barley – molecular breeding iamz 2015 patrick hayes dept. crop and soil science oregon state...

Barley – Molecular BreedingIAMZ 2015

Patrick HayesDept. Crop and Soil Science

Oregon State UniversityCorvallis, Oregon USAwww.barleyworld.org

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

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. Necessary outcomes2. Tools3. Traits4. 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

General considerations

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

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

Selection tools

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

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…..

Barley traits

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

The framework for climate change

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

Putting it together