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July - November 2020
During the first six months of 2020, no executive summary has been published. The 2019-2020 activity report, however, does cover the changes/implementations that have happened in this period. Due to the Covid-19 pandemic, the ICAR-Interbull Meeting scheduled for June 2020 in Leeuwarden was postponed to April 2021 instead. In order to give our community the possibility to ask any questions in relation to the 2019-2020 activity and finance reports, strategic plan as well as the videos that were posted online on the Interbull website, two online Q&A sections were organized on 20 August and 8 September 2020 which were followed by a total of 63 people.
After 5½ years, Haifa Benhajali decided to leave the Centre to focus more on big data handling and machine learning. We thank Haifa for all the good years she has spent at the Centre and for all her contributions. We wish her best of luck in this new chapter of her career. The recruitment process for a geneticist has started, with full details available on https://www.slu.se/en/about-slu/work-at-slu/jobs-vacancies/
Mohammed Abdallah Ahmed Sallam has successfully finished his Master thesis at SLU working with Interbull data (IG-BSW data) on comparing multi-trait to single-trait International genomic evaluations. He has since then been employed at the Centre with a temporary position until the end of 2020. He is focusing on revising the GE form questions and harmonizing the information collected so far in the context of Interbull Centre’s role as the European Union’s Reference Centre. . After this time at the Centre he will start a PhD position at SLU.
Steering Committee’s Membership Renewal
As announced in the online meetings, Enrico Santus will hold his membership with SC for one year longer until April 2021 when also other SC memberships will be up for election. This has been also endorsed by the ICAR board. The process of collecting new candidate names from representative countries is ongoing at the SC level.
New post-processing windows for MACE correlations: Following the ITC recommendation to review such windows every 5 years, the Centre has, during the first half of 2020, reviewed such values which were last reviewed in 2015. With the help of the post-processing working group, new values have been identified and set equal to the 10th percentile of all country correlations within groups. This change would allow the post-processing correlations to be more in line with the real estimated ones. Implementation of the new post-processing windows is planned for the January 2021 test run.
InterGenomics-HOL: all research and developments have been implemented and during the September 2020 test run a dedicated Intergenomics HOL (IG-HOL) test run has been carried out. The first official IgHOL evaluation is therefore scheduled to take place in December 2020, with the involvement of 4 participating countries (Ireland, Israel, South Korea and Slovenia), and 3 contributing countries (Germany, Denmark/Finland/Sweden and France).
Clinical Mastitis Evaluation (cma):
The current mastitis evaluation, combining SCS and clinical mastitis information, has lately brought up two main arguments towards the possibility to have a dedicated clinical mastitis evaluation. These were: 1) the low correlations for national bulls between national and MACE proofs and 2) the need, in the genomic era, to have a foreign reference population for clinical mastitis not affected by the inclusion of SCS data. the Interbull Centre has, therefore, worked on the feasibility to offer a dedicated cma evaluation where the number of daughters are based solely on clinical mastitis information with a minimum number for inclusion set to 10 daughters in 10 herds. Such new evaluation will be considered as a new service towards SNP training. Therefore, its results will only be provided to the participating countries, and may not be used for publication purposes. The associated new service fee is currently being finalized by the Business Funding Model Task Force. A first official test run for such new evaluation is envisioned for the January 2021 test run with the official evaluation set for April 2021.
GenoEX PSE: Opportunities to increase participation are being pursued through the adjustment of the thresholds for data requirements, and expansion from Parentage Verification to Parentage Discovery. The software for the Parentage Discovery accreditation test is in its last phase of development and the ICAR DNA Working Group is now working with ICAR to expand the relevant accreditation procedure and fee structure which will be needed for taking part in the GenoEx-PSE Parentage Discovery service.
GENOEX GDE: was launched in August 2020 for use in InterGenomics-BSW only. It is envisioned to implement GenoEx-GDE for InterGenomics-HOL next and expand the service to other users outside the InterGenomics service after that. First feedback from IG-BSW users has been collected since its release and the database has already been improved by implementing some key points raised. These include amongst others: better ways to accept and handle new SNP map requests as well as managing the data sharing permissions.
snpMACE: The snpMACE software (“METAGS”) has been developed by Agriculture Victoria Research following recommendations by the snpMACE Working Group. The Interbull Centre is working now with National Genetic Evaluation Centres to test the software on different systems, and a data call for a pilot run is in preparation.
Interbull-ICAR 2021 meeting
As events continue to unfold, the format for the next Interbull-ICAR meeting is being adapted. At this stage, a hybrid meeting, combining physical presence, virtual sessions and pre-recorded presentations is been considered. More information will be provided as soon as it is available.