Nahla Bassil, B. Gilmore, D. Main, C. Peace, T. Mockler, L. Wilhelm, E. van de Weg, T. Davis, D. Chagne, S. Gardiner, R. Crowhurst, I. Verde, B. Sosinski, S. Scalabrini, K. Folta, V. Shulaev, P. Arus, R. Velasco, M. Troggio, A. Cestaro, G. Fazio, J. Norelli, J. Rees and A. Iezzoni RosBREED Deploys Genome- Wide Scans in Peach, Apple, and Cherry

Integration of modern genomics tools with traditional breeding approaches will transform crop improvement in Rosaceae, significantly improving profitability and sustainability of U.S. rosaceous crop industries & contribute to the increased consumption and enjoyment of these fruit, nut and floral products. Overview Oral Presentation, Fruit Breeding and Genetics, Monday at 12:15 pm, Cameron Peace 4 yrs $7.2M federal $7.2M matching Amy Iezzoni, Michigan State Univ Cameron Peace, WA State Univ This project is supported by the Specialty Crop Research Initiative of USDA’s National Institute of Food and Agriculture RosBREED - Vision

Reference Genomes Now Available Apple, peach & diploid strawberry genome Image courtesy of NSF Images courtesy of Jim Hancock

High Throughput SNP Genome Scans G1 G4 G3 G2 G6 G7 G8 G5 ≤5cM QTL Markers for any trait of interest for MAB

3 posters

Re-sequencing of SNP Detection Panel: Illumina Alignment to reference genome: apple, peach SNP detection: SOAP, CLC BIO Jasper Rees, ARC, SA David Chagne, PFR, NZ Ignazio Verde, Italy Pere Arus, Spain Reference-Scaffold 1 Elberta O’Henry Bolinha 80 bp PE reads Infinium Chip Development

SNP validation: GoldenGate SNP Consortium Community chooses parameters for Infinium chip: SNP Summit Final filtering for Infinium chips ASOs 384 SNPs 480 DNA samples Infinium Chip Development

Criteria for SNP Choice for GoldenGate Assay G1 Genic-40% Intronic-20% Promoter-20% Intergenic-20% Equidistant SNPs Elberta O’Henry Accession- specific-20% Bolinha Zoomed-in-20%

GoldenGate Assay Validation Results

Effect of SNP Location Cindy Lawley, Illumina

Effect of Number of Peach Accessions Containing Sequence Data

Haplotype Diversity at Zoomed-in Regions Haplogroup 6 Haplogroup 3 Haplogroup 4 Haplogroup 1 Haplogroup 5 Haplogroup 2 YesNo 160 accessions  35 unique haplotypes  6 haplogroups Haplotype Diversity at Ma Locus

Infinium iSelect® HD Custom Genotyping 3,0001 M Attempted Beadtypes 24 samples per chip Sample Table SNP Table SNP Graph AA AB BB Fully customizable Low DNA input, 200 ng iScan

Choosing SNPs for Infinium Chips Peach chromosome 1. Infinium II SNPs (one SNP per beadtype) 2. Validated SNPs, RosCOS, candidate genes 9 K chips, publicly available SNP

Choosing SNPs for Infinium Chips Position of SNP-Peach genome Tarts: no. reads Tarts: freq of rare base (AAAB, AABC) Tarts: skew from 1:1 (Chi2 value) Tarts: suspected sub- genome SNP bases (common -rare) Chromosome 1 SNP971,900, fruA-G SNP989,112, avG-A SNP9916,224, fruC-G SNP10023,498, avC-T Sweet cherry (4,180), tart cherry (1,551) RosCOS (227), candidate genes (2)

Peach, Cherry and Apple SNPs: Downloadable from GDR

Deploying 9K Infinium Chip in Peach 953 peach samples 1400 SNP markers added to map QTLs for bacterial spot resistance in peach leaf (LEA) and fruit (FRU) in NC and SC, in 2008, 2009 and 2011 G1

Deploying 6K Infinium Chip in Cherry

Deploying 9K Infinium Chip in Apple 5554 (72.2%) pol. SNPs Chagné et al. 2011, manuscript in prep.

Infinium Chips will be used via Pedigree- Based Analysis to identify and validate marker-locus-trait associations for application in breeding RosBREED Use of SNP Genome Scans

MARKER-ASSISTED BREEDING PIPELINE

To Achieve Our Dream Ultra-crisp tasty apples sweet juicy peaches flavorful cherries luscious strawberries Enjoyed by consumers, regularly Consistent quality, available & affordable Sustainably produced throughout the U.S. & worldwide

OSU Todd Mockler Larry Wilhelm Chris Sullivan Mark Dasenko MSU Jeff Langraff Rutgers David Sidote Intuitive Genomics Doug Bryant Todd Mockler GDR, WSU Stephen Ficklin IGA, Italy Simone Scalabrin PFR, NZ Ross Crowhurst Illumina Mark Hansen Sequencing and Bioinformatic Support

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

MSU Amy Iezzoni (PD) Jim Hancock Dechun Wang Cholani Weebadde WSU Cameron Peace Dorrie Main Kate Evans Karina Gallardo Raymond Jussaume Vicki McCracken Nnadozie Oraguzie Mykel Taylor Cornell Susan Brown Kenong Xu Clemson Ksenija Gasic Gregory Reighard Texas A&M Dave Byrne Univ. of CA-Davis Tom Gradziel Carlos Crisosto Univ. of New Hamp. Tom Davis Univ. of Minnesota Jim Luby Chengyan Yue Oregon State Univ. Alexandra Stone Plant Research Intl, Netherlands Eric van de Weg Marco Bink USDA-ARS Nahla Bassil Gennaro Fazio Chad Finn Univ. of Arkansas John Clark