1. Breeding Jersey cattle for Africa in the era of genomics Prof Norman Maiwashe 1,2 (PhD, Pri. Sci. Nat) 1 ARC-Animal Production Institute Private Bag X2 Irene 0062 2 University of the Free State P.O. Box 339 Bloemfontein 9300 20 th International WJCB Conference, Western Cape, South Africa, 17 Sept 2014

2. Presentation Outline A breeder’s dilemma –Inbreeding versus Genetic progress How will genomics: –Complicate or Simplify breeding Summary

3. Genetic Improvement is a balancing act Minimal Inbreeding Rapid Genetic Progress

4. The curse is in the principle! –Superior animals (sires) are provided more breeding opportunities While: –Inferior animals (sires) are denied breeding opportunities Consequently: Most of the progeny are from few outstanding sires and are «likely to be outstanding themselves» When this progeny in turn become parents, they are more «likely to mate with their siblings»

5. Question 1: Is the rate of inbreeding reaching critical levels in Jersey populations?

6. Inbreeding level in SA dairy cattle

7. Inbreeding level in SA Jersey 4.8% Du Toit et al. (2012)

8. Inbreeding in Canadian Jerseys Du Toit et al. (2012)

9. Inbreeding depression Inbreeding has a negative impact on longevity in SA Jersey cattle ( Du Toit et al., 2012 ) -0.14% Mean longevity -0.35% - 0.22% Lact. 1Lact. 2 Lact. 3 A 1% increase in inbreeding is associated with ~0.5% reduction in longevity

10. Inbreeding in the genomic era ΔF will increase due to shorter rapid generation interval Management of inbreeding will become more important Opportunity –Genomics may allow for new ways to control inbreeding e.g. use of DNA to calculate genomic relatedness and inbreeding

11. Answers to Question 1: Inbreeding is real and should be managed –Use superior bulls that are less related to the population Genomics could lead to rapid inbreeding –but offer better tools for managing inbreeding (genomic mating programs) Remember: Inbreeding is not bad per se – it is rapid inbreeding that is bad Mild inbreeding with intense selection is good

12. Question 2: How was the Jersey breeder’s life before genomics?

13. Genetic trend for Calving Interval

14. Conformation and Udder Traits Figure: Genetic trends for « conformation » and « udder » in SA Jersey Theron et al. (2012)

15. Answers to Question 2 How was the Jersey breeder’s life before genomics? Answer: Good genetic progress made on measured traits (often with high h 2 ) albeit at a relatively slow pace Little progress on lowly heritable traits Progress was costly (time and money )

16. Question 3 How is the Jersey breeder’s life during genomics?

17. Genomic opportunities 1.Genomics for managing deleterious haplotype carriers (e.g JH1, JH2 and Fertility 1) –Decreased reproductive efficiency (is accessible to the breeder) 2.Genomic selection (more about this later) –Selection of young animals with DNA test (with reasonable reliability ~60%) 3.Parentage verification or discovery of missing ancestors (is accessible to the breeder)

18. Genomic selection Requires a large number of animals with accurate proofs e.g. >1000 animals Genotyping costs are still high –Use of cows in the reference population is a possibility –Genotyping a small group of animals with high density chips and using imputation Important question: –Can I use genomic proofs from another country? Answer: –Advise: tread carefully –Genomic proofs are population-specific and their reliabilities may erode in a different population Using foreign scale could be hazardous for traits with low international genetic correlations (Partry and Ducrocq, 2014)

19. Priorities during the Genomic Era Genomic exploitation strategy: –High value animals (influential) genotype with 50K or higher density SNP chip –Low value animals genotyped using low density chips for: –Parentage verification –Genomic inbreeding –Deleterious haplotypes

20. The KEY to genomic selection Aggressive data collection (milk/performance recording) What kind of data? –Fertility –Adaptation to heat stress –Weights / growth –Feed efficiency –Methane production –Health

21. Answer to Question 3 How is the Jersey breeder’s life during genomics? Answer? Genomics for parentage verification and managing deleterious haplotypes is a reality and beneficial Genomics proofs presented on foreign scale should be treated cautiously

22. Summary Inbreeding is a threat to long-term genetic improvement and should be managed Genomics presents an opportunity for fast-tracking genetic improvement More emphasis should be placed on: –collection of data on traits that are difficult to improve through conventional selection Both public and private (industry) investment is key to exploitation of genomics selection

23. Thank You Dankie vir u andaag Ndi a livhuwa