W. Eric Van de Weg
,
Plant Breeding Wageningen University & Research centre, Wageningen, Netherlands
Nahla Bassil
,
USDA/ARS, NCGR, Corvallis, OR
Thomas M. Davis
,
University of New Hampshire, Durham, NH
Hailong Zhang
,
University of New Hampshire, Durham, NH
Lise Mahoney
,
University of New Hampshire, Durham, NH
Stephen P. Ficklin
,
Washington State University, Pullman, WA
Dorrie Main
,
Washington State University, Pullman, WA
Sook Jung
,
Washington State University, Pullman, WA
Cameron Peace
,
Washington State University, Pullman, WA
Amparo Monfort
,
IRTA, Centre for Research in Agricultural Genomics, Bellaterra (Barcelona), Spain
Iraida Amaya
,
IFAPA, Malaga, Spain
Laurent R. Bellon
,
Affymetrix Inc., Santa Clara, CA
Béatrice Denoyes
,
INRA UMR, Villenave d'Ornon, France
Amy Iezzoni
,
Michigan State University, East Lansing, MI
Michael Mittmann
,
Affymetrix Inc., Santa Clara, CA
Ali Pirani
,
Affymetrix, Inc., Santa Clara, CA
Teresa A. Webster
,
Affymetrix, Inc., Santa Clara, CA
Fiona Brew
,
Affymetrix UK Ltd, High Wycombe, United Kingdom
Luca Bianco
,
FEM-IASMA, San Michele all'Adige, Italy
Michela Troggio
,
FEM-IASMA, San Michele all'Adige, Italy
Riccardo Velasco
,
FEM-IASMA, San Michele all'Adige, Italy
Charles Eric Durel
,
INRA, Institut de Recherche en Horticulture et Semences , Beaucouzé Cedex 1, France
François Laurens
,
IRHS-INRA, Angers, France
Ross N Crowhurst
,
The New Zealand Institute for Plant & Food Research Ltd, Auckland, Niger
Ivo Gut
,
Centre Nacional d'Anàlisi Genòmica, Barcelona, Spain
Sophia Derdak
,
Centre Nacional d'Anàlisi Genòmica, Barcelona, Spain
Sergi Beltran Beltran
,
Centre Nacional d'Anàlisi Genòmica, Barcelona, Spain
Cynthia Lawley
,
Illumina, Hayward, CA
Mark Hansen
,
Illumina Inc., San Diego, CA
A central goal of the RosBREED and FruitBreedomics consortia has been to establish SNP arrays for peach, cherry, apple, and strawberry, to facilitate QTL discovery and marker-assisted breeding. This goal has been advanced by the release of three Illumina® Infinium® arrays for apple, peach, and cherry (8K, 9K and 6K, respectively). Here, we report on the development of a 90K Strawberry Affymetrix Axiom® and a 20K Apple Infinium® genotyping array.
The cultivated strawberry is an allo-octoploid. This level and type of ploidy creates challenges which we addressed in several ways. First, the large size of the array permits success despite a lower conversion rate of candidate to functional SNPs than for diploid crops. Second, we exploited both site-specific, biological as well as designed reductions in ploidy. The array will target several polymorphism types, including indels and di- and multi-allelic SNPs.
For apple, the new SNP markers are located in focal points of max 10 KB, an approach that favours the design of multi-allelic haplotypes. Focal points have an average of 8 SNPs selected to evenly represent the members of the discovery panel. Issues related to the duplicated nature of the apple genome are accounted for in several ways, including the use of double haploids.
We will describe our approaches for the design of these two SNP arrays. We also report on a new bioinformatics pipeline, which includes local re-alignment around indels and polymorphism type-specific filtering strategies. Both arrays will be commercially available in early 2013.
