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MARKER-ASSISTED BREEDING in APPLE, PEACH, & CHERRY TARGETS VALUABLE FUNCTIONAL ALLELES Cameron Peace, Washington State University with: Nahla Bassil, Michael.

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Presentation on theme: "MARKER-ASSISTED BREEDING in APPLE, PEACH, & CHERRY TARGETS VALUABLE FUNCTIONAL ALLELES Cameron Peace, Washington State University with: Nahla Bassil, Michael."— Presentation transcript:

1 MARKER-ASSISTED BREEDING in APPLE, PEACH, & CHERRY TARGETS VALUABLE FUNCTIONAL ALLELES Cameron Peace, Washington State University with: 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

2 Outline of Presentation  The RosBREED Project  Available “Jewels in the Genome”  Jewels in Breeding Application  What’s Next? RosBREED 2

3 The RosBREED Project

4 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

5 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

6 Application of Genomics Knowledge Known QTLs DNA information Linkage maps Expression profiles Whole genome sequences Genetic/ allelic diversity GMO Application in current cultivars Application in breeding Find trait- controlling genes Application

7 Application of Genomics Knowledge Known QTLs DNA information Linkage maps Expression profiles Whole genome sequences Genetic/ allelic diversity GMO Application in current cultivars Application in breeding Find trait- controlling genes Practical application What DNA information is available? What is the practical goal? Various ways to get there

8 Application of Genomics Knowledge Breeding markers DNA testing services QTL priorities Crossing schemes Trial MASS Simple validation Allele effects & distributions Seedling selection schemes

9 Application of Genomics Knowledge Breeding markers DNA testing services QTL priorities Crossing schemes Trial MASS Simple validation Allele effects & distributions Seedling selection schemes

10 1.Tool utility =predictive power in germplasm of a breeding program Application in Breeding - Requirements 2.Tool itself =assay (DNA markers) usable by a breeding program

11 1.Tool utility =predictive power in germplasm of a breeding program Application in Breeding - Requirements 2.Tool itself =assay (DNA markers) usable by a breeding program  ready-to-use marker-locus-trait associations  DNA tests for contrasting alleles at loci for valuable traits

12 1.Tool utility =predictive power in germplasm of a breeding program Application in Breeding - Requirements 2.Tool itself =assay (DNA markers) usable by a breeding program  ready-to-use marker-locus-trait associations  DNA tests for contrasting alleles at loci for valuable traits Idiosyncratic! One size does not fit all!...all breeding-program-specific

13 Available “Jewels in the Genome”

14

15 Strawberry: Red Stele Resistance Validation of marker by inoculations: - 75% match genotype-phenotype - 20% individuals have other resistance sources disease threshold Is presence of certain SSR allele associated with red stele resistance? Genotypic data also used to identify many cases of incorrect parentage Marker(s)?1 SSR Application? Parents: crossing Seedlings: culling Selections: advance

16 Apple: Skin Coloration Cover amount over apple skin surface Allele & Genotype frequencies in 192 cvsrf Rf rfrf RfRf Rfrf 1000 seedlings – how many with score >4? Rfrf x RfRf ---> 647 RfRf x RfRf ---> % efficiency! probability Marker(s)?1-3 SNPs from 8K array genome scan Application? Parents: crossing Selections: distinguish Rfrf / RfRf

17 Peach: Maturity Date July days July days AA:AA GA:AA AA:AG GA:AG 168:168156:168 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 Marker(s)?2 SNPs from 9K array...or... 1 SSR Application? Parents: crossing Seedlings: culling Selections: advance

18 Apple: Acidity Two loci Ma – LG16 “A” – LG8 Not quite additive – some epistasis  Use together Marker(s)?2 SNPs from 8K array genome scan Application? Parents: crossing Selections: distinguish low/med/high

19 Apple: Multiple Traits Around Ma Locus Ma Mb Maturity date cM Every individual has 2 haplotypes HoneycrispGolden Del.BraeburnGalaPink Lady LELL Target B? LL Marker(s)?1 SSR Application? Parents: crossing Seedlings: culling Selections: advance Target A? LL

20 Cherry: G2 Fruit Size and Firmness – An Economic Trade-Off Socio-economic value ($ per lb) G2 locus haplotype G2 locus diplotype BL AL L E C B H m F CE BE AA AB AE AD AC BD AH Am AN BN Bm AF Population average D A N O SE value = value of reaching threshold x probability of achieving it Marker(s)?SSRs – 2 flanking the QTL Application? Parents: crossing Seedlings: culling Selections: advance

21 Jewels in Breeding Application

22 Cost per initial seed Marker-Assisted Seedling Selection in the Washington Apple Breeding Program Savings DNA testing $8 $4 $0 $6 $10 $2 Rearing & evaluating those kept Early rearing $62K 2010 estimated projected resource savings $38K 2011 $60K 2012 seedlings tested seedlings culled

23 What’s Next? RosBREED 2

24 A Planned New RosBREED Project Socio- economics information DNA information Innovative, superior, risk-mitigating new cultivars Efficient, accurate, creative breeding Accessible natural diversity PRODUCTION PROCESSING MARKETING Post-breeding Breeding Pre-breeding Seedling selection Parent selection Cultivar commercialization Germplasm development

25 Acknowledgements This project is supported by the Specialty Crop Research Initiative of USDA’s National Institute of Food and Agriculture

26 Questions?


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