Axiom Analysis Suite

Axiom Analysis Suite performs genotyping data analysis across Axiom arrays and enables copy number analysis on select arrays to support high-throughput genetic studies.

Key Features:

• Genotyping across Axiom arrays: Performs genotyping data analysis for all Axiom arrays.
• Copy number analysis: Performs copy number analysis on select Axiom arrays.
• Integration with Applied Biosystems™ Axiom™ Pear 70K Genotyping Array: Supports the Applied Biosystems™ Axiom™ Pear 70K Genotyping Array and its SNP content.
• Two-step design strategy: Uses a draft array to screen a subset of samples and select robust and informative SNPs for incorporation into the final array.
• High-quality SNP identification: Identified 66,616 high-quality polymorphic SNPs representing 93% of tiled SNPs from 1416 pear accessions from the USDA National Clonal Germplasm Repository (NCGR).
• High-density SNP content for downstream analyses: Provides dense SNP coverage to support genetic diversity studies and genome-wide association analyses.
• Linkage map construction: Enabled construction of high-density linkage maps in a bi-parental population.
• Performance benchmarking versus GBS: Includes comparative evaluations against genotyping-by-sequencing (GBS) and restriction enzyme reduced representation sequence-based genotyping methods, demonstrating greater robustness for SNP screening.

Scientific Applications:

• Genetic diversity analysis: Enables assessment of genetic diversity in Pyrus spp. using dense SNP datasets.
• Genome-wide association studies (GWAS): Supports GWAS in pear and related species using high-density SNP genotypes.
• Linkage mapping: Facilitates high-density linkage map construction in bi-parental populations.
• SNP discovery and validation: Identifies and validates robust, polymorphic SNPs for downstream analyses.
• Breeding and conservation: Informs cultivar development and conservation strategies within USDA NCGR and Pyrus collections.
• Method comparison and benchmarking: Supports comparative evaluation of SNP array performance against GBS and restriction enzyme reduced representation sequencing approaches.

Methodology:

Two-step array design using a draft array to screen a subset of samples and select robust SNPs for the final 70K array. SNP calling and quality filtering produced 66,616 high-quality polymorphic SNPs (93% of tiled SNPs) from 1416 pear accessions from the USDA National Clonal Germplasm Repository (NCGR). Comparative analyses were performed against genotyping-by-sequencing (GBS) and restriction enzyme reduced representation sequence-based genotyping methods.