Transcript General considerations

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