genome scans new qtls discovered pba: crop-wide pba: breeding program breeding markers screening...
TRANSCRIPT
GENOME SCANS
New QTLs discovered
PBA: crop-wide
PBA: breeding program
Breeding markersScr
eenin
g
serv
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Mar
ker
prior
ities
Cross
ing
sche
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Trial
MASS
Socio-economics
information
DNA information
Efficient routine breeding operations
Better fruit
STANDARDIZED PHENOTYPING
GERMPLASM CHOICE
TRAIT & MARKET SEGMENT BREEDING TARGET ESTABLISHMENT
GDR, COMPARATIVE GENOMICS
5. Fast-tracked pipelining
MA
B P
IPE
LIN
ING
MA
B P
IPE
LIN
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Promising targets
BREEDERS’ TOOLBOX
DEVELOPMENT
Seedli
ng
selec
tion
sche
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What is Fast-Tracked Pipelining?
• Doing Pipelining quickly – conducting Pipeline stages without the full infrastructure yet in place
• Only as far as MAPS (aiding crossing)
This… …before we can do this
Why Are We Fast-Tracking?
• Examine promising markers now
• Practice for Demo Breeders
• Success stories and pitfalls
• Test Pipeline approach in many situations
What Are We Fast-Tracking?
• Peach1. Texture: Freestone/Clingstone, Melting/Non-
melting, fruit softening rate, softening location – endoPG F-M locus
2. Flavor: sweetness and acidity – QTL, linked to F-M locus
• Cherry (sweet and tart)1. Fruit quality: fruit size, fruit firmness
– QTL (linked to sweetness QTL)
2. Flavor: acidity – QTL (linked to fruit color MTL)
What Are We Fast-Tracking?
• Apple1. Flavor and Texture: acidity, crispness, juiciness
– MTL/QTL (Ma locus)
2. Texture: Firmness – QTL (Md-Exp7 gene)
www.solo.be
What Are We Fast-Tracking?
• StrawberryLack of available fruit quality M-L-T associations
Using instead:
1. Red stele root rot resistance – unpublished QTL (PRI, Netherlands)
www.omafra.gov.on.ca www.urbanext.illinois.eduwww.forestryimages.org
What Are We Fast-Tracking?
What Are We Fast-Tracking?Crop Trait Locus MarkerPeach Fruit flesh softening type
(melting, non-melting, non-softening) and
flesh adhesion to stone (freestone/clingstone). Also mealiness, firmness, flesh bleeding in storage
F-M locus on Prunus chromosome 4
SSR: endoPG-1 and SCAR: endoPG-6
Peach Fruit sweetness (SSC) and acidity (TA)
QTL on Prunus chromosome 4
SSR: BPPCT023
Apple Fruit acidity, crispness, and juiciness
Ma locus with QTLs on Malus chromosome 16
SSRs: CH05c06 and Hi04e04
Apple Fruit firmness QTL on Malus chromosome 1 SSR: Md-Exp7
Cherry Fruit size, firmness, and flavor
QTL on Prunus chromosome 2
SSRs: CPSCT038 and BPCT034
Cherry Fruit acidity QTL on Prunus chromosome 3
SSR: BPPCT039
PBA: crop-wide
PBA: breeding program
Breeding markersScr
eenin
g
serv
ices
Mar
ker
prior
ities
Cross
ing
sche
me
MA
B P
IPE
LIN
ING
MA
B P
IPE
LIN
ING
Promising targets
How Are We Fast-Tracking?
Efficient routine breeding operations
PBA: crop-wide
PBA: breeding program
Breeding markersScr
eenin
g
serv
ices
Mar
ker
prior
ities
Cross
ing
sche
me
Promising targets
How Are We Fast-Tracking?
1.
PRIORITIZATION. Many M-L-T assocs to choose from (e.g. RosBREED table).Made shortlist of ~6 each crop; current breeding priorities, apparent strength* Proxy for $ x G x H
PBA: crop-wide
PBA: breeding program
Breeding markersScr
eenin
g
serv
ices
Mar
ker
prior
ities
Cross
ing
sche
me
Promising targets
How Are We Fast-Tracking?
2. * Proxy for any future service breeders can access
GENETIC SCREENING EFFICIENCY. Nahla’s Corvallis lab designated as project’s Genotyping Center
3.
IMPROVED MARKERS. Tested known markers, all worked.* Normally will have
to access GDR to develop then test new mkrs at locus
PBA: crop-wide
PBA: breeding program
Breeding markersScr
eenin
g
serv
ices
Mar
ker
prior
ities
Cross
ing
sche
me
Promising targets
How Are We Fast-Tracking?
4.
VALIDATION. * Needs repres. segregating germplasm, phenotypes for traits of interest, genotypes for specific trait locus markers. We are using CR Sets,
Yr 1 phenotypic data, mkrs of previous slides
Currently collating that data
Then analysis - PBA
Genotyping:Nahla & April, Ksenija & Terrence
Phenotyping:All crop teams
Germplasm…
Data quality control…
PBA: crop-wide
PBA: breeding program
Breeding markersScr
eenin
g
serv
ices
Mar
ker
prior
ities
Cross
ing
sche
me
Promising targets
How Are We Fast-Tracking?
5.
UTILITY. As for Validation but ensure use breeding program germplasm
Output = functional genotypes of imp. breeding parents
PBA: crop-wide
PBA: breeding program
Breeding markersScr
eenin
g
serv
ices
Mar
ker
prior
ities
Cross
ing
sche
me
Promising targets
How Are We Fast-Tracking?
6.
MAPS (CROSS PLANNING). Functional genotypes simply used to inform crossing.Avoid inferior crossesTarget superior crosses
Cross
ing
sche
me
Use of Fast-Tracked Information
Enough time? Who needs it when?
Yr 1 data enough?
Supplement with prior data?
Consider in light of prior studies?
Use at least for 2012 crossing… and MASS
2011 spring crossing decision support.