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MARKER-ASSISTED BREEDING in APPLE, PEACH, & CHERRY TARGETS VALUABLE FUNCTIONAL ALLELES
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Transcript of MARKER-ASSISTED BREEDING in APPLE, PEACH, & CHERRY TARGETS VALUABLE FUNCTIONAL ALLELES
MARKER-ASSISTED BREEDING in APPLE, PEACH, & CHERRY
TARGETS VALUABLEFUNCTIONAL ALLELES
Cameron Peace, Washington State Universitywith: Nahla Bassil, Michael Coe, Gennaro Fazio, Karina Gallardo,
Ksenija Gasic, Jim Luby, Dorrie Main, Jim McFerson, Cholani Weebadde, Eric van de Weg, Chengyan Yue, & Amy Iezzoni
Outline of Presentation
The RosBREED Project
Available “Jewels in the Genome”
Jewels in Breeding Application
What’s Next? RosBREED 2
The RosBREED Project
• Goal: Enable MAB for U.S. Rosaceae crops
• PI: Amy Iezzoni, Michigan State University
• 4 years, Sep 2009 – Aug 2013
• Funded by SCRI(USDA-NIFA’s Specialty Crop Research Initiative)
• $14.4 M ($7.2 M SCRI, $7.2 M in-kind Partners)
• Collaboration U.S.-wide and international
The RosBREED Project
QTL discovery(looks promising...)
MAB Pipelining(polishing...)
Breeding(assembling into masterpieces)
“Jewels in the Genome”- discovering, polishing, using
Jewels= valuable genetic discoveries ready for breeding application= marker-locus-trait associations validated in a breeding program
Application of Genomics Knowledge
Known QTLs
DN
A in
form
atio
n
Linkage maps
Expression profiles
Whole genome
sequences
Genetic/allelic
diversity
GMO
Application in current cultivars
Application in breeding
Find trait-controlling genes
Application
Application of Genomics Knowledge
Known QTLs
DN
A in
form
atio
n
Linkage maps
Expression profiles
Whole genome
sequences
Genetic/allelic
diversity
GMO
Application in current cultivars
Application in breeding
Find trait-controlling genes P
ractical application
What DNA information is
available?
What is the practical
goal?
Various waysto get there
Application of Genomics Knowledge
Known QTLs
Application in breeding
Breeding markersDNA te
sting
servi
cesQTL
priori
ties
Crossin
g
sche
mes
Trial
MASS
Simple validation
Allele effects& distributions
Seedli
ng
selec
tion
sche
mes
Application of Genomics Knowledge
Known QTLs
Application in breeding
Breeding markersDNA te
sting
servi
cesQTL
priori
ties
Crossin
g
sche
mes
Trial
MASS
Simple validation
Allele effects& distributions
Seedli
ng
selec
tion
sche
mes
1.Tool utility = predictive power in germplasm
of a breeding program
Application in Breeding - Requirements
2.Tool itself = assay (DNA markers) usableby a breeding program
1.Tool utility = predictive power in germplasm
of a breeding program
Application in Breeding - Requirements
2.Tool itself = assay (DNA markers) usableby a breeding program
ready-to-usemarker-locus-trait associations
DNA tests for contrasting alleles at locifor valuable traits
1.Tool utility = predictive power in germplasm
of a breeding program
Application in Breeding - Requirements
2.Tool itself = assay (DNA markers) usableby a breeding program
ready-to-usemarker-locus-trait associations
DNA tests for contrasting alleles at locifor valuable traits
Idiosyncratic!One size does not fit all!
...all breeding-program-specific
Available“Jewels in the Genome”
Sweetness & acidity
Maturity date
Bitter pit susceptibility
Self-fertility
Fruit size
Ever-bearing
Fruit skin color
Fruit color
Fruit storability
Melting vs. Non-melting flesh
Freestone vs. clingstoneFruit size
Available “Jewels in the Genome”
Red stele resistance
Leaf spot resistance
Acidity
Sunburn susceptibility
Firmness
“Fresh sensation”(crispness, tartness, juiciness)
Fruit color
Strawberry: Red Stele Resistance
• Validation of marker by inoculations:- 75% match genotype-phenotype- 20% individuals have otherresistance sources
0 1 2 3 4 5
3.43 disease
threshold
Is presence of certain SSR allele associated with red stele resistance?
• Genotypic data also used to identifymany cases of incorrect parentage
Red stele resistance
Marker(s)? 1 SSR Application? Parents: crossing Seedlings: culling Selections: advance
Apple: Skin Coloration
Cover amount over apple skin surface
Allele & Genotype frequencies in 192 cvs
rfRf rfrf
RfRf
Rfrf
1000 seedlings – how many with score >4?
Rfrf x RfRf ---> 647
RfRf x RfRf ---> 818
+26% efficiency!
prob
abilit
y
Marker(s)? 1-3 SNPs from 8K array genome scan Application? Parents: crossing Selections: distinguish Rfrf / RfRf
Peach: Maturity Date
-40 -20 20 July
+20 +40 days
-40 -20 20 July
+20 +40 days
AA:AAGA:AA
AA:AG GA:AG 168:168 156:168
Three 2-SNP haplotypes (AA,GA,AG) in four combinations
Two SSR alleles(168,156) in two combinations
One trait locus,two ways of genotyping
Maturity date
Marker(s)? 2 SNPs from 9K array ...or ... 1 SSR Application? Parents: crossing Seedlings: culling Selections: advance
Apple: Acidity
• Two lociMa – LG16“A” – LG8
Acidity
• Not quite additive – some epistasis
Use together Marker(s)? 2 SNPs from 8K array genome scan Application? Parents: crossing Selections: distinguish low/med/high
“Fresh sensation”(crispness, tartness, juiciness)
Apple: Multiple Traits Around Ma Locus
Bitter pit susceptibilityMa
Fruit size
Mb0
2
4
6Maturity date
cM0
101520
5
2530
• Every individual has 2 haplotypesHoneycrisp Golden Del. Braeburn Gala Pink Lady
L E L L
Target B?
LL
Marker(s)? 1 SSR Application? Parents: crossing Seedlings: culling Selections: advance
Target A?
LL
Cherry: G2 Fruit Size and Firmness– An Economic Trade-Off
Socio-economic value ($ per lb)
0.10
0
0.08
0.06
0.04
0.02
G2 locus haplotype
G2 locus diplotypeBL ALL
ECB
Hm F
CE
BEAAABAEAD AC
BDAHAm AN BN BmAF
Population average
DA
N O
SE value=
value of reaching threshold
xprobability of achieving it
Fruit sizeFirmness
Marker(s)? SSRs – 2 flanking the QTL Application? Parents: crossing Seedlings: culling Selections: advance
Jewels in Breeding Application
Cost per initial seed
Marker-Assisted Seedling Selectionin the Washington Apple Breeding Program
Savings
DNA testing
$8
$4
$0
$6
$10
$2
Rearing & evaluating those kept
Early rearing
$62K2010 estimated
projected resource savings
$38K2011
$60K2012
seedlings tested
seedlings culled
8000
5000
5417
2937
7452
4403
“Fresh sensation”(crispness, tartness, juiciness)
Fruit storability
What’s Next? RosBREED 2
A Planned New RosBREED Project
Socio-
economics
informatio
n
DNA
informatio
n
Innovative, superior,
risk-mitigating new cultivars
Efficient, accurate, creative breeding
Accessible natural diversity
PRODUCTIONPROCESSINGMARKETING
Post-breeding
Breeding
Pre-breeding
NATURAL DIVERSITY
CONSUMPTION
Seedling selectionParent selection
Cultivar commercialization
Germplasm development
Acknowledgements
This project is supported by the Specialty Crop Research Initiative of USDA’s
National Institute of Food and Agriculture
Questions?