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

Publication Overview
TitleDevelopment and preliminary evaluation of a 90 K Axiom SNP array for the allo-octoploid cultivated strawberry Fragaria × ananassa
AuthorsBassil NV, Davis TM, Zhang H, Ficklin S, Mittmann M, Webster T, Mahoney L, Wood D, Alperin ES, Rosyara UR, Koehorst-Vanc Putten H, Monfort A, Sargent DJ, Amaya I, Denoyes B, 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
TypeJournal Article
Journal NameBMC genomics
Volume16
Issue1
Year2015
Page(s)1310
CitationBassil NV, Davis TM, Zhang H, Ficklin S, Mittmann M, Webster T, Mahoney L, Wood D, Alperin ES, Rosyara UR, Koehorst-Vanc Putten H, Monfort A, Sargent DJ, Amaya I, Denoyes B, 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. Development and preliminary evaluation of a 90 K Axiom SNP array for the allo-octoploid cultivated strawberry Fragaria × ananassa. BMC genomics. 2015 Dec; 16(1):1310.

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.

Features
This publication contains information about 138,099 features:
Feature NameUniquenameType
AX-89850202AX-89850202genetic_marker
AX-89850203AX-89850203genetic_marker
AX-89906462AX-89906462genetic_marker
AX-89906463AX-89906463genetic_marker
AX-89906464AX-89906464genetic_marker
AX-89850204AX-89850204genetic_marker
AX-89850205AX-89850205genetic_marker
AX-89850206AX-89850206genetic_marker
AX-89906465AX-89906465genetic_marker
AX-89906466AX-89906466genetic_marker
AX-89906467AX-89906467genetic_marker
AX-89906468AX-89906468genetic_marker
AX-89850207AX-89850207genetic_marker
AX-89850208AX-89850208genetic_marker
AX-89850209AX-89850209genetic_marker
AX-89850210AX-89850210genetic_marker
AX-89850211AX-89850211genetic_marker
AX-89850212AX-89850212genetic_marker
AX-89906469AX-89906469genetic_marker
AX-89906470AX-89906470genetic_marker
AX-89850213AX-89850213genetic_marker
AX-89906471AX-89906471genetic_marker
AX-89906472AX-89906472genetic_marker
AX-89850214AX-89850214genetic_marker
AX-89850215AX-89850215genetic_marker

Pages

Featuremaps
This publication contains information about 1 maps:
Map Name
Strawberry-HK-F1-SNP