Development and preliminary evaluation of a 90K Axiom® SNP array for the allo-octoploid cultivated strawberry Fragaria ×ananassa

Authors: Bassil, Nahla; DAVIS, THOMAS - University Of New Hampshire; ZHANG, HAILONG - University Of New Hampshire; FICKLIN, STEPHEN - Washington State University; MITTMAN, MICHAEL - Affymetrix, Inc; WEBSTER, TERESA - Affymetrix, Inc; MAHONEY, LISE - University Of New Hampshire; WOOD, DAVE - University Of New Hampshire; Alperin, Elisabeth; ROSYARA, UMESH - Michigan State University; KOEHORST-VAN PUTTEN, HERMA - Wageningen University And Research Center; MONFORT, AMPARO - Institute De Recerca I Tecnologia Agroalimentaries (IRTA); AMAYA, IRAIDA - Research And Training Institute For Agricultural And Fisheries Of Andalusia, Ifapa; DENOYES, BEATRICE - Institut National De La Recherche Agronomique (INRA); SARGENT, DANIEL - Fondazione Edmund Mach; BIANCO, LUCA - Fondazione Edmund Mach; VAN DIJK, THIJS - Wageningen University And Research Center; PIRANI, ALI - Affymetrix, Inc; IEZZONI, AMY - Michigan State University; MAIN, DORRIE - Washington State University; PEACE, CAMERON - Washington State University; YANG, YILONG - University Of New Hampshire; WHITAKER, VANCE - University Of Florida; VERMA, SUJEET - University Of Florida; BELLON, LAURENT - Affymetrix, Inc; BREW, FIONA - Affymetrix, Inc; HERRERA, RAUL - Universidad De Chile; VAN DE WEG, ERIC - Wageningen University And Research Center

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/1/2015
Publication Date: 8/1/2015
Citation: Bassil, N.V., Davis, T., Zhang, H., Ficklin, S., Mittman, M., Webster, T.A., Mahoney, L.L., Wood, D.J., Alperin, E.S., Rosyara, U., Koehorst-Van Putten, H., Monfort, A., Amaya, I., Denoyes, B., Sargent, D.J., Bianco, L., Van Dijk, T., Pirani, A., Iezzoni, A., Main, D., Peace, C., Yang, Y., Whitaker, V., Verma, S., Bellon, L., Brew, F., Herrera, R., Van De Weg, E.W. 2015. Development and preliminary evaluation of a 90K Axiom® SNP array for the allo-octoploid cultivated strawberry Fragaria ×ananassa. Biomed Central (BMC) Genomics. 16:155.

Interpretive Summary: In strawberry, the RosBREED consortium has focused on developing tools to characterize the DNA sequences and enable DNA-informed breeding. This characterization is an important step in the development of genetic tools to improve the efficiency of plant breeding. This goal was met by the public release of a commercially available computer chip that is being used by the worldwide scientific community. Development of this technology in strawberry has lagged behind mostly due to the challenges caused by its complex genetic make-up generated from multiple chromosome sets. We describe the development of a computer chip in strawberry, the first of its kind in a crop with eight chromosome sets. Preliminary evaluation of this chip in 306 strawberry samples identified thousands of useful DNA markers as we demonstrate in a strawberry family resulting from a cross between the strawberry cultivars Holiday and Korona. We expect this data set to enable in-depth characterization of commercial strawberry and to identify the genes responsible for traits of economic significance in this important fruit crop. This chip will enable an detailed genetic analyses in this high value crop.

Technical Abstract: A high-throughput genotyping platform is needed to enable marker-assisted breeding in the allo-octoploid cultivated strawberry Fragaria ×ananassa. Short-read sequences from one diploid and 19 octoploid accessions were aligned to the diploid Fragaria vesca ‘Hawaii 4’ reference genome to identify single nucleotide polymorphisms (SNPs) and indels for incorporation in a 90K Affymetrix® Axiom® array. We report the development and preliminary evaluation of this array. About 36 million sequence variants were identified in a 19 member germplasm. Strategies and filtering pipelines were developed to identify and incorporate markers of several types: di-allelic SNPs (66.6%), multi-allelic SNPs (1.8%), indels (10.1%), and ploidy-reducing “haploSNPs” (11.7%). SNPs discovered in diploid progenitor F. iinumae (3.9%), and speculative “codon-based” SNPs (5.9%), were included. In genotyping 306 octoploid accessions, SNPs were assigned to six classes with Affymetrix’s “SNPolisher” R package. The highest quality classes, PolyHigh Resolution (PHR), No Minor Homozygote (NMH), and Off-Target Variant (OTV) comprised 25%, 38%, and 1% of array markers, respectively, providing markers suitable for genetic studies as demonstrated by generation in the full-sib family ‘Holiday’בKorona’ of a genetic linkage map consisting of 6,594 PHR SNPs evenly distributed across 28 chromosomes with an average density of approximately one marker per 0.5 cM, exceeding our goal of one marker per cM. The Affymetrix® IStraw90 Axiom® array is the first high-throughput genotyping platform for cultivated strawberry and is commercially available to the worldwide scientific community. The array’s high success rate is likely driven by the presence of naturally occurring variation in ploidy level within the nominally octoploid genome, and by effectiveness of the employed array design and SNP genotyping strategies. This array enables genetic analyses including generation of high-density linkage maps, identification of QTLs for economically important traits, and genome-wide association studies, thus providing a basis for marker-assisted breeding in this high value crop.