Genome-wide QTL Analyses Uncovers SNP Marker-based Functional Alleles for Apple “Fresh Sensation” Traits

Tuesday, July 23, 2013: 12:45 PM
Springs Salon D/E (Desert Springs J.W Marriott Resort )
Sujeet Verma , Hort&LA, Washington State University, Pullman, WA
Cari Schmitz , Dept. of Horticultural Science, University of Minnesota, St, Paul, MN
Matthew Clark , Dept. of Horticultural Science, University of Minnesota, St. Paul, MN
Yingzhu Guan , Washington State University, Wenatchee, WA
Benjamin Orcheski , Cornell University, Geneva, NY
Julia Harshman , Washington State University, Wenatchee
Katherine Evans , Washington State University, TFREC, Wenatchee, WA
Susan K. Brown , Cornell University, Geneva, NY
James R. McFerson , Washington Tree Fruit Research Commission, Wenatchee, WA
Nahla Bassil , USDA–ARS, NCGR, Corvallis, OR
Umesh Rosyara , Horticulture, Michigan State University, East Lansing, MI
Marco Bink , Wageningen University and Research Center, Droevendaalsesteeg, Netherlands
James Luby , Dept of Horticultural Science, University of Minnesota, St. Paul, MN
Eric van de Weg , Wageningen University and Research Center, Droevendaalsesteeg, Netherlands
Amy F. Iezzoni , Michigan State University, East Lansing, MI
Cameron Peace , Washington State University, Pullman, WA
Crispness, juiciness, and acidity are traits that collectively determine the “fresh sensation” of apple flesh and greatly affect consumer liking of apple cultivars. Unfortunately, our lack of genetic understanding of these attributes has slowed progress in apple breeding programs. The RosBREED project has developed genotypic and phenotypic resources to enable DNA-informed breeding in apple and other Rosaceae crops. For example, an 8 K SNP chip for scanning genomes of approximately 1000 individuals of the U.S. apple breeding germplasm has been developed. Pedigree based analysis approach, using FlexQTL™ and Pedimap softwares, has been implemented for location specific (Washington, Minnesota, and New York) genome-wide QTL analysis for “fresh sensation” traits and linkage groups with significant QTLs have been identified for further analysis. LG02 and LG16 have QTLs for all three fresh sensation traits. We have also confirmed an additional QTL for acidity on LG08, crispness on LGs 05, and 12, and sensory juiciness on LGs 05 and 12. We have identified SNP based functional alleles and estimated effects of major “fresh sensation” loci for important breeding parents. Identified “fresh sensation” QTL variants would be useful for DNA-informed breeding and new cultivar development.
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