Applied Biosystems™ Axiom™ Strawberry FanaSNP 50k Genotyping Array, mini-96 format

• Array was designed by the University of California, Davis Strawberry Breeding Program in collaboration with Affymetrix Expert Design Program (Hardigan et al 2020)
• The array offers genome-wide coverage of polymorphic SNPs across the cultivated and wild octoploid strawberry species
• The Axiom FanaSNP Strawberry 50K Genotyping Array is also available in 384-HT format (Cat. Number 551041)

Array Content

• Comprehensive content
  • 850,000 SNPs subgenome specific SNPs from diverse octoploid strawberry accessions from around the globe
  • Collectively, 446,644 of 850,000 marker probes produced QC-passing polymorphic SNP genotype clusters showing disomic (allopolyploid) segregation
  • The complete set of 446,644 validated probes is made available for public use
• Production scale array also design
  • The most performant set of 49,483 SNPs was tested and validated for production activities
  • 5,809 SNPs from the iStraw 35K array were maintained for connectivity to previous platforms
• Tied to multiple reference genomes
  • SNP positions ascertained by WGS alignment to the `Camarosa` v1 reference genome (Edger et al 2019) and have since been updated to the `UCD Royal Royce` (FaRR1) reference genome (Hardigan et al 2022)
• Global represented and validated
  • Variants were discovered by WGS resequencing of 47 x ananassa, 24 F. chiloensis, and 22 F. virginiana individuals
  • Subgenome-specific marker performance variants were validated in a genetically diverse sample of 384 octoploid strawberry accessions

Applications

• Molecular genetics research and inference
  • QTL discovery and Genome-wide association
  • Kinship and parentage analysis
• Genomic and molecular breeding
  • Genomic prediction and selection
  • Marker-assisted selection
• Release of new cultivars
  • Accelerate and increase efficiency of cultivar development
  • Identify the presence of important markers in existing strawberry germplasm
  • Use genetic information to identify germplasm that will perform well in specific growing regions
• Intellectual property protection and verification
  • Clonal source and purity confirmation
  • Validation of parent-offspring relationships

Required Products

• GeneChip Command Console Software
• GeneTitan Multi-Channel Instrument
• Axiom Analysis Suite Software
• Axiom Long Format Export Tool (AxLE)