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Monitoring of animal genetic resources in Germany: sheep / goat
Project
Project code: 08BE001
Contract period: 18.12.2009
- 17.12.2012
Purpose of research: Inventory & Assessment
The revision of the German law for animal breeding assigns a monitoring of genetic diversity within certain breeds for all farm animal species. The animal breeding associations are committed to provide results to Federal Office for Agriculture and Food (BLE) useful for description and evaluation of the available resp. remaining genetic diversity within their supervised breeds.
The umbrella organizations of the German Sheep Breeding Associations (VDL) and of the German Goat Breeding Associations (BDZ) applied for the project and got the award. VDL/BDZ appointed the breeding associations as subcontractors for data delivery and 'United Data Systems for Animal Production' (vit) for the technical execution of the project, the hosting and analysis of the collected herdbook data.
The breeding associations were in charge of
• providing necessary herdbook data using defined data interfaces,
• data consolidation in cooperation with vit,
• mutual harmonization with other breeding associations to achieve unique animal identifications for all living animals and their ancestors across associations and breeds, and
• providing additional information, i.e. about the history and applied breeding program of a population, as supplement for the monitoring report.
Vit was in charge of
• definition of the necessary interfaces for data transfer into the joint herdbook data base,
• collection and combination of data from different herdbook systems,
• data consolidation in coordination with the breeding associations,
• technical organisation and execution of data consolidation,
• analysis of the required parameters to monitor the actual genetic diversity of a population,
• compiling the monitoring reports for all breeds, and
• transmission of the monitoring data base (individual records) to BLE.
The vit department 'IT Services for Herdbook Keeping' was responsible for data collection and consolidation and the department 'Biometrics and Genetic Evaluation' was responsible for the ensuing genetic analyses.
Pedigree information of several different herdbook systems of breeding associations was combined into the common database serv.it OVICAP in the first step. In a second iterative step jointly executed by vit and breeding associations pedigree information was harmonized across the different herdbook systems in order to get i.e. unique identifications for all living animals and their ancestors. This consolidation of pedigree data was time consuming, but a very important part of the project previous
to the statistical analyses. During the project the necessary database was significantly improved concerning data completeness and data quality means.
The analyses to quantify the remaining genetic diversity within populations were conducted for 21 sheep breeds and 4 goat breeds (see attached table). The monitoring parameters were estimated on the base of currently alive parents, born 2004 – 2011 and having a (Pedigree Completeness Index over 4 generations) PCI > 0.70, and their ancestors.
The following parameters were calculated:
- Pedigree Completeness Index (PCI)
- Average percent of foreign blood within the actual breeding population
- Average increase of inbreeding over birth years
- Average generation interval within the four selection paths
- Effective population size derived from relative increase of inbreeding and generation interval
- Number of effective founders (fe)
- Number of effective ancestors (fa) with marginal genetic contributions to the actual breeding population (used as predictors for bottle necks)
- Average relationship between the available parents of the actual breeding population
- Relationship between alive sires and alive dams
Statistical methods, programs and job stream originating from a similar BLE project for cattle breeds were refined and adapted to sheep and goat data during the first year. Methods, programs and job stream were already documented in the intermediate report (July 2011). Preliminary monitoring reports for 5 sheep breeds were part of this report.
In the second project year methods and programs were further improved and applied on the consolidated data base for the monitoring of all 21 requested sheep breeds and three goat breeds. Only for the goat breed 'Harzer Ziege' the analyses were not feasible because of an insufficient data base. For all breeds monitoring reports are conducted. The reports contain descriptions about breed history, breeding goals and breeding programs, breed organization and location and results about remaining
genetic diversity of the active breeding population. In the end of the reports interpretation of the monitoring results including recommendations for future breeding plans are given.
Monitoring analyses are conducted for all requested sheep and goat breeds. Caused by incomplete pedigree information and pedigree structure not all planned methods were appropriate to answer the question of remaining genetic diversity within breeds. Whereas the effective population size (Ne) derived by the relative increasing of inbreeding did not lead to reasonable results, the estimation of effective founders and effective ancestors results in plausible figures. The main results and the derived recommendations are summarized in the attached table.
All used methods are documented in the final report including cited literature. Detailed documentation of the process flow is given in the appendix. The whole monitoring process, starting with data export from the database, data preparation, plausibility checks, statistical analyses and composing of the monitoring report is automated by a large extend.
As requested in the project call and already practiced in 2011 vit is able to provide individual data of monitored breeds to BLE using the agreed data interface (csv-files).
This data delivery is already conducted for all breeds. Repeated monitoring investigations by request will be possible and reasonable within a regular time span mainly for populations with already limited genetic variability. An estimation of expenditure of time and costs is given in the final report, too.
A final workshop of the project is scheduled to present the monitoring results to breeding associations and public administration units. Interpretation and derived recommendations concerning future breeding programs of the single breeds will be additional items of the agenda.
Section overview
Subjects
- Animal breeding
- Genetic Resources
Framework programme
Funding programme
Excutive institution
Consortium of German Sheep Breeding Associations and German Goat Breeding Associations
