Development and preliminary evaluation of a 90 K Axiom® SNP array for the allo-octoploid cultivated strawberry Fragaria × ananassa
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Author
Bassil, Nahla V.
Davis, Thomas M.
Zhang, Hailong
Ficklin, Stephen
Mittmann, Mike
Webster, Teresa
Mahoney, Lise
Wood, David
Alperin, Elisabeth S.
Rosyara, Umesh R.
Putten, Herma Koehorst-vanc
Sargent, Daniel J.
Amaya, Iraida
Denoyes, Beatrice
Bianco, Luca
van Dijk, Thijs
Pirani, Ali
Iezzoni, Amy
Main, Dorrie
Peace, Cameron
Yang, Yilong
Whitaker, Vance
Verma, Sujeet
Bellon, Laurent
Brew, Fiona
Herrera, Raul
van de Weg, Eric
Publication date
2015-03-07ISSN
1471-2164
Abstract
Background: 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 into a 90 K Affymetrix® Axiom® array. We report the development and preliminary evaluation of this array.
Results: About 36 million sequence variants were identified in a 19 member, octoploid germplasm panel. 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%). The remaining SNPs included those discovered in the diploid progenitor F. iinumae (3.9%), and speculative “codon-based” SNPs (5.9%). 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. These markers were suitable for genetic studies as demonstrated in the full-sib family ‘Holiday’ × ‘Korona’ with the generation 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, thus exceeding our goal of one marker per cM.
Conclusions: 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 ploidy-reducing strategies. This array enables genetic analyses including generation of high-density linkage maps, identification of quantitative trait loci for economically important traits, and genome-wide association studies, thus providing a basis for marker-assisted breeding in this high value crop.
Document Type
Article
Document version
Published version
Language
English
Subject (CDU)
633 - Field crops and their production
Pages
30
Publisher
BMC
Is part of
BMC Genomics
Citation
Bassil, Nahla V, Thomas M Davis, Hailong Zhang, Stephen Ficklin, Mike Mittmann, Teresa Webster, and Lise Mahoney et al. 2015. "Development And Preliminary Evaluation Of A 90 K Axiom® SNP Array For The Allo-Octoploid Cultivated Strawberry Fragaria × Ananassa". BMC Genomics 16 (1). doi:10.1186/s12864-015-1310-1.
Grant agreement number
MICINN/Programa Nacional de Proyectos de Investigación Fundamental/AGL2010-21414/ES/ANALISIS GENETICO DE LOS CARACTERES DE CALIDAD NUTRICIONAL DE FRUTO EN FRESA SILVESTRE Y CULTIVADA/
Program
Genòmica i Biotecnologia
This item appears in the following Collection(s)
- ARTICLES CIENTÍFICS [2646]
Except where otherwise noted, this item's license is described as http://creativecommons.org/licenses/by/4.0/