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-89906303AX-89906303genetic_marker
AX-89906304AX-89906304genetic_marker
AX-89906305AX-89906305genetic_marker
AX-89850035AX-89850035genetic_marker
AX-89906306AX-89906306genetic_marker
AX-89850036AX-89850036genetic_marker
AX-89906307AX-89906307genetic_marker
AX-89850037AX-89850037genetic_marker
AX-89906308AX-89906308genetic_marker
AX-89850038AX-89850038genetic_marker
AX-89850039AX-89850039genetic_marker
AX-89850040AX-89850040genetic_marker
AX-89850041AX-89850041genetic_marker
AX-89906309AX-89906309genetic_marker
AX-89850043AX-89850043genetic_marker
AX-89850044AX-89850044genetic_marker
AX-89850045AX-89850045genetic_marker
AX-89906310AX-89906310genetic_marker
AX-89906311AX-89906311genetic_marker
AX-89850046AX-89850046genetic_marker
AX-89906312AX-89906312genetic_marker
AX-89906313AX-89906313genetic_marker
AX-89906315AX-89906315genetic_marker
AX-89850047AX-89850047genetic_marker
AX-89850048AX-89850048genetic_marker

Pages

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