1. Barley – Molecular Breeding IAMZ 2015 Patrick Hayes Dept. Crop and Soil Science Oregon State University Corvallis, Oregon USA www.barleyworld.org

2. Class Outline 1.General considerations for molecular breeding 2.Selection tools and molecular breeding 3.Barley traits and targets for molecular breeding 4.The framework for climate change – a molecular breeding strategy 5.Putting it together – a collaborative exercise in breeding program design

3. Where to start? DNA RNA Protein Metabolite Phenotype Epigenetics General considerations

4. Don’t forget the all-important environment “natural” and “human-made” And the even more important: Genotype x Environment interaction General considerations

5. Technology and targets DNA RNA Protein Metabolite Phenotype Epigenetics General considerations

6. Starting at the beginning DNA The barley genome sequence and the Plant Breeder General considerations

7. Ending at the end Phenotype Breeding goals and the Plant Breeder General considerations

8. “When to rely on genotype to predict phenotype?” General considerations

9. “When to rely on genotype to predict phenotype?” Needs Resources General considerations

10. Needs Molecular breeding: 1- 2 % per year gain from phenotypic selection: is it enough? Choosing between a new and better way vs. grabbing the latest fashion. A problem demanding new technology vs. technology in search of a problem? General considerations

11. Resources Knowledge Is knowing the genetic basis sufficient? Data access Time “Throughput” Money 50 vs. 2,000 50 vs. 50 50 vs. 10 General considerations

12. “Ready to take the molecular breeding plunge?” 1.Necessary outcomes 2.Tools 3.Traits 4.Resource allocation General considerations

13. “Ready to take the molecular breeding plunge?” Outcomes Public vs. private sector Fundamental knowledge vs. varieties Tools Traits Resource allocation General considerations

14. “Ready to take the molecular breeding plunge?” Tools Marker assisted selection Genomic selection Transgenics/Cisgenics Genome editing Traits Resource allocation General considerations

15. “Ready to take the molecular breeding plunge?” Traits Prior knowledge: genes/QTLs/GxE/germplasm Heritability Cost/ease/accuracy of phenotyping Resource allocation General considerations

16. “Ready to take the molecular breeding plunge?” Resource allocation Time: Design, Implementation, Data Management, Application, Validation $: Low per unit costs BUT scale dependent General considerations

17. Molecular breeding - selection tools 1.Phenotypic (yes, it is an essential component!) 2.Genotypic (marker assisted selection) 3.Genomic (genomic selection) 4.Genic (trans/cis and editing) Selection tools

18. Phenotypic All indirect selection requires direct validation The phenotype is what sells Heritability and its discontents You’ll always need to plant, grow, and harvest Cost Selection tools

19. Genotypic Marker Assisted Selection Knowledge (vacuums) The more you want, the worse it gets: how many genes can your target? Validation and reasonable expectations: “germplasm specificity” Technology and obsolescence Cost Selection tools

20. Genomic Genomic selection The simple beauty of a black box: from cows to barley Principle vs. practice: technology and algorithms Cost Selection tools

21. Genic Trans, cis and editing Knowledge (vacuums) The limits of conservatism Intellectual property Cost Selection tools

22. Barley traits 1.Spike type: 2-row, 6-row 2.Growth habit: Spring, winter, facultative 3.End use: Feed/Forage, Food, Malting 4.Disease resistance: Qualitative/Quantitative 5.Herbicide resistance Barley traits

23. Spike type: 2-row, 6-row Single gene + 2-row dominant Many ways to achieve 6-row Fact and fiction/ Pride and prejudice A good target for molecular breeding? F1, F2, DH, pure lines….. Barley traits

24. Growth habit: Spring, winter, facultative Key players: Vernalization (VRN) sensitivity, short day photoperiod (PPD) sensitivity Spring: No VRN, PPD can vary Winter: VRN, PPD can vary Facultative: No VRN, Short day PPD essential VRN – 3 genes + PPD (sd) – 1 gene + Good targets for molecular breeding? F1, F2, DH, pure lines….. Barley traits

25. End use: Feed/Forage, Food, Malting Feed/Forage: most acreage worldwide Yield, high test weight Complex genetics Food: limited acreage worldwide: a prospect Naked seed, beta glucan, starch type Yield Simple to complex genetics Malt: Most $ value worldwide Balance of starch and protein Yield Complex genetics Good targets for molecular breeding? F1, F2, DH, pure lines….. Barley traits

26. Disease resistance: Qualitative/Quantitative Bacterial, fungal, viral Insects, nematodes Durability One gene + …… complex inheritance Good targets for molecular breeding? F1, F2, DH, pure lines….. Barley traits

27. The “genics” to come One gene + Good target for molecular breeding? F1, F2, DH, pure lines….. Barley traits

28. The framework for climate change and collaboration: Performance Growth habit Value The framework for climate change

29. Performance Yield Disease resistance Biotic stress resistance Abiotic stress resistance Winterhardiness/Water use efficiency Input residues The framework for climate change

30. Facultative growth habit Plant anytime of year Low temperature tolerance – no cost under spring planting The framework for climate change

31. Value Feed/forage - the specter of maize Food - the new horizon: 2-row/6-row Malt - meeting specifications: 2-row The framework for climate change

32. Putting it together The job description The goals The tools The budget The plan Putting it together

33. The job description Public sector Knowledge Instruction Varieties Putting it together

34. The goals Meet or beat the check for agronomics Facultative Low temperature tolerant 2-row Malt or Food Putting it together

35. The selection tools Phenotypic: $20 per plot Genotypic: $20 per haplotype; 384 minimum Genomic $20 per plant; 384 minimum Genic: $200 per positive transformant Putting it together

36. The budget Your salary paid (generously) One technician paid (adequately) All equipment available (field, lab, analysis) Page charges, travel paid $300,000 per year for 5 years Putting it together

37. The plan Small group breakout session Each group reports Questions for each group Conclusions Putting it together