Genomics - introduction into cattle breeding

1. Genomics - introduction into cattle breeding Egbert Feddersen, DHV/ Germany 2010 EHRC SECRETARIES MEETING 16 June 2010, Zadar/ Croatia

2. Operation of the session • Introductory paper • Introduction and practical application of genomics • International collaboration • Interbull and official approval • Impact of genomics on herd-book associations • Discussion with the entire audience: • How are countries intending to administer this technology • The likely impact on recording and classification of progeny test daughters?

3. Genomics • Technology with the largest impact on dairy genetics since the introduction of artificial insemination

4. A review – two years ago • The use of quantitative genetic concepts • Ranking based on estimated breeding values (EBVs) • Coming from traditional breeding programs with their necessary elements • performance recording (Milk yield, SCC, type traits, etc.) • pedigree data • good data structure (across herds/environments) • Genetic evaluation • BLUP methodology, which result in highly reliable EBVs (85-99%) • for bulls with a progeny test of 100-150 daughters • Transformation of these EBVs since15 years via Interbull MACE • results in bulls that are marketed world wide

5. … but • High generation interval due to progeny test • Expensive, due to keeping of many waiting bulls • Tests of many daughters • Genetic gain per year is limited • Even if selection of young bulls for progeny test on very reliable EBVs • Bull dams ~60% r² and bull sires~95% r² the reliability of a pedigree index (= 0,5 EBV sire + 0.5 EBV dam) is low: PA = 25-35%

6. In 2009: SNP - Technology New opportunities: • SNP = Single-nucleotide polymorphism • SNPs are by far the most common source of genetic variation • Genotype = Frequency of the nucleotides C-G, A-T an animal carries • 50K chip: Ca. 50.000 SNPs at a cost of about 150 - 200 EUR

7. Practical application • Availability of high throughput analysing equipment • New in the system: well equipped labs • SNP-data per se has no information • Calculation (regression) formula to reach a good estimation of gEBVs (Meuwissen et al 2001) • Genotype animals that have reliable EBVs from ‚conventional‘ genetic evaluation (reference population) • Calculate regression formulas from a ‚reference population‘ so that SNPs explain well the conventional EBV • Use the regression formulas derived by historic data to evaluate gEBVs of young animals • Need of validation • Select among these young animals

8. Size of reference population • Key factor for reliable breeding values Goddard

9. Increase of reliability in BV of AI bulls Reents, Riga 2010

10. Increase of reliability in BV of cows Reents, Riga 2010

11. International co-operations • North America consortium: USA/ CDN (HOL) • Intergenomics (BSW) (AUT, CHE, DEU, FRA, ITA, SLO, USA) • EuroGenomics (HOL) (DEU, DFS, FRA, NLD) • IGenoP: Smaller countries (12) • (International (AUS, BEL, CHE, ESP, IRL, ISR, ITA, GenomicPartnership) JPN, NZL, POL, SFA, UK)

12. Official approval of gEBVs in Europe • Interbull will offer a validation procedure for official approval of genomic evaluations systems (1st step: protein yield) • Two research runs on a validation procedure in early 2010 • Necessary refinements are incorporated in a final version that will be distributed to national genetic evaluation centres on 14 June 2010 • Data for official validation to be sent back until 5 July 2010 • The genomic evaluation systems that pass the test will then be displayed on the ICAR webpage on 9 August 2010 • in order to fulfil the requirements of the EC regulation 427/2006 for wide use of semen also from young sires.

13. Interbull: Further steps • Validation of all other traits of the Interbull portfolio will be added for a research run in early September 2010 • Review of the technical bodies and the Interbull steering committee in early October 2010. • Validation test for all traits in the future and the results will be made public for general information. • The research runs for GMACE (MACE including genomic information) showed larger challenges than expected. It was therefore decided to first proceed with a simplified version of GMACE and test its properties, until the technical issues with the full GMACE system are solved.

14. The impact of Genomics on herdbooks To be considered: • How may genomics change the provision of services currently offered by herd-books, including milk recording? • How may genomics change the breed development goals of the herd-books? • How will genomics change the collection, distribution and use of data by herd-books and industry? • How might access to genomic services affect herd-books and is there a common position herd-books could reach on this issue?

15. 1. Provision of Services • Decrease of numbers of bulls with progeny testWhat is the impact on type classification (less classification, less income) • Genomics will increase the reliability of gEBVs for type traitsWill this reduce the demand for classification for mating programs? • Parentage verification through SNPs will become possible With the same reliability as today? • Frequency of services (classification, milk recording, etc.) can decrease. How does this impact the data used by herd-book breeders? • Private companies with commercial offers of genomics How does that interact with the public herd-book/government provision?

16. 2. Breed Development Goals • Higher increase in traits with low heritability • Faster progress in fertility and health traits • Reduced generation interval • but …. • Increase of inbreeding is possible • Phenotypic data is still needed in future

17. 3. Changes in collection and use of data • Data bases need to store the genomic information and to print genomic breeding values on pedigrees • How will this information be collected and shared? • Will herd-books have access to all genomic information available? • How do countries exchange genomic information on cows? • Who owns the results of a genomic test on specific animals?

18. 4. Access to data • Have herd-books access to Genomics in all countries? • Are there common interests to protect the interests of members? • Will all genomic information be available to public?

19. Summary • Different systems around in Europe • Pure HB-associations • HB-associations with DHI (ESP, CZE, LUX) • Breeding organisation HB/AI (DEU) • Breeding companies (NLD) • 2. Organisations to review their services to farmers • Need to become an overall service provider in cattle breeding • 3. In that respect performance recording is essential • Registration • Parentage verification • classification • milk recording • etc. • 4. The ability to verify parentage through SNPs may change the accepted methods of parentage verification

20. Summary • The number of bulls put through progeny test will decrease. This will have an impact on type classification services • If reasonable reliability for type traits is reached, it could reduce the demand for classification for management purposes. • Possibility to score new traits ? • Cooperate activities with other breed associations • The position of purebreds in the industry may change. (Due to genomics herd-book animals could become less but get more importance) • Chance to find outcrosses, but risk to increase inbreeding

21. Thanks for your attention