1. GENOME SCANS New QTLs discovered PBA: crop-wide PBA: breeding program Breeding markers Screening services Marker priorities Crossing scheme 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 MAB PIPELINING Promising targets BREEDERS’ TOOLBOX DEVELOPMENT Seedling selection scheme

2. 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

3. Why Are We Fast-Tracking? Examine promising markers now Practice for Demo Breeders Success stories and pitfalls Test Pipeline approach in many situations

4. What Are We Fast-Tracking? Peach 1.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

5. 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?

6. Apple 1.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?

7. Strawberry Lack of available fruit quality M-L-T associations Using instead: 1.Red stele root rot resistance – unpublished QTL (PRI, Netherlands) www.omafra.gov.on.cawww.urbanext.illinois.edu www.forestryimages.org What Are We Fast-Tracking?

8. CropTraitLocusMarker PeachFruit 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 PeachFruit sweetness (SSC) and acidity (TA) QTL on Prunus chromosome 4 SSR : BPPCT023 AppleFruit acidity, crispness, and juiciness Ma locus with QTLs on Malus chromosome 16 SSRs : CH05c06 and Hi04e04 AppleFruit firmness QTL on Malus chromosome 1 SSR : Md-Exp7 CherryFruit size, firmness, and flavor QTL on Prunus chromosome 2 SSRs : CPSCT038 and BPCT034 CherryFruit acidityQTL on Prunus chromosome 3 SSR : BPPCT039

9. PBA: crop-wide PBA: breeding program Breeding markers Screening services Marker priorities Crossing scheme MAB PIPELINING Promising targets How Are We Fast-Tracking? Efficient routine breeding operations

10. PBA: crop-wide PBA: breeding program Breeding markers Screening services Marker priorities Crossing scheme Promising targets How Are We Fast-Tracking? 1. P RIORITIZATION. 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

11. PBA: crop-wide PBA: breeding program Breeding markers Screening services Marker priorities Crossing scheme Promising targets How Are We Fast-Tracking? 2. * Proxy for any future service breeders can access G ENETIC S CREENING E FFICIENCY. Nahla’s Corvallis lab designated as project’s Genotyping Center 3. I MPROVED M ARKERS. Tested known markers, all worked. * Normally will have to access GDR to develop then test new mkrs at locus

12. PBA: crop-wide PBA: breeding program Breeding markers Screening services Marker priorities Crossing scheme Promising targets How Are We Fast-Tracking? 4. V ALIDATION. * 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…

13. PBA: crop-wide PBA: breeding program Breeding markers Screening services Marker priorities Crossing scheme Promising targets How Are We Fast-Tracking? 5. U TILITY. As for Validation but ensure use breeding program germplasm Output = functional genotypes of imp. breeding parents

14. PBA: crop-wide PBA: breeding program Breeding markers Screening services Marker priorities Crossing scheme Promising targets How Are We Fast-Tracking? 6. MAPS (C ROSS P LANNING ). Functional genotypes simply used to inform crossing. Avoid inferior crosses Target superior crosses

15. Crossing scheme 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.

16. Fast-Tracked MAB Pipelining Peach 1.Texture: endoPG F-M locus 2. Flavor: sweetness & acidity QTL Cherry 1.Fruit quality: fruit size and firmness QTL 2. Flavor: acidity QTL Apple 1.Flavor and Texture: acidity, crispness, juiciness MTL/QTL 2.Texture: Firmness QTL for Fruit Quality