Abstract
BackgroundA 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.ResultsAbout 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.ConclusionsThe 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.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1310-1) contains supplementary material, which is available to authorized users.
Highlights
A high-throughput genotyping platform is needed to enable marker-assisted breeding in the allo-octoploid cultivated strawberry Fragaria × ananassa
This goal has been realized in part through the development of three single nucleotide polymorphisms (SNPs) arrays: a 9 K whole genome scanning array for peach [2], an 8 K apple and 1 K pear array [3,4], and a 6 K array for cherry [5]
These three projects utilized the Illumina® Infinium® genotyping platform. These arrays have been used for the generation of linkage maps [4,6,7,8,9,10,11], evaluation of the quality of physical maps [12], fine mapping and validation of quantitative trait loci (QTL) [9,13], elucidation of marker-trait associations [10,14], genomewide association studies [15], genomic selection studies [16], validation of pedigrees and verification of trueness to type of breeding lines and accessions [17], and for design of the future generation of arrays [18]
Summary
Sequence resources The genomes of 19 octoploid and six diploid strawberry accessions were sequenced to serve as resources for SNP discovery and interpretation (Table 1). The diploids included three representatives of F. vesca, one of F. mandshurica, and two of F. iinumae (Table 1). Of the latter, accession F1D is an intraspecific hybrid that is being used as a parent in an F. iinumae linkage mapping project (Mahoney et al, manuscript in preparation). ×ananassa breeding accessions and cultivars (Table 2, Additional file 1); 51 “non-ananassa” octoploid accessions; three widely studied accessions of diploid F. vesca; and a pedigree-connected population of diploid F. iinumae that included crossing parents J17 and J4, their first generation hybrid F1D, and 21 second generation ‘F2D’ progeny. The 51 “non-ananassa” octoploid accessions included 10 parents and progeny from a F. ×ananassa reconstruction population [46] named FVC, and 41 individuals of multiple pedigreeconnected families from the New Hampshire breeding program (UNH_1 through UNH_41)
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