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

作者：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; Monfort Amparo; 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; de Weg Eric van

来源：BMC Genomics, 2015, 16(1): 155.

DOI：10.1186/s12864-015-1310-1

• Fragaria
• Genotyping array
• Plant breeding
• Polyploidy
• Strawberry
• Single nucleotide polymorphism
• Reduced ploidy

Background: A high-throughput genotyping platform is needed to enable marker-assisted breeding in the allo-octoploid cultivated strawberry Fragaria x 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 (R) Axiom (R) 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' x '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.

• 出版日期2015-3-7