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GENOME SCANS

5. Fast-tracked pipelining. TRAIT & MARKET SEGMENT BREEDING TARGET ESTABLISHMENT. GDR, COMPARATIVE GENOMICS. Socio-economics information. GENOME SCANS. Marker priorities. Promising targets. Breeding markers. Screening services. MAB PIP ELINING. GERMPLASM CHOICE. DNA information.

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GENOME SCANS

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  1. 5. Fast-tracked pipelining TRAIT & MARKET SEGMENT BREEDING TARGET ESTABLISHMENT GDR, COMPARATIVE GENOMICS Socio-economics information GENOME SCANS Marker priorities Promising targets Breeding markers Screening services MAB PIPELINING GERMPLASM CHOICE DNA information PBA: crop-wide STANDARDIZED PHENOTYPING New QTLs discovered PBA: breeding program Crossing scheme Efficient routine breeding operations Better fruit MAB PIPELINING Seedling selection scheme Trial MASS BREEDERS’ TOOLBOX DEVELOPMENT

  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 • Texture: Freestone/Clingstone, Melting/Non-melting, fruit softening rate, softening location – endoPG F-M locus • Flavor: sweetness and acidity – QTL, linked to F-M locus

  5. What Are We Fast-Tracking? • Cherry (sweet and tart) • Fruit quality: fruit size, fruit firmness – QTL (linked to sweetness QTL) • Flavor: acidity – QTL (linked to fruit color MTL)

  6. What Are We Fast-Tracking? • Apple • Flavor and Texture: acidity, crispness, juiciness – MTL/QTL (Ma locus) • Texture: Firmness – QTL (Md-Exp7 gene) www.solo.be

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 • Strawberry • Lack of available fruit quality M-L-T associations • Using instead: • Red stele root rot resistance – unpublished QTL (PRI, Netherlands) www.omafra.gov.on.ca www.urbanext.illinois.edu www.forestryimages.org

  8. What Are We Fast-Tracking?

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

  10. How Are We Fast-Tracking? Prioritization. Many M-L-T assocs to choose from (e.g. RosBREED table). Made shortlist of ~6 each crop; current breeding priorities, apparent strength 1. * Proxy for $ x G x H Marker priorities Promising targets Breeding markers Screening services PBA: crop-wide PBA: breeding program Crossing scheme

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

  12. How Are We Fast-Tracking? Validation. * Needs repres. segregating germplasm, phenotypes for traits of interest, genotypes for specific trait locus markers. Marker priorities Promising targets Breeding markers Screening services We are using CR Sets, Yr 1 phenotypic data, mkrs of previous slides PBA: crop-wide 4. Phenotyping: All crop teams Currently collating that data Then analysis - PBA PBA: breeding program Genotyping: Nahla & April, Ksenija & Terrence Crossing scheme Germplasm… Data quality control…

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

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

  15. Use of Fast-Tracked Information • 2011 spring crossing decision support. 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 Crossing scheme

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

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