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Barley – Molecular Breeding IAMZ 2015 Patrick Hayes Dept. Crop and Soil Science Oregon State University Corvallis, Oregon USA www.barleyworld.org Class Outline 1. 2. 3. 4. General considerations for molecular breeding Selection tools and molecular breeding Barley traits and targets for molecular breeding The framework for climate change – a molecular breeding strategy 5. Putting it together – a collaborative exercise in breeding program design General considerations Where to start? • DNA • RNA • Protein • Metabolite • Phenotype Epigenetics General considerations Don’t forget the all-important environment • “natural” and “human-made” And the even more important: Genotype x Environment interaction General considerations Technology and targets • DNA • RNA • Protein • Metabolite • Phenotype • Epigenetics General considerations Starting at the beginning DNA • The barley genome sequence and the Plant Breeder General considerations Ending at the end Phenotype • Breeding goals and the Plant Breeder General considerations “When to rely on genotype to predict phenotype?” General considerations “When to rely on genotype to predict phenotype?” • Needs • Resources General considerations 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 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 “Ready to take the molecular breeding plunge?” 1. 2. 3. 4. Necessary outcomes Tools Traits Resource allocation General considerations “Ready to take the molecular breeding plunge?” Outcomes • Public vs. private sector • Fundamental knowledge vs. varieties Tools Traits Resource allocation General considerations “Ready to take the molecular breeding plunge?” Tools • • • • Marker assisted selection Genomic selection Transgenics/Cisgenics Genome editing Traits Resource allocation General considerations “Ready to take the molecular breeding plunge?” Traits • Prior knowledge: genes/QTLs/GxE/germplasm • Heritability • Cost/ease/accuracy of phenotyping Resource allocation General considerations “Ready to take the molecular breeding plunge?” Resource allocation • Time: Design, Implementation, Data Management, Application, Validation • $: Low per unit costs BUT scale dependent Selection tools Molecular breeding - selection tools 1. 2. 3. 4. Phenotypic (yes, it is an essential component!) Genotypic (marker assisted selection) Genomic (genomic selection) Genic (trans/cis and editing) Selection tools 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 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 Genomic • Genomic selection • The simple beauty of a black box: from cows to barley • Principle vs. practice: technology and algorithms • Cost Selection tools Genic • Trans, cis and editing • Knowledge (vacuums) • The limits of conservatism • Intellectual property • Cost Barley traits Barley traits 1. 2. 3. 4. Spike type: 2-row, 6-row Growth habit: Spring, winter, facultative End use: Feed/Forage, Food, Malting Disease resistance: Qualitative/Quantitative 5. Herbicide resistance Barley traits 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 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 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 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 The “genics” to come • One gene + Good target for molecular breeding? • F1, F2, DH, pure lines….. The framework for climate change The framework for climate change and collaboration: • Performance • Growth habit • Value The framework for climate change Performance • Yield • Disease resistance • Biotic stress resistance • Abiotic stress resistance • Winterhardiness/Water use efficiency • Input residues The framework for climate change Facultative growth habit • Plant anytime of year • Low temperature tolerance – no cost under spring planting The framework for climate change Value • Feed/forage - the specter of maize • Food - the new horizon: 2-row/6-row • Malt - meeting specifications: 2-row Putting it together Putting it together • The job description • The goals • The tools • The budget • The plan Putting it together The job description • Public sector • Knowledge • Instruction • Varieties Putting it together The goals • Meet or beat the check for agronomics • Facultative • Low temperature tolerant • 2-row • Malt or Food Putting it together 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 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 The plan • Small group breakout session • Each group reports • Questions for each group • Conclusions