Barley – Molecular Breeding IAMZ 2015 Patrick Hayes Dept. Crop and Soil Science Oregon State...
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![Page 1: Barley – Molecular Breeding IAMZ 2015 Patrick Hayes Dept. Crop and Soil Science Oregon State University Corvallis, Oregon USA .](https://reader035.fdocuments.in/reader035/viewer/2022062421/56649da95503460f94a96e39/html5/thumbnails/1.jpg)
Barley – Molecular BreedingIAMZ 2015
Patrick HayesDept. Crop and Soil Science
Oregon State UniversityCorvallis, Oregon USAwww.barleyworld.org
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Class Outline
1. General considerations for molecular breeding2. Selection tools and molecular breeding 3. Barley traits and targets for molecular breeding4. The framework for climate change – a molecular
breeding strategy5. Putting it together – a collaborative exercise in breeding
program design
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Where to start?• DNA• RNA• Protein• Metabolite• Phenotype
Epigenetics
General considerations
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Don’t forget the all-important environment • “natural” and “human-made”
And the even more important:
Genotype x Environment interaction
General considerations
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Technology and targets
• DNA• RNA• Protein• Metabolite
• Phenotype
• Epigenetics
General considerations
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Starting at the beginning
DNA • The barley genome sequence and the Plant
Breeder
General considerations
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Ending at the end
Phenotype
• Breeding goals and the Plant Breeder
General considerations
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“When to rely on genotype to predict phenotype?”
General considerations
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“When to rely on genotype to predict phenotype?”
• Needs• Resources
General considerations
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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
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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
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“Ready to take the molecular breeding plunge?”
1. Necessary outcomes2. Tools3. Traits4. Resource allocation
General considerations
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“Ready to take the molecular breeding plunge?”
Outcomes• Public vs. private sector• Fundamental knowledge vs. varieties
Tools
Traits
Resource allocation
General considerations
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“Ready to take the molecular breeding plunge?”
Tools• Marker assisted selection• Genomic selection• Transgenics/Cisgenics• Genome editing
Traits
Resource allocation
General considerations
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“Ready to take the molecular breeding plunge?”
Traits• Prior knowledge:
genes/QTLs/GxE/germplasm• Heritability• Cost/ease/accuracy of phenotyping
Resource allocation
General considerations
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“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
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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
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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
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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
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Genomic• Genomic selection• The simple beauty of a black box: from cows to barley• Principle vs. practice: technology and algorithms• Cost
Selection tools
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Genic• Trans, cis and editing • Knowledge (vacuums)• The limits of conservatism • Intellectual property • Cost
Selection tools
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Barley traits
1. Spike type: 2-row, 6-row2. Growth habit: Spring, winter, facultative3. End use: Feed/Forage, Food, Malting4. Disease resistance: Qualitative/Quantitative
5. Herbicide resistance
Barley traits
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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
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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
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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
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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
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The “genics” to come
• One gene +
Good target for molecular breeding?• F1, F2, DH, pure lines…..
Barley traits
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The framework for climate change and collaboration: • Performance • Growth habit• Value
The framework for climate change
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Performance• Yield • Disease resistance• Biotic stress resistance• Abiotic stress resistance• Winterhardiness/Water use efficiency• Input residues
The framework for climate change
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Facultative growth habit• Plant anytime of year• Low temperature tolerance – no cost under spring
planting
The framework for climate change
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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
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Putting it together • The job description• The goals• The tools• The budget• The plan
Putting it together
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The job description• Public sector• Knowledge• Instruction• Varieties
Putting it together
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The goals• Meet or beat the check for agronomics • Facultative• Low temperature tolerant• 2-row• Malt or Food
Putting it together
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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
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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
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The plan• Small group breakout session• Each group reports • Questions for each group• Conclusions
Putting it together