ArticleBMC genomics2015
Development and preliminary evaluation of a 90 K Axiom® SNP array for the allo-octoploid cultivated strawberry Fragaria × ananassa.
Article in BMC genomics, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 105 papers.
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105 citing papers in PubMed, 201 citations in OpenAlex.
- Genetic architecture of angular leaf spot resistance in cultivated strawberry shaped by epistasis and genotype-by-environment interactions.The plant genome · 2026Article
- Genome-wide association study of exotic Fragaria germplasm accessions for resistance to Phytophthora crown rot in strawberry.BMC plant biology · 2026Article
- Modeling production curves in a strawberry breeding program to optimize early season productivity.Frontiers in plant science · 2026Article
- Integrative genomics for mango genetics and breeding.Horticulture research · 2026Article
- Accounting for population structure in genomic prediction of strawberry sweetness at a global scale.Scientific reports · 2025Article
- Marker-trait association mapping for perpetual flowering habit in an octoploid ancestral strawberry, Fragaria virginiana.The plant genome · 2025Article
- The PeachSNP170K array facilitates insights into a large-scale population relatedness and genetic impacts on citrate content and flowering time.Communications biology · 2025Article
- Genetic analysis of predicted vegetative biomass and biomass-related traits from digital phenotyping of strawberry.The plant genome · 2025Article
- A haplotype-phased genome characterizes the genomic architecture and causal variants for RXf1 conferring resistance to Xanthomonas fragariae in strawberry (F. × ananassa).BMC genomics · 2025Article
- Within-family genomic selection in strawberry: Optimization of marker density, trial design, and training set composition.The plant genome · 2025Article
- Genome-wide association studies in a diverse strawberry collection unveil loci controlling agronomic and fruit quality traits.The plant genome · 2024Article
- How to handle high subgenome sequence similarity in allopolyploid Fragaria x ananassa: linkage disequilibrium based variant filtering.BMC genomics · 2024Article
- Accelerating genetic gains for quantitative resistance to verticillium wilt through predictive breeding in strawberry.The plant genome · 2024Article
- Development and Assessment of SNP Genotyping Arrays for Citrus and Its Close Relatives.Plants (Basel, Switzerland) · 2024Article
- Transgressive segregation, hopeful monsters, and phenotypic selection drove rapid genetic gains and breakthroughs in predictive breeding for quantitative resistance toHorticulture research · 2024Article
- Strawberry soluble solids QTL with inverse effects on yield.Horticulture research · 2024Article
- Genetic loci associated with tissue-specific resistance to powdery mildew in octoploid strawberry (Frontiers in plant science · 2024Article
- Advances in genomics and genome editing for improving strawberry (Frontiers in genetics · 2024Review
- Improvement of crop production in controlled environment agriculture through breeding.Frontiers in plant science · 2024Review
- A medium-density genotyping platform for cultivated strawberry using DArTag technology.The plant genome · 2023Article
45 more citing papers are in PubMed but not listed here.
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Authors and funding
28 authors at 11 institutions in 6 countries.
Funding
No grant is acknowledged in the PubMed record.
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.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.