GENOME SCANS New QTLs discovered PBA: crop-wide PBA: breeding program Breeding markers Screening services Marker priorities Crossing scheme Trial MASS.

GENOME SCANS

New QTLs discovered

PBA: crop-wide

PBA: breeding program

Breeding markersScr

eenin

g

serv

ices

Mar

ker

prior

ities

Cross

ing

sche

me

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

ING

Promising targets

BREEDERS’ TOOLBOX

DEVELOPMENT

Seedli

ng

selec

tion

sche

me

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 Red stele root rot resistance – unpublished QTL (PRI, Netherlands)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.

Fast-Tracked MAB Pipelining

Peach1. Texture: endoPG F-M

locus

2. Flavor: sweetness & acidity QTL

Cherry1. Fruit quality: fruit size and

firmness QTL

2. Flavor: acidity QTL

Apple1. Flavor and Texture:

acidity, crispness, juiciness MTL/QTL

2. Texture: Firmness QTL

for Fruit Quality