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

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.

HaploSNP affinities and linkage map positions illuminate subgenome composition in the octoploid, cultivated strawberry ( Fragaria×ananassa )

“…Capitalizing on the availability of a high quality genome sequence for the genus, a medium density whole genome genotyping array (named the Axiom® IStraw90® array) has been developed for the cultivated strawberry by Bassil and Davis et al [17], who utilized alignments of extensive resequencing data from a panel of 19 F. ×ananassa cultivars, breeding selections and mapping population progeny, and a further six diploid Fragaria accessions to the FvH4 genome sequence. The array was built using the Affymetrix Axiom® platform and comprises 95,062 marker loci, most of which reside in coding or intronic regions of the genome.…”

“…The array was built using the Affymetrix Axiom® platform and comprises 95,062 marker loci, most of which reside in coding or intronic regions of the genome. Included on the array was an innovative marker category known as 'haploSNPs' [17], which conferred an effective reduction of ploidy in relation to marker genotyping by exploiting the coupling of marker SNPs with nearby homoeologous sequence variants (HSVs) [18].…”

“…In the array design process [17], this destabilization site was required to have two alleles, both of which were present in all members of the octoploid discovery panel, and one of which was defined as the 'critical' allele on the basis that segregation of the coupled marker SNP occurred only in the presence of the critical destabilization site allele. The haploSNP probes were then designed to anneal in the presence of the critical destabilization site allele, but not in the presence of the alternate (noncritical) allele, thus providing a degree of subgenome exclusivity to probe hybridization.…”

Genetic mapping in polyploids

“…Examples of the former include alfalfa (Li et al, 2014b), chrysanthemum (van Geest et al, 2017c, potato (Hamilton et al, 2011;Felcher et al, 2012;Vos et al, 2015), rose and sour cherry (Peace et al, 2012). Examples of allopolyploid SNP arrays include cotton (Hulse-Kemp et al, 2015), oat (Tinker et al, 2014), oilseed rape (Dalton- Morgan et al, 2014;Clarke et al, 2016), peanut (Pandey et al, 2017), strawberry (Bassil et al, 2015) and wheat (Akhunov et al, 2009;Cavanagh et al, 2013;Wang et al, 2014b;Winfield et al, 2016). Untargeted approaches such as genotyping-by-sequencing have also been applied, for example in autopolyploids such as alfalfa Yu et al, 2017), blueberry (McCallum et al, 2016), bluestem prairie grass (Andropogon gerardii) (McAllister and Miller, 2016), cocksfoot (Dactylis glomerata) (Bushman et al, 2016), potato (Uitdewilligen et al, 2013;Sverrisdóttir et al, 2017), sugarcane (Balsalobre et al, 2017;Yang et al, 2017b) and sweet potato (Shirasawa et al, 2017), and in allopolyploids such as coffee (Moncada et al, 2016), cotton (Islam et al, 2015;Reddy et al, 2017), intermediate wheatgrass (Thinopyrum intermedium) (Kantarski et al, 2017), oat (Chaffin et al, 2016), prairie cordgrass (Spartina pectinata) (Crawford et al, 2016), shepherd's purse (Capsella bursa-pastoris) (Cornille et al, 2016), wheat (Poland et al, 2012;Edae et al, 2...…”

Development of a Core Collection of Strawberry Cultivars Based on SSR and CAPS Marker Polymorphisms

“…We consider the approach in this study is the best under the current conditions; however, further validation is necessary when the complete strawberry genome is available in the future. Additionally, single nucleotide polymorphism (SNP) markers, which can be polymorphic among strawberry cultivars, have recently been developed (Bassil et al, 2015;Sargent et al, 2015). Because SNPs are usually detected more frequently than SSRs in the cultivated strawberry genome, the development of an improved core collection set is expected using SNPs and the genome-wide genetic differences among strawberry cultivars.…”