1. DEPARTMENT OF PRIMARY INDUSTRIES 1 Discovering Genes for Beef Production Mike Goddard University of Melbourne and Department of Primary Indusries, Victoria

2. DEPARTMENT OF PRIMARY INDUSTRIES 2 Traditional Genetic Improvement Genes Breeding Value

3. DEPARTMENT OF PRIMARY INDUSTRIES 3 Introduction Genomics Identify genes for economic traits

4. DEPARTMENT OF PRIMARY INDUSTRIES Background on Genomics Genomics revolution Human genome project Based on –high throughput techniques –computer analysis of databases Spin-off to agriculture –knowledge –techniques

5. DEPARTMENT OF PRIMARY INDUSTRIES 5 Genomics - International investment MetaMorphix invests $10m with Cargill to find genes for meat quality Ovita in NZ in sheep Vialactia in NZ in dairy cattle Dairy CRC NRE and AgResearch Beef CRC $5M AWI - MLA sheep genomics $30M

6. DEPARTMENT OF PRIMARY INDUSTRIES 6 Applications to Beef Industry Selection of bulls and cows carrying the favourable genes Non-genetic manipulation of physiology Transgenic cattle

7. DEPARTMENT OF PRIMARY INDUSTRIES 7 Introduction This talk Discovering genes for economic traits Progress in Beef CRC research Using these genes in beef cattle breeding

8. DEPARTMENT OF PRIMARY INDUSTRIES 8 Discovering Gene Function High Throughput Techniques DNA sequence Naturally occurring variants –gene mapping Gene expression pattern –microarrays

9. DEPARTMENT OF PRIMARY INDUSTRIES 9 Naturally occurring gene variants Genes are a sequence of DNA eg AGTCTAG Genetic differences are due to differences in DNA sequence eg AGTCTAG AGTGTAG

10. DEPARTMENT OF PRIMARY INDUSTRIES 10 Naturally occurring gene variants Number of genes causing variation in a trait At least 20 experimentally Hayes and Goddard (2001) 50-100 segregating Effect varies from small to medium

11. DEPARTMENT OF PRIMARY INDUSTRIES 11 Distribution of effects of genes on quantitative traits

12. DEPARTMENT OF PRIMARY INDUSTRIES 12 Naturally occurring gene variants Problem Finding the differences in DNA sequence (ie genes) that cause differences in performance

13. DEPARTMENT OF PRIMARY INDUSTRIES 13 Naturally occurring gene variants Research strategy Map genes for traits to chromosomal region Find candidate genes in correct region of chromosome Test natural variants in candidate genes for affect on the trait

14. DEPARTMENT OF PRIMARY INDUSTRIES 14 Gene mapping

15. DEPARTMENT OF PRIMARY INDUSTRIES 15 Bull chromosomes

16. DEPARTMENT OF PRIMARY INDUSTRIES Gene mapping M1+ sire M2- offspring M1 + M2-

17. DEPARTMENT OF PRIMARY INDUSTRIES Linkage equilibrium M1+ sire1 M2- M1- sire2 M2+

18. DEPARTMENT OF PRIMARY INDUSTRIES 18 Fine scale mapping Linkage map gene to about 30 cM Depends on size of effect Fine scale map by linkage disequilibrium

19. DEPARTMENT OF PRIMARY INDUSTRIES 19 Linkage disequilibrium... A chunk of an ancestral animal’s chromosome is conserved in the current population 1Q12 Marker Haplotype

20. DEPARTMENT OF PRIMARY INDUSTRIES 20 Candidate gene approach Select genes with a physiological role in trait (eg muscle growth) Find variations in DNA sequence Test gene variants for effect on trait

21. DEPARTMENT OF PRIMARY INDUSTRIES 21 Candidate genes Problem –Thousands of possible candidates –Only 5-10 with moderate effect

22. DEPARTMENT OF PRIMARY INDUSTRIES 22 Position candidate genes Among the genes that map to the right chromosome region Find list of all genes in a region of bovine chromosome from homologous human chromosome

23. DEPARTMENT OF PRIMARY INDUSTRIES 23 * * HumanCattle

24. DEPARTMENT OF PRIMARY INDUSTRIES 24 CRC for Cattle and Beef Quality Project 2.1 Genetic Markers Overall Aim Genetic markers for Marbling Tenderness Meat yield Tropical adaptation Food conversion efficiency That can be used regardless of family

25. DEPARTMENT OF PRIMARY INDUSTRIES 25 Organizations CSIRO AGBU VIAS Uni of Adelaide Trangie

26. DEPARTMENT OF PRIMARY INDUSTRIES 26 Overall Strategy Linkage analysis  chromosomal region Fine scale map  small chromosomal region haplotype of markerstest positional candidate direct markers commercial test

27. DEPARTMENT OF PRIMARY INDUSTRIES 27 Linkage mapping results Trait Tenderness and retail beef yield

28. DEPARTMENT OF PRIMARY INDUSTRIES 28 Linkage mapping of LD Peak Force CBX experiment Maximum Likelihood Summed over sires November 1998 CAST (calpastatin) Strong evidence

29. DEPARTMENT OF PRIMARY INDUSTRIES 29 CAST effects on LD Peak force (kg) BreedC11C12 C22 Angus0.170-0.21 Brahman0.080-0.18 Belmont Red0.100-0.22 Hereford-0.360-0.11 Murray G0.880-0.15 Santa G0.02 0-0.12 Shorthorn-0.140-0.10 Allbreeds0.060-0.16

30. DEPARTMENT OF PRIMARY INDUSTRIES 30 Marbling Gene star New gene patented February

31. DEPARTMENT OF PRIMARY INDUSTRIES 31 Other traits Meat yield fine scale mapping gene Tick resistance linkage mapping NFI genes mapped to chromosomes in Jersey x Limousin starting project to map and identify in Angus

32. DEPARTMENT OF PRIMARY INDUSTRIES 32 Using DNA information Independent of EBVs Combine into EBVs

33. DEPARTMENT OF PRIMARY INDUSTRIES 33 Combining DNA and other information phenotype pedigree DNA EBVs

34. DEPARTMENT OF PRIMARY INDUSTRIES 34 Introduction Assay DNA sequence change + phenotypes and pedigrees --> more accurate EBVs at a younger age

35. DEPARTMENT OF PRIMARY INDUSTRIES 35 Factors affecting the gain in accuracy from DNA data Accuracy of existing EBV Proportion of genetic variance explained by DNA data Accuracy of estimating QTL allele effects Generation length

36. DEPARTMENT OF PRIMARY INDUSTRIES 36 Gene Expression Where and when a gene is expressed tells you a lot about its function Now measure mRNA in 20,000 genes at once with microarrays

37. Collect RNA Make cDNA libraries PCR purification Microarray slide 0.1nlprint Prepare mRNA target hybridise Overview of Microarray Technology

38. Detection of signal analysis overlay images

39. Close up at column 3, row 1 Channel 1 Lactating Channel 2 Pregnant Overlay

40. Microarray Technology at VIAS y-axis: log 2 ratio of fluorescence intensity Cy3/Cy5 + more highly expressed in lactating MG - more highly expressed in pregnant MG x-axis: total fluoresence intensity

41. DEPARTMENT OF PRIMARY INDUSTRIES 41 Conclusion Genomics new knowledge applications selection of bulls and cows transgenic cows non-genetic manipulation

42. DEPARTMENT OF PRIMARY INDUSTRIES 42 Conclusions 5-10 genes explain 50% variation in a typical economic trait Genomics is helping us to find these genes

43. DEPARTMENT OF PRIMARY INDUSTRIES 43 Conclusions Identifying genes with natural variants Two genes patented for marbling One commercialised One gene commercialised for tenderness Others genes mapped for beef yield and NFI Experiments under way for tick count

44. DEPARTMENT OF PRIMARY INDUSTRIES 44 Conclusions In 20 years we will know 200 genes that affect beef production We will use these genes and existing technology to breed the right cattle for each task

45. DEPARTMENT OF PRIMARY INDUSTRIES 45 Conclusions Transgenic cattle Non-genetic manipulation of growth and composition