Differences between revisions 4 and 7 (spanning 3 versions)

Minutes from Interbeef Technical Committee Meeting

Aarhus, May 27, 2013
Hotel Scandic Aarhus City

Participants

Brian Wickham (WG Chairman), Lubos Vostry, Pavel Bucek, Zdenka Vesela, Clara Diaz Martin, Eric Venot, Ross Evans, Thierry Pabiou, Raphael Mrode, Anders Fogh, Valentina Palucci, Mohammad Nilforooshan, João Dürr, Eva Hjerpe, Japie van der Westhuizen, Laurent Griffon, Fritz .

1. Opening and adoption of agenda

The Interbeef Chairman Dr Joao Durr, welcomed all the participants. The agenda proposed contained many reports both from Interbull Centre and the countries. Spain did not receive all the reports sent by countries via email. The chairman reminded the group to use the Interbeef forum so to avoid problems such this in the future.

ADOPTED AGENDA

Opening and adoption of agenda
Minutes from meeting in Uppsala - Dec 2012
Results from the Adjusted Weaning Weight test run
1. Variance components (Mohammad Nilforooshan)
2. Breeding values (Mohammad Nilforooshan)
3. Reliabilities (Mohammad Nilforooshan)
4. Country reports on results
Calving traits pilot run
1. Data reception (Eva Hjerpe)
2. Report from CZE (Pavel Bucek)
Heterosis and recombination coefficients (Thierry Pabiou)
Genetic parameter survey (Ross Evans)
Inclusion of new countries in AWW evaluations
Timeline for new traits
Technical committee terms of reference
Recommendations to the working group
Adjourn

2. Minutes from meeting in Uppsala

The minutes from the previous technical meeting held in Uppsala in December 2012 were fully accepted by all participants.

3. Results from AWW test run

a. Variance components b. breeding values prediction c. reliabilities

Mohammad presented an overview of data used at Interbull Centre for variance components estimation, breeding value prediction and reliabilities estimation; the preliminary checks done on the data and the results for correlations, international EBV and reliabilities for all countries and the breeds they participated with. While EBV prediction got a general approval, the main concern from the participants was still on parameter estimation procedure and reliabilities.
Eric Venot pointed out to do not put much attention on the EBV results until we are more confident that variance components estimation is correct. Eric also highlighted the importance to have the standard errors of the estimates available so to have a better understanding of the quality and soundness of the results. Unfortunately MIX99 does not provide such estimates.
Ross Evans commented that the difference options on conversion creteria might have an impact on the final results and wondered if Interbull Centre had tried some different options, Mohammad reported that indeed different scenarios were tested. Several suggestions were proposed:
Raphael Mrode proposed to validate the results on converging by running a bivariate analysis from two countries;
Clara Diaz proposed to estimate variance components with a bayesian analysis instead of Mix99, in this way we could see what the probability of a correlation being above a certain treshold would be.

Joao reminded the participants that estimation of genetic parameters was still an open issue. Interbull Center tried to provide some trials to go ahead and provide some results although the complexity of the topic still requires a common effort between Interbull Center and ICBF.

d. Countries report

SPAIN: EBV results were acceptable but there were some concerns on reliability which values seemed to be too low. Mohammad commented that some differences in international/national reliability were due to the different value of heritability used in the international analysis compared to the heritability used nationally.

FRANCE: They would like to receive more feedback on the amoount of data used for international evaluation and how the data were used.They proposed a change in the distribution file format: having the information displayed vertically rather than horizontally. Joao informed that a similar change in format is undergoing also in dairy and that therefore it would not be a problem to implement. They also pointed out an issue with a certain amount of pedigree information marked as invalid by the authoritative organization but still included in the analysis. Valentina explained that the reason for it was that that particular animal was associated with a performance value elsewhere and most likely being an old animal being exported as very young animal and its ID not properly recorded in the country of first registration. It was decided to assess the problem to see how many of these animals were included in the analysis, check their birthdate and try to find a way to discriminate these animals from the other validated animals. There seemed to be some issue with reliabilities results as there were no results for the range 0.0-0.08. The reason for this absence was unclear and it was agreed that Interbull Centre will look into it. In general international reliabilities were higher than national reliabilities, a possible explanation for it could be the different value of heritability used and the benefit from using international data.
Eric suggested two ways for validating the results 1) for Interbull Centre to run a new variance components estimation with zero correlations and using the same variances as used by the countries; 2) as the French national evaluation includes also animals not sent to Interbull Centre it could be good for France to run an evaluation with a data set as close as possible to the data sent to Interbull Centre, so to reduce the source of variation.

IRELAND: as Interbeef evaluation did not include crossbreed animals the results were not yet very useful in Ireland. Inclusion of crossbreeding animals within a given breed of evaluation would definetely increase the importance of such evaluation in Ireland.

DENMARK: results for Charolaise seem reasonable as the trend of IEBV is quite similar with the national trend, the trend for Limousin presents some differences, national trend appear to be much steeper than international trend.

CZECH REPUBBLIC: The results looked much better than the ones evaluated in December. Anyhow there still seems to be some issues in the genetic parameter estimation.

UNITED KINGDOM: There seems to be an issue in the scale of expression for IEBV. Last results looked better than the ones presented in December, there was a significant amount of reranking.

SWEDEN: The report sent by email showed to be in line with the other countries' report.

Final remarks: International EBV estimation using Mix99 have proved to work well, majority of trends were good although for some countries there could be a scale issue to investigate. For genetic parameters and reliabilities estimation Mix99 might not be the best choice. It was suggested to estimate genetic parameters and reliability using a small dataset and running with both Mix99 and a second software (either DMU or ASREML) and compare results. DMU would be a better choice as it could also provide standard errors of the estimates. Having a comparison with another software we could ask MTT to inspect better the differences and provide a plausible explanation.

4. Calving traits

a. Data Reception

Eva presented an overview of the data received from the participating countries on calving traits, the most common errors in preparing the necessary files and the amount of data sent to Czech Republic for analysis.

As all the information of pedigree have been recoded prior sending them to CZE, it was agreed that for better understanding and presenting the results the Czech could get the full international ID of all their national animals plus BREED+COUNTRY for every other international ID.

b. Report from CZE

Pavel presented a general introduction of the data received. There research group was waiting for some extra information coming from some countries in order to continue the research.

5. Heterosis and recombination

Thierry Pabiou presented the results on the possibility to calculate recombination and heterosis starting from the Interbull international pedigree. In his study he compared the results between the ICBF database and Interbull. The main point was the availability in ICBF of additional information in case of missing pedigree, i.e. availability of the breed of the sire/dam, which helped in the calculation of breed composition and therefore in the recombination results comparing to the Interbull database where such information are at the moment not available. Thierry's study pointed out that breed composition and recombination are therefore highly affected by the source of additional information and therefore change drastically between Interbull and ICBF. One of the many questions raised was what should be collected and make available in the Interbull database. Some suggested to store breed fraction of founders and breed of missing parents. Fritz commented the risk to have such information recorded in a permanent database such as the one stored at Interbull. The issue was that as the pedigree is a permanent one, as soon as a pedigree from a founder is provided or corrected this will change the breed composition of all other animals linked via the pedigree to this founder, therefore the breed composition will change overtime.

6. Genetic parameter survey

Ross Evans presented a survey on genetic parameter estimation as carry out in most countries. Interbull Centre is still open for collaboration and is still available for running analysis if it is needed but the research development is within the ICBF team. Some suggestions were provided on how to try to improve the estimation of variance components. Work with a well connected data but looking also at the data structure:having enough contemporary groups level and good numbers of herds among sampled data. Limit pedigree information to 5 generations. Run analysis with Mix99 and DMU and compare results.

ICBF and ITBC will present a research proposal quite soon.

7. Inclusion of new countries in AWW evaluations

A new evaluation is scheduled for September 2013. Due to the amount of evaluation already scheduled at the Interbull Center the evaluation in September would be a routine run, this means that no genetic parameters would be estimated in September. Due to the fact that Germany is ready to send data and therefore is ready to participate to the September evaluation it would be anyhow necessary to re-estimate variance components. It was proposed that Germany would send proper file for AWW and pedigree to Interbull Centre by July. Interbull Centre would run variance components in July using the new data from Germany and the old data from the other countries, so that the September run would still be a routine run in which Germany would be able to participate having the variance components being estimated earlier.

8. Timelines for new traits

The participants expressed high interest for carcass traits to be the next new trait to start researching. It was agreed that the group involve in carcass traits, United Kingdom and Ireland, will present a research proposal and a timeline.

9. Technical committee terms of reference

Due to lack of time it was agreed that everybody would read the documentation and send comments/recommendations to the forum.

10. Recommendations to the working group

Joao summarized the main topics and decision of the meeting which he will present the next day at the Interbeef Working Group meeting:

Need of detailed description of data and evaluation results from the Interbull Centre to participating countries.
Mix99 is a well tested software for EBV estimation and results look consistent
Genetic parameters:
- Impact ranks and reliabilities - need to be comfortable
- Still a research topic:ICBF
  - Survey among users
  - Sample data looking at connectedness and data structure
  - Limit number of generations with data
  - Try alternative methods
  - Compare Mix99 with alternative software
Reliabilities:
- Compare Mix99 with alternative software (fit one country data only to compare results)
- Investigate gaps at very low reliability values (0.0-0.08)
- Check Maternal effects in Mix99
- Compare sources of information considered both at national and international evaluations.
Pedigree:
- investigate issue on invalid animals
- see how many there are in the analysis and how old they are
- Propose way to distinguish between invalid and unverified animals.
Calving data:
- send COU+BREED combination to CZE for research.
Breed fraction: continue discussion
Terms of reference: will be review and discussed online

11. Adjourn

The Chairman thanked all participants and adjoured the meeting.

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-. technical committee terms of reference
+. Technical committee terms of reference
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-=== 2. Administrative matters ===
==== a. Technical Committee terms of reference ====
Terms of reference (ToR) are needed for the Interbeef technical committee (TC-Beef) in order to clearly define the mandate of this group. The Interbeef WG ToR already describe the main roles of the TC-Beef and the Interbull Technical Committee ToR can also be used as a reference. A proposal will be posted in the TC-Beef discussion forum by the Interbull Centre (ITBC) for discussion before being sent to the WG for approval.
+=== 2. Minutes from meeting in Uppsala ===
The minutes from the previous technical meeting held in Uppsala in December 2012 were fully accepted by all participants.
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+Line 34:
-==== b. Calendar of TC meetings ====
The group agreed to have ordinary meetings once a year at the ICAR annual meetings, preferably before the WG meets. Eventually, if more urgent matters require, extraordinary meetings may be organized according to the TC-Beef members. It is suggested that the TC-Beef can help the WG organizing technical sessions focused on genetic evaluation of beef breeds and traits during the ICAR meetings.
+=== 3. Results from AWW test run ===
==== a. Variance components b. breeding values prediction c. reliabilities ====
Mohammad presented an overview of data used at Interbull Centre for variance components estimation, breeding value prediction and reliabilities estimation; the preliminary checks done on the data and the results for correlations, international EBV and reliabilities for all countries and the breeds they participated with. While EBV prediction got a general approval, the main concern from the participants was still on parameter estimation procedure and reliabilities. <<BR>> Eric Venot pointed out to do not put much attention on the EBV results until we are more confident that variance components estimation is correct. Eric also highlighted the importance to have the standard errors of the estimates available so to have a better understanding of the quality and soundness of the results. Unfortunately MIX99 does not provide such estimates. <<BR>>Ross Evans commented that the difference options on conversion creteria might have an impact on the final results and wondered if Interbull Centre had tried some different options, Mohammad reported that indeed different scenarios were tested. Several suggestions were proposed: <<BR>>Raphael Mrode proposed to validate the results on converging by running a bivariate analysis from two countries; <<BR>>Clara Diaz proposed to estimate variance components with a bayesian analysis instead of Mix99, in this way we could see what the probability of a correlation being above a certain treshold would be.
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-==== c. Research infrastructure ====
 * As it was previously agreed, research will be carried out by research partners and not by the Interbull Centre. Mix99 was successfully used by the ITBC to calculate international breeding values and variance components for adjusted weaning weight. The software is very efficient and takes only about two hours for EBV estimation. Also other genetic centers, like ICBF and SRUC, have had a positive experience with Mix99. Some other genetic centers, like Sweden and Denmark, have positive experience with DMU instead.
 * A secure access to data for the research partners has been discussed. Due to very large amount of data that need to be made available to the research partners and also due to the concern from the service users about its security, the ITBC proposed to provide access to a virtual machine in the cloud with the same environment used at the ITBC (Linux, Fortran compiler, Mix99) as well as access to research data (pedigree and phenotypes). The cost for such virtual machine is not accounted for in the Interbeef budget, and therefore should be covered by the research partner.
 * Mix99 doesn’t necessary need to be the software used by the research partners. Interbull Centre simply offers the partners the possibility to use it.
 * It is very important to have research agreements. One type of agreement should regulate the use by research partners of the Mix99 programs licensed to the ITBC. MTT has agreed to allow access to Interbeef research partners as long as they agree not to use the software for other purposes outside the project. Interbull Centre has already a similar agreement with Holstein USA which could be taken as a model. The other type of research agreement will have clearly stated that data are used for research purposes only. Brian Wickham will prepare a first draft of it as well as of a research agreement with each partner.The research agreement should be made available soon.
 * About publications, Raphael reported on the practice at Interbull: the organization that does the research should refer back to all organizations that have provided data which should have access to the paper and the results prior to publication.
+Joao reminded the participants that estimation of genetic parameters was still an open issue. Interbull Center tried to provide some trials to go ahead and provide some results although the complexity of the topic still requires a common effort between Interbull Center and ICBF.
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-=== 3. Calving traits pilot run ===
==== a. Data Format ====
A question was raised on how to handle calves that are born dead without an identification and thus without an entry in the pedigree database. To avoid populating Interbull database with fake IDs for dead animals and to avoid creation of multiple file formats, Interbull Centre proposed to report data such as stillbirth and birth weight as a maternal trait. Therefore, for such traits the record sld refer to the dam. Effect of the sire, sex of the calf, ID of the calf (if available) can be entered as environmental effects. In the current file format description for file 602 the environmental effects are reported with length of 10 characters. It was therefore agreed to expand their length to 20 characters to allow inclusion, for instance, of the sire international ID with 19 characters. The ITBC will take care of updating the Interbeef guidelines with the corrected file format and add a specification on how to report calving traits since the field interpretation varies.
+'''d. Countries report<<BR>>'''
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-==== b. Research plan (CMSCH, VUZV) ====
Pavel Bucek presented the research plan for calving traits that will be carried out in Czech Republic. He showed that his research team has got enough finances to cover all research steps. As for research infrastructure Pavel informed the group that they will start working first with SAS, BLUPF90 family then move to MIX99 when available as they do not have MIX99 and it will take time for his group to get acquainted with it. They have sufficient hardware at the research institute, and have also access to CMBC hardware and to their own IT specialists. Timetable: they will start as soon as they will receive the data. The research will take approximately 1 year considering a starting day of end of January 2013. It would be useful to have discussions on partial results, this can be done via forum, emails and/or special meetings. He envisions a summary report every two months to inform the group about the research progress. The following is a summary of what each country will be able to provide:
||<tablestyle="margin-left:32.2pt;border-collapse:collapse;border:none;mso-border-alt:solid windowtext .5pt;mso-yfti-tbllook:1184;mso-padding-alt:0cm 5.4pt 0cm 5.4pt" tableclass="MsoTableGrid"rowstyle="mso-yfti-irow:0;mso-yfti-firstrow:yes"width="154px" style="border:solid windowtext 1.0pt;mso-border-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt;vertical-align:top">'''''Country''''' ||<width="154px" style="border:solid windowtext 1.0pt;border-left:none;mso-border-left-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt;vertical-align:top">'''''Breed''''' ||<width="154px" style="border:solid windowtext 1.0pt;border-left:none;mso-border-left-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt;vertical-align:top">'''''Calving ease''''' ||<width="154px" style="border:solid windowtext 1.0pt;border-left:none;mso-border-left-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt;vertical-align:top">'''''Stillbirth''''' ||<width="154px" style="border:solid windowtext 1.0pt;border-left:none;mso-border-left-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt;vertical-align:top">'''''Birth weight''''' ||
||<rowstyle="mso-yfti-irow:1"width="154px" style="border:solid windowtext 1.0pt;border-top:none;mso-border-top-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt;vertical-align:top">France ||<width="154px" style="border-top:none;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt;vertical-align:top">CHA, LIM ||<width="154px" style="border-top:none;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt;vertical-align:top">X ||<width="154px" style="border-top:none;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt;vertical-align:top">- ||<width="154px" style="border-top:none;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt;vertical-align:top">X ||
||<rowstyle="mso-yfti-irow:2"width="154px" style="border:solid windowtext 1.0pt;border-top:none;mso-border-top-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt;vertical-align:top">Czech Republic ||<width="154px" style="border-top:none;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt;vertical-align:top">CHA, LIM ||<width="154px" style="border-top:none;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt;vertical-align:top">X ||<width="154px" style="border-top:none;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt;vertical-align:top">- ||<width="154px" style="border-top:none;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt;vertical-align:top">X ||
||<rowstyle="mso-yfti-irow:3"width="154px" style="border:solid windowtext 1.0pt;border-top:none;mso-border-top-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt;vertical-align:top">Ireland ||<width="154px" style="border-top:none;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt;vertical-align:top">CHA, LIM ||<width="154px" style="border-top:none;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt;vertical-align:top">X mostly on crossbreeds ||<width="154px" style="border-top:none;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt;vertical-align:top">Few observations ||<width="154px" style="border-top:none;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt;vertical-align:top">Few observations ||
||<rowstyle="mso-yfti-irow:4"width="154px" style="border:solid windowtext 1.0pt;border-top:none;mso-border-top-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt;vertical-align:top">Denmark ||<width="154px" style="border-top:none;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt;vertical-align:top">CHA, LIM ||<width="154px" style="border-top:none;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt;vertical-align:top">X ||<width="154px" style="border-top:none;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt;vertical-align:top">X ||<width="154px" style="border-top:none;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt;vertical-align:top">X ||
||<rowstyle="mso-yfti-irow:5"width="154px" style="border:solid windowtext 1.0pt;border-top:none;mso-border-top-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt;vertical-align:top">Sweden ||<width="154px" style="border-top:none;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt;vertical-align:top">CHA, LIM ||<width="154px" style="border-top:none;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt;vertical-align:top">X ||<width="154px" style="border-top:none;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt;vertical-align:top">? ||<width="154px" style="border-top:none;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt;vertical-align:top">X ||
||<rowstyle="mso-yfti-irow:6"width="154px" style="border:solid windowtext 1.0pt;border-top:none;mso-border-top-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt;vertical-align:top">Spain ||<width="154px" style="border-top:none;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt;vertical-align:top">LIM ||<width="154px" style="border-top:none;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt;vertical-align:top">- ||<width="154px" style="border-top:none;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt;vertical-align:top">- ||<width="154px" style="border-top:none;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt;vertical-align:top">x ||
||<rowstyle="mso-yfti-irow:7"width="154px" style="border:solid windowtext 1.0pt;border-top:none;mso-border-top-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt;vertical-align:top">Finland ||<width="154px" style="border-top:none;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt;vertical-align:top">? ||<width="154px" style="border-top:none;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt;vertical-align:top">? ||<width="154px" style="border-top:none;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt;vertical-align:top">? ||<width="154px" style="border-top:none;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt;vertical-align:top">? ||
||<rowstyle="mso-yfti-irow:8;mso-yfti-lastrow:yes"width="154px" style="border:solid windowtext 1.0pt;border-top:none;mso-border-top-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt;vertical-align:top">Great Britain ||<width="154px" style="border-top:none;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt;vertical-align:top">LIM ||<width="154px" style="border-top:none;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt;vertical-align:top">X ||<width="154px" style="border-top:none;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt;vertical-align:top">- ||<width="154px" style="border-top:none;border-left:none;border-bottom:solid windowtext 1.0pt;border-right:solid windowtext 1.0pt;mso-border-top-alt:solid windowtext .5pt;mso-border-left-alt:solid windowtext .5pt;mso-border-alt:solid windowtext .5pt;padding:0cm 5.4pt 0cm 5.4pt;vertical-align:top">X ||
+__SPAIN__: EBV results were acceptable but there were some concerns on reliability which values seemed to be too low. Mohammad commented that some differences in international/national reliability were due to the different value of heritability used in the international analysis compared to the heritability used nationally.
-Line 62:
+Line 44:
+__FRANCE__: They would like to receive more feedback on the amoount of data used for international evaluation and how the data were used.They proposed a change in the distribution file format: having the information displayed vertically rather than horizontally. Joao informed that a similar change in format is undergoing also in dairy and that therefore it would not be a problem to implement. They also pointed out an issue with a certain amount of pedigree information marked as invalid by the authoritative organization but still included in the analysis. Valentina explained that the reason for it was that that particular animal was associated with a performance value elsewhere and most likely being an old animal being exported as very young animal and its ID not properly recorded in the country of first registration. It was decided to assess the problem to see how many of these animals were included in the analysis, check their birthdate and try to find a way to discriminate these animals from the other validated animals. There seemed to be some issue with reliabilities results as there were no results for the range 0.0-0.08. The reason for this absence was unclear and it was agreed that Interbull Centre will look into it. In general international reliabilities were higher than national reliabilities, a possible explanation for it could be the different value of heritability used and the benefit from using international data. <<BR>>Eric suggested two ways for validating the results 1) for Interbull Centre to run a new variance components estimation with zero correlations and using the same variances as used by the countries; 2) as the French national evaluation includes also animals not sent to Interbull Centre it could be good for France to run an evaluation with a data set as close as possible to the data sent to Interbull Centre, so to reduce the source of variation.
-Line 63:
+Line 46:
+__IRELAND__: as Interbeef evaluation did not include crossbreed animals the results were not yet very useful in Ireland. Inclusion of crossbreeding animals within a given breed of evaluation would definetely increase the importance of such evaluation in Ireland.
-Line 64:
+Line 48:
+__DENMARK__: results for Charolaise seem reasonable as the trend of IEBV is quite similar with the national trend, the trend for Limousin presents some differences, national trend appear to be much steeper than international trend.
-Line 65:
+Line 50:
-=== 4. Other research projects ===
==== a. Genetic correlations (ICBF) ====
ICBF should provide guidelines for parameter estimation from start to finish. It will be a very useful document as there is no such a thing available in today's literature. There is certainly the risk that data may not be balanced among countries: some countries with large amount of data some others with very few data. The initial recommendation is to create a subset of well-connected animals from which estimate variance components.
+__CZECH REPUBBLIC__: The results looked much better than the ones evaluated in December. Anyhow there still seems to be some issues in the genetic parameter estimation.
-Line 69:
+Line 52:
-==== b. Inclusion of crossbred animals (ICBF) ====
We need to be sure to have a pedigree deep enough to allow detection of breed composition. Ross Evans will provide a list of animals with phenotypes in Ireland (pure and crossbreds) from which the ITBC will extract a pedigree. The Irish will then check how good the calculation of breed composition is using the extracted pedigree. It would be important to be able to determine the breed composition of ancestors in case of truncated pedigree. One solution would be to rely on farmer declaration of the breed of sire. It will be useful to gather information on how countries evaluate breed composition. Then Ireland will study the inclusion of crossbred animal on a trait of their choice among the ones considered in Interbeef.
+__UNITED KINGDOM__: There seems to be an issue in the scale of expression for IEBV. Last results looked better than the ones presented in December, there was a significant amount of reranking.
-Line 72:
+Line 54:
-==== c. Carcass traits (SRUC) ====
Raphael Mrode informed that GBR has started collecting data and genotyopes for carcass traits for Limousine. He will have an updated report ready for the next meeting in Stansted.
+__SWEDEN__: The report sent by email showed to be in line with the other countries' report.
-Line 75:
+Line 56:
-==== d. Fertility traits (INIA) ====
There is a problem in Spain with budget cuts for cattle federation. Before committing to any timeline for research Clara Diaz needs to see how the budget problem gets solved. Clara has received information from the ITBC (Hossein Jorjani) about international fertility evaluation in dairy breeds and the Spanish team is currently studying it, and the intention is to have a report ready for the meeting in Stansted.
+__Final remarks:__ International EBV estimation using Mix99 have proved to work well, majority of trends were good although for some countries there could be a scale issue to investigate. For genetic parameters and reliabilities estimation Mix99 might not be the best choice. It was suggested to estimate genetic parameters and reliability using a small dataset and running with both Mix99 and a second software (either DMU or ASREML) and compare results. DMU would be a better choice as it could also provide standard errors of the estimates. Having a comparison with another software we could ask MTT to inspect better the differences and provide a plausible explanation.
-Line 78:
+Line 58:
-=== 5. Calendar of evaluations for 2013 ===
The wish from the Technical Committee members is to have two evaluations per year, possibly in January and August. João pointed out the fact that in August Interbull Centre is already committed with a dairy routine run beginning late July - early August and right after a dairy test run in September. There is also the need to enable holidays in late June-early July for the Interbull Centre team. Time of evaluation will be further discussed in January in Stansted.
+=== 4. Calving traits ===
==== a. Data Reception ====
Eva presented an overview of the data received from the participating countries on calving traits, the most common errors in preparing the necessary files and the amount of data sent to Czech Republic for analysis.
-Line 81:
+Line 62:
-=== 6. Adjusted Weaning Weight Test run results ===
Most of the work for data preparation and data analysis presented at the meeting was performed by Eva Hjerpe from the Interbull Centre. Unfortunately, due to a minor surgery, she was not able to attend the meeting.
+As all the information of pedigree have been recoded prior sending them to CZE, it was agreed that for better understanding and presenting the results the Czech could get the full international ID of all their national animals plus BREED+COUNTRY for every other international ID.
-Line 84:
+Line 64:
-==== a. Description of implementation flow ====
 * Check on incoming data: Interbull Centre has prepared a Python program to check correctness of incoming data. In particular the program checks the correctness of file format. The program can be made available to the service users in the future. Many thanks to Spain for providing performance data in advance so that Eva could test the correct functioning of the program.
 * Software used: Python for creation of input file and Mix99 for VCE and EBV estimation.
 * Correlations between countries: the proposal was that we should start by estimating EBVs adopting arbitrary correlations, but since MIX99 requires a (co)variance matrix as input the ITBC was forced to estimate them from the data.
+==== b. Report from CZE ====
Pavel presented a general introduction of the data received. There research group was waiting for some extra information coming from some countries in order to continue the research.
-Line 89:
+Line 67:
-==== b. Description of pedigrees ====
Valentina reported on the database activity during the period June-September 2012. All countries succeeded on uploading new pedigree files, verifying pedigree records reported by other countries and update their own database according to the feedback received by IDEA. Limousin and Charolais pedigrees were then traced back starting with animal with performance record. The Charolais pedigree used for the analysis contained 3,681,308 while the one for Limousine contained 2,203,324 pedigree records. Interbull Centre thanked all the countries for the effort they made on uploading pedigree and recommended to keep the verification process active all the time. Eric reported on a possible error in the French pedigree as appearing in the Interbull database. For some reason pedigree information are not fully displayed for some French animals despite the fact that France had uploaded full pedigrees. Eric and Valentina will further investigate on what could have caused the problem.
+=== 5. Heterosis and recombination ===
Thierry Pabiou presented the results on the possibility to calculate recombination and heterosis starting from the Interbull international pedigree. In his study he compared the results between the ICBF database and  Interbull. The main point was the availability in ICBF of additional information in case of missing pedigree, i.e. availability of the breed of the sire/dam, which helped in the calculation of breed composition and therefore in the recombination results comparing to the Interbull database where such information are at the moment not available. Thierry's study pointed out that breed composition and recombination are therefore highly affected by the source of additional information and therefore change drastically between Interbull and ICBF. One of the many questions raised was what should be collected and make available in the Interbull database. Some suggested to store breed fraction of founders and breed of missing parents. Fritz commented the risk to have such information recorded in a permanent database such as the one stored at Interbull. The issue was that as the pedigree is a permanent one, as soon as a pedigree from a founder is provided or corrected this will change the breed composition of all other animals linked via the pedigree to this founder, therefore the breed composition will change overtime.
-Line 92:
+Line 70:
-==== c. Phenotypic data editing ====
Mohammad presented all the editing that were further applied to the countries' performance data before entering the EBV estimation.
+=== 6. Genetic parameter survey ===
Ross Evans presented a survey on genetic parameter estimation as carry out in most countries. Interbull Centre is still open for collaboration and is still available for running analysis if it is needed but the research development is within the ICBF team. Some suggestions were provided on how to try to improve the estimation of variance components. Work with a well connected data but looking also at the data structure:having enough contemporary groups level and good numbers of herds among sampled data. Limit pedigree information to 5 generations. Run analysis with Mix99 and DMU and compare results.
-Line 95:
+Line 73:
- * the applied editing were:
  * Discard animals in performance file without an entry in the Interbull pedigree database
  * Birth year kept between 1991 - 2011
  * Exclusion of Twins and ET
  * Kept adjusted weaning weight records between 50 and 500 kg.
  * Check on consistency of sire(dam)/breed
  * Covariates check_ no edit, report to country
  * Contemporary group with at least 3 observation
  * Minimum 3 progeny per sire
  * Minimum 10 records per fixed effect
+ICBF and ITBC will present a research proposal quite soon.
-Line 106:
+Line 75:
-The Technical Committee agreed that each country should provide to Interbull Centre only edited data used in the national evaluation. Therefore Interbull Centre should no longer apply extra editing on the data received. Nevertheless, Interbull Centre still has the need to check that the data received by each country has indeed being edited.
+=== 7. Inclusion of new countries in AWW evaluations ===
A new evaluation is scheduled for September 2013. Due to the amount of evaluation already scheduled at the Interbull Center the evaluation in September would be a routine run, this means that no genetic parameters would be estimated in September. Due to the fact that Germany is ready to send data and therefore is ready to participate to the September evaluation it would be anyhow necessary to re-estimate variance components. It was proposed that Germany would send proper file for AWW and pedigree to Interbull Centre by July. Interbull Centre would run variance components in July using the new data from Germany and the old data from the other countries, so that the September run would still be a routine run in which Germany would be able to participate having the variance components being estimated earlier.
-Line 108:
+Line 78:
- * New editing rules were agreed:
  * Animals in performance file with no record in Interbull pedigree database: exclude animals from the evaluation and send the list of animal IDs to the country
  * Birth year edit: no editing. Reinforce that country should send to Interbull Centre only edited data used in national evaluation.
  * Twins: some countries, such as Sweden, Denmark and Czech Republic, do include twins in the model. Countries will specify in the parameter file if they include or not twins. If they say yes then the checking program will leave the twins in the file.
  * E.T.: each country will create an additional file listing all embryo-transferred animals without a performance record. This list will be used to include such animals in the breed-specific pedigree. E.T animals performances will be excluded from the evaluation but as they are included in the pedigree they will receive an international EBV.
  * Biological range: no edit is to be applied in the dependent variable. Calculate AWW distribution and send result back to the countries for verification.
  * Check on consistency of sire(dam)/breed: check that sire and dam are from the same breed (either both CHA or LIM). If sire is missing and dam is of the same breed as the calf (either CHA or LIM) then the record will be kept. If the dam is missing the record will be deleted.
  * Covariates: no edit, send distribution back to country.
  * Ireland should from now on provide only non-adjusted weaning weight because that is the trait used in national evaluations (most animals have only one weight recorded and AWW needs at least two).
  * Contemporary group: it is country responsibility to send to Interbull Centre data with enough number of observations per contemporary groups. Interbull Centre should check their distribution. Countries will specify in the parameter file the minimum number of observation per contemporary group to be adopted in the evaluation.
  * Number of progeny per sire: no edit
  * Number of records per fixed effects: check distribution and report to country.
+=== 8. Timelines for new traits ===
The participants expressed high interest for carcass traits to be the next new trait to start researching. It was agreed that the group involve in carcass traits, United Kingdom and Ireland, will present a research proposal and a timeline.
-Line 121:
+Line 81:
-==== d. Correlation matrix ====
A new estimation of variance components was done at Interbull Centre using Mix99. Variances and co-variances were re-estimated for all participating countries for both breeds. There was no problem in setting up the model. Computationally speaking the two jobs were quite heavy and had to be discontinued after a couple of weeks. Judging from the little changes in the estimates, convergence shouldn't be too far to reach. Variance and co-variances as estimated at the time of last iteration were used for the breeding values prediction. Full data were used to analyzed VCE.  Correlation matrix looks much better than earlier although some combinations are still too low (.30). Lack of connectedness can still be the major issue. Technical Committee advised to re-estimate VCE using a smaller better-connected data set.  Reduction on the amount of data would probably give better estimates and speed up analysis.
+=== 9. Technical committee terms of reference ===
Due to lack of time it was agreed that everybody would read the documentation and send comments/recommendations to the forum.
-Line 124:
+Line 84:
-==== e. Summary of results ====
Good activity uploading and verifying pedigree data. Variance and co-variances estimable with Mix99, Interbull Centre should consider re-estimating them using a smaller, well-connected subset. Country should also try to improve connectedness by keeping active the verification process in the pedigree database. New set of editing rules for Interbull centre were agreed. Countries should send only edited data used in national evaluation in the next data submissions.
+=== 10. Recommendations to the working group ===
Joao summarized the main topics and decision of the meeting which he will present the next day at the Interbeef Working Group meeting:
-Line 127:
+Line 87:
-==== f. Country reports on test run results ====
 * France: can send to Interbull Centre more info on how smaller well-connected subset were obtained in the previous evaluation.
+ * Need of detailed description of data and evaluation results from the Interbull Centre to participating countries.
 * Mix99 is a well tested software for EBV estimation and results look consistent
 * Genetic parameters:
  * Impact ranks and reliabilities - need to be comfortable
  * Still a research topic:ICBF
   * Survey among users
   * Sample data looking at connectedness and data structure
   * Limit number of generations with data
   * Try alternative methods
   * Compare Mix99 with alternative software
 * Reliabilities:
  * Compare Mix99 with alternative software (fit one country data only to compare results)
  * Investigate gaps at very low reliability values (0.0-0.08)
  * Check Maternal effects in Mix99
  * Compare sources of information considered both at national and international evaluations.
 * Pedigree:
  * investigate issue on invalid animals
  * see how many there are in the analysis and how old they are
  * Propose way to distinguish between invalid and unverified animals.
 * Calving data:
  * send COU+BREED combination to CZE for research.
 * Breed fraction: continue discussion
 * Terms of reference: will be review and discussed online
-Line 130:
+Line 111:
-It would be helpful if Interbull Centre can provide a table of statistics.

 * Czech Republic: nothing to report because results were distributed too close to the meeting.
 * Spain: correlation national/international ebv is low (.65) while it seems ok for accuracy (.90). The scale in both cases is similar. They have received only very few animals back (only 5,000 out of 52,000).
 * UK: They received fewer animals than than expected (4,000 instead of 6,000). Mean was lower than the national evaluation. Correlations were also low. Look at correlation – all animals .08 but high rel animal 0.9.  JD – new run with amended editing rules.  Results will be distributed.

=== 7. Recommendations of changes ===
==== a. Guidelines ====
Interbull centre will update Interbeef guidelines with the new agreed file formats and specification on how to report calving traits. The new guidelines will be available on the ICAR website as soon as possible.

==== b. International genetic evaluation ====
Interbull Centre will re-estimate international EBV for adjusted weaning weight applying the new set of editing rules agreed during this meeting. Results will be distributed back to countries. Review estimation of reliabilities: female reliabilities indicate a probable overestimation that might be related to the way maternal effects are accounted for.

=== 8. Publication rules and use of Interbeef results ===
 * Distribution of Pedigree: there is no agreement to send back pedigree information used in the evaluation.
 * Different rules should be applied for distribution of males and females.
 * Two set of files should be distributed: a distribution file containing all animals, and a publication file containing only animals that are publishable in all countries.
 * Publication decided by each Service User based on transparent criteria.
 * Final decisio to be taken by the WG in Stansted.

=== 9. Other matters ===
There were none

=== 10. Adjourn ===
Brian shortly summarizes the main outcome of the current meeting:

 * Due to changes in the file format decided at the current meeting countries will need to re-send calving data. Countries should aim at sending new data to Interbull Centre by mid-January 2013.
 * Have a research agreement ready and finalized at Stansted meeting.
 * Ireland will provide cross bred animals to Interbull Centre so that the Centre could trace back a pedigree file from which Ireland will to study  heterosis/recombintation. Based on the results, Ireland will provide recommendations to the technical committee on what is needed to include cross bred and will choose a trait to carry out research.
 * João will provide report and recommendations to the working group meeting on 17th January.
 * Next meeting for the Working Group is scheduled for January 17th at Stansted airport.

Brian thanked all participants and closed the meeting. Attachments: [[attachment:Testrun_overview.pdf]] [[attachment:Editing_procedures.pdf]] [[attachment:Pedigree_Description.pdf]] [[attachment:Research_plan_CZE.pdf]]
+=== 11. Adjourn ===
The Chairman thanked all participants and adjoured the meeting.