1. Graeme Martin Professor, UWA Institute of Agriculture Leader, UWA Future Farm 2050 Graeme Martin Professor, UWA Institute of Agriculture Leader, UWA Future Farm 2050 Steps to Sustainable Livestock Elegant genetic strategies 30 min incl. questions

2. Nature (2014) 507, 32-34 Elegant genetic solutions Six major challenges 1)Animal health, welfare, nutrition 2)Human nutrition – health, balance 3)Relevance to culture 4)Livestock consuming human food 5)Environmental footprint 6)Breeds suited to environment

3. This presentation: Examples and principles 1)Developing countries: genotype for environment 2)Developed countries (Australia): a)Disease resistance b)Methane emissions Next presentation: Ellen Goddard on genomic selection Elegant genetic solutions

4. Indigenous animal breeds: 21% in danger of extinction Elegant genetic solutions Developing countries: genotype for environment Holstein Bred for 30 litres milk per day, perfect diet, intensive management, temperate climate Imported into Africa, Asia, but … Not resistant to heat, humidity, tropical diseases, parasites World’s most infertile farm animal Solution: Native local breeds + Modern genomics

5. Dr Frederick Obese, Ghana Strategy: upgrade local breeds Developing countries: genotype for environment Sanga Friesian x Sanga 0.8 1.0 1.2 1.4 1.6 1.8 2.02.212345678910 Daily milk yield (kg) Weeks postpartum Elegant genetic solutions

6. Developing countries: genotype for environment Australia: a) Disease resistance/resilience

7. Gastro-intestinalnematodes Trichostrongylus colubriformis Ostertagia circumcincta MyiasisFlystrike Lucilia cuprina Eggs in faeces Diarrhoea Nematode larvae Nematode-Fly Disease Complex

8. MyiasisFlystrike

9. Gastro-intestinalnematodes Trichostrongylus colubriformis Ostertagia circumcincta Myiasis Lucilia cuprina Eggs in faeces Diarrhoea Nematode larvae The problem 1)Nematodes now resistant to anthelminthic drugs 2)‘Mulesing’ to prevent flystrike no longer acceptable Nematode-Fly Disease Complex

10. Gastro-intestinalnematodes Trichostrongylus colubriformis Ostertagia circumcincta Myiasis Lucilia cuprina Eggs in faeces Diarrhoea Nematode larvae Effective solutions 1)Anthelmintic forages a)Cornelia Grace b)Reza Ferasyi c)Sophie Vandermeulen d)Eremophila glabra Nematode-Fly Disease Complex

12. John Karlsson & Johan Greeff Schalk Cloete Gastro-intestinalnematodes Trichostrongylus colubriformis Ostertagia circumcincta Myiasis Lucilia cuprina Eggs in faeces Diarrhoea Nematode larvae Effective solutions 1)Anthelmintic forages 2)Genetic resistance a)Nematode infestation b)Flystrike Nematode-Fly Disease Complex

13. -250 -200 -150 -100 -50 0 50100 Change in worm eggs per gram faeces 1988199119941997200020032006 Year of birth Heritability : 0.6 Random Selection Selected for Low WEC Nematode resistance: genetic progress

14. 8 years of selection for resistance: Medication16% less $ Weight at weaning1.0 kg heavier Weight at 16 months1.5 kg heavier Wool fibre diameter0.3 micron finer Nematode resistance: benefits of breeding

15. Gastro-intestinalnematodes Trichostrongylus colubriformis Ostertagia circumcincta Myiasis Lucilia cuprina Eggs in faeces Diarrhoea Nematode larvae Genetic resistance to nematode infestation Where to next? 1)How does it work? Molecular basis of immunity Hypersensitivty (allergy) 2) Genomic selection Rapid industry uptake The Nematode-Fly Disease Complex

16. Genetic resistance to flystrike The Nematode-Fly Disease Complex

17. Unexplained 78% Genetic resistance to flystrike The Nematode-Fly Disease Complex Faecal contamination

18. SusceptibleResistant 2.5%9%94%103% Flystrike: Extreme-Resistance Genotypes Sniffer dogs can identify the groups … odour!

19. Steps to Sustainable Livestock Challenge 6: Environmental footprint Elegant genetic solutions Developing countries: genotype for environment Developed countries:a) Disease resistance b) Methane emissions

21. 1)Feed Additives 2)Manipulating the Rumen 3)Novel Forages 4)Production Efficiency = kg CH 4 per kg product 5)Genetics 1)Heritability of CH 4 outputs 2)International Ruminant ‘Pan-Genome’ Project

22. 1)Heritability of CH 4 outputs 1)Feed Additives 2)Manipulating the Rumen 3)Novel Forages 4)Production Efficiency = kg CH 4 per kg product 5)Genetics Gross CH 4 production (Australia, NZ) nh 2 Source Sheep12770.27 ± 0.05 Pinares-Patiño et al 2013 Robinson et al 2010 Robinson et al 2014 Beef cattle5300.27 ± 0.11 Donoghue et al 2015

23. 1)Feed Additives 2)Manipulating the Rumen 3)Novel Forages 4)Production Efficiency = kg CH 4 per kg product 5)Genetics 1)Heritability of CH 4 outputs Gross CH 4 production (beef cattle) h 2 Source Pedigree0.27Donoghue et al 2015 Genomic0.28Hayes et al 2015 Genomic selection Suits hard to measure traits Accuracy + Generation interval = Genetic gain

24. 1)Feed Additives 2)Manipulating the Rumen 3)Novel Forages 4)Production Efficiency = kg CH 4 per kg product 5)Genetics 1)Heritability of CH 4 outputs 2)International Ruminant ‘Pan-Genome’ Project Phil Vercoe Reduce Methanogenesis Increase Efficiency of Feed Use

25. Pan-Genome? Pan-genome: superset of all genes in all strains of a species Challenge: extend concept to link between host genome to its rumen microbiome Why? Understand interactions among genes that influence efficiency: Within host Within rumen microbiome Between host and rumen microbiome

26. Pan-Genome? Phenotype =Genotype + Environment + (GxE) Ruminant: What defines G and E?

27. G m + E r + G m x E r Rumen Phenotype = G a + E e + G a x E e Host Animal Phenotype = Pan-genome G a x G m x E e x E r

28. Pan-Genome

29. The power of genetics Don’t let geneticists make decisions!

30. Six major challenges 1)Animal health, welfare, nutrition 2)Human nutrition – health, balance 3)Relevance to culture 4)Livestock consuming human food 5)Environmental footprint 6)Elegant genetic solutions Steps to Sustainable Livestock Examples and principles a)Genotype for environment b)Disease resistance c)CH 4 emissions Indigenous breeds: Conserve, utilise Manage the genes Clean: Less hormones, medication Green: Reduce CH 4 intensity Ethical: Better animal welfare Next: Be clever with genomics

32. $280,000,000 every year

33. Rumen Pangenome Project Connecting the host genome with its ruminal microbiome Rumen metagenomics Genomics and selection Nutrition Methane Feed efficiency N efficiency Milk Production Meat Production Wool Production Host genome and rumen microbiome Optimise Genetics x Environment x Management Optimise Genetics x Environment x Management Beef, sheep and dairy cattle genetic resources GWAS Host Rumen

34. Rumen Pangenome Project Connecting the host genome with its ruminal microbiome Methane Feed efficiency N efficiency Milk Production Meat Production Wool Production Host genome and rumen microbiome Optimise Genetics x Environment x Management Optimise Genetics x Environment x Management Genetic resources: sheep, beef and dairy cattle GWAS Host Rumen metagenomics Nutrition Genomics and selection