Katrine Haugaard and Toine Roozen.
Validation Services
Validation test
A new enhanced GEBVtest software has been released on August 2024. The software includes a revised methodology, based on VanRaden's de-regressed GEBV (described in the 2021 Interbull bulletin paper, https://journal.interbull.org/index.php/ib/article/view/82) as the official prediction target. The VanRaden dGEBV replaces the previously used dEBV target described by Mantysaari et al (2010). Predicting later GEBV or dGEBV from earlier GEBV is conceptually easier to understand and to verify than predictions of dEBV. The new tests are also more suitable for validating single-step models, where genomic preselection effects are properly accounted in GEBVf, GEBVr and dGEBV,
whereas dEBV include genomic preselection bias. More information about the enhanced software is available in the Interbull Code of Practice, Appendix VIII (https://interbull.org/ib/cop_appendix8). The new software is available for downloading from the Interbull Centre webpage, https://interbull.org/ib/gebvtest_software_2024.
Data Exchange Services
International Genotype Exchange Platform (GenoEx)
The GenoEx Platform was most recently updated in September 2024 to improve the user experience for both PSE and GDE modules. The update includes, among other things, the following improvements for the users:
- The “system data” page will now also be accessible from the GenoEx entry page so that information about available arrays, laboratories, breeds and countries can be retrieved without the need to log in.
- The feedback provided by the system to any possible errors related to input file format problems has been improved in its content.
- When performing extractions, a short summary of the selection criteria applied will now be available in the comment section of the history table, so that users can always double check the information received against the selection criteria applied.
- The job status page will now also display information about the number of extracted genotypes and the size of the extraction file.
New features strictly related to the GDE module and, at this moment, mostly relevant to the InterGenomics BSW users, have been added:
- A delta-extraction is now available, where the user will have the possibility to select only genotypes that have NOT been previously downloaded by their organization.
- The support program gxapi.py has been improved to also include the new delta-extraction feature.
These and other features will be addressed in the upcoming GenoEx Webinar (information can be found in the Communications and Collaboration section of this document).
Genetic Traits Exchange
Interbull’s Genetic Traits Exchange services are in place for Holstein and Brown Swiss cattle through collaboration with the World Holstein Friesian Federation (WHFF) and the InterGenomics (Brown Swiss) community respectively.
The WHFF Council have recently approved the addition of Muscle Weakness to the WHFF Genetic Traits Master list. Muscle Weakness will be included in Interbull’s Genetic Traits Exchange service from the December 2024 Routine evaluation. Please see the table below for the full list of traits included.
ANAFIBJ (Italy) is the most recent organsitation signing up to the Genetic Traits Exchange Service for the Holstein breed. Participants for Holstein are now: Italy, Canada, United Kingdom, The Netherlands and Germany. Participants in the Genetic Traits Exchange for Brown Swiss are: Canada, USA, Germany, Austria, Italy and Switzerland.
Traits included in Interbull’s Genetic Traits Exchange Service
PREP Database: The Performance Recording, Evaluation and Publication database (PREPdb) has now been populated with specific electronic forms for dairy udder health, longevity and workability traits. The newly added forms have been pre-filled for each organisation according to their available information in the old Genetic Evaluation (GE) forms. Organisations are invited to check all remaining parts of such forms and complete them as necessary. All traits currently included in an international genetic evaluation (dairy and beef) have now their respective electronic form in PREPdb. From now on the usage of the former National Genetic Evaluation (GE) forms will be disbanded. Instead, organisations are expected to provide updates on their national genetic evaluations directly inside PREPdb. Development of electronic forms for reporting descriptive information regarding GENOMIC evaluations is expected to be completed in 2025.
Research & Development
New Traits
Following the 2024 Business Meeting discusssions on the information collected in the PREPdb for introducing new traits into Interbull’s portfolio, a data call was issued on 21 August 2024 to all current MACE users with information on the new traits and trait groups that will be included in a research run:
- Metabolic disease: Clinical Ketosis; Sub-clinical Ketosis; Milk fever.
- Claw health: Digital dermatitis; Interdigital dermatitis; Interdigital hyperplasia; Sole haemorrhage; Sole Ulcer; White Line Disease.
- Gestation Length will be added to the Trait Group ‘Calving’.
Organisations that wish to participate but have not informed the Interbull Centre yet for which breed*trait combinations, should do so as soon as possible; Actual data can be submitted until 31 October 2024. Participants in the research run are NOT under any obligation to participate in any Routine evaluations that may follow.
Interbull Genomic Reliability (GREL) WG
The working group is continuing to investigate the applicability of the Interbull guidelines to small breeds and new traits as well as work on improving the current guidelines with references to best practices for weekly genomic evaluation.
Interbull Trend Validation Tests WG
The working group will continue exploring new approaches for an enhanced Trend Test method III, in order to be able to apply the test to young genomic bulls as well, and review the Mendelian Variance Test.
Review Service Calendar WG
A survey has been sent out to all MACE users to collect their feedback on the current service calendar and their suggestions for improvements. The survey has been completed by many organisations, marking the relevance of the topic. On the basis of the feedback collected the working group will proceed preparing some proposals to be further discussed within the Interbull Technical Committee.
Communication and Collaboration
GenoEx Webinar
The Interbull Centre webinar series is continuing. The next webinar is scheduled for 10 October 2024, and will cover the functionalities of GenoEx-GDE and the accompanying support programs gxprep.py and gxapi.py. Registration is possible until 8 October 2024 by sending an email to Interbull@slu.se .
Interbull Bulletin
The proceedings of the 2024 Interbull Open Meeting in Bled, Slovenia, were published on 4 September 2024 in Interbull Bulletin Issue No. 60. All submitted papers can be accessed here: https://journal.interbull.org .
2025 Interbull Annual Meeting
The 2025 Interbull Annual Meeting will be held in conjunction with ADSA in Louisville, KY, USA. Interbull Business Meetings, Open Meetings and joint Sessions will be organised on Saturday 21, Sunday 22 and Monday 23 June 2025. Information about the venue and registration will become available on the ADSA website https://www.adsa.org/Meetings/2025-Annual-Meeting. Specific information about the Interbull meeting will be made available on the Interbull event page https://interbull.org/ib/2025_adsa_interbull.