Axiom Expert Designed Genotyping Arrays

Axiom™ Porcine Genotyping Array (Applied Biosystems™)

Axiom Porcine Genotyping Array (Axiom_PigHDv1) for pig genotyping was designed through the Affymetrix- Expert Design Program by Dr. Martien Groenen at Wageningen University, Netherlands, and Dr. Alan Archibald at The Roslin Institute, United Kingdom.

Axiom Porcine Genotyping Array is available in 96-array format and includes 658,692 markers discovered using whole-genome sequence data from 210 animals covering a broad range of commercial and non-commercial pig breeds that were selected for their relevance to world-wide breeding programs.1 Powered by Axiom Genotyping Solution, the array offers the highest data completeness, call rates, and reproducibility of any technology available today.

This high-density array offers the power and resolution for a wide range of applications in pig breeding and genomics that include studying marker-trait association, evaluating pure lines, identifying multi-line reference populations, as well as research applications for genome-wide analysis and selective sweep analysis studies. A key benefit of using Axiom Porcine Genotyping Array is the ability to genotype samples without experiencing marker dropout or missing data, which have been observed when using other porcine genotyping products.

Features of Axiom Porcine Genotyping Array
Expert design: developed by key opinion leaders in the porcine community
High resolution
   - 658,692 markers on the array
   - Equal spacing on chromosomes
   - Bias towards common variants
   - 56,000 of the most informative markers from an existing in-market 60,000 marker array, allowing compatibility with previous studies
High diversity: includes markers from a diverse set of commercially relevant breeds, including rare/traditional breeds

Applications of Axiom Porcine Genotyping Array
• Construction of high-resolution genetic maps
• Genetic improvement of pure lines
• Fine mapping of quantitative trait loci
• Developing training populations for calculating breeding values with genomic selection models

Required Products
GeneChip Command Console Software
GeneTitan Multi-Channel Instrument

Axiom Canine Genotyping Array Set A (Applied Biosystems™)

Axiom™ Canine Genotyping Array Sets A and B were designed as part of the Expert Array Design program. The arrays offer access to approximately 1.1M markers that were discovered by the National Human Genome Research Institute of the National Institutes of Health. The content, distributed over two arrays, offers dense genotyping for validation and discovery of variants associated with specific phenotypes. All of the new content was discovered through high quality sequencing of over 300 dog genomes. The content on the array was aligned with the CanFam3 reference genome.

Canis Familiaris also serves as a model organism in understanding the human disease drug discovery process. Axiom canine genotyping arrays offer dense genotyping for isolating the variants associated with specific phenotypes. Understanding these genotypes allows breeders to anticipate the phenotypes of potential offspring, maximizing the potential to ensure dogs are mated with minimal inbreeding and to screen for possible genetic disorders.

Features of Axiom Canine Genotyping Array Set A
This array includes over 460,000 markers and includes legacy content from in-market arrays including new rare variants. The legacy content on the array offers the capability to continue your studies while getting access to new functional variants. The array includes:
• Markers from legacy in-market genotyping arrays
• Functional variants of biological relevance
• Intergenic variants based on newly available long non-coding RNA (lnc RNA) data
• miRNA variants
• Breed-specific markers

Learn more about Canine Array Set B ›

Applications of Axiom Canine Genotyping arrays
• Genome-wide association studies
• Veterinary research
• Direct-to-consumer applications
• As a model organism to help us understand complex human diseases such as cancer and diabetes

Data from the Axiom Canine Genotyping arrays are analyzed with Axiom Analysis Suite and Axiom CNV Summary Tools Software. Automated genotyping analysis with Axiom Analysis Software enables accurate genotyping of samples from various breeds including samples that exhibit in-breeding, a common occurrence in canine species.

Axiom™ Strawberry Genotyping Array (Applied Biosystems™)

Axiom Strawberry Genotyping Array was designed through the Affymetrix Expert Design Program in collaboration with the International RosBREED SNP consortium that spans multiple nations, states, and institutions dedicated to genetic improvement of rosaceous crops.* The array offers genome-wide coverage of polymorphic SNPs across the cultivated garden strawberry hybrid (Fragaria ananassa).

Features of Axiom Strawberry Genotyping Array:
Comprehensive content: 95,062 SNPs and indels derived from octoploid and diploid cultivars, including:
   - 1,761 multi-allelic SNPs
   - 3,751 SNPs derived from diploid cultivars; the remaining markers are derived from octoploid cultivars
Multiple cultivars represented: SNP discovery was facilitated with a diverse worldwide breeding germplasm panel that included:    - Holiday, Korona, and F1 seedlings from the cross Holiday x Korona
   - Two likely diploid progenitors, Fragaria mandschurica, F. iinumae
   - One known diploid F. vesca

Applications of Axiom Strawberry Genotyping Array:
Complex trait research
   - QTL discovery
   - Identify traits of economic significance
Molecular breeding
   - Genome-wide scanning
   - Marker-assisted breeding
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

Notes about the data analysis: Axiom Strawberry Genotyping Array requires advanced analysis. Genotyping many different varieties together may create multiple clusters during the analysis that interfere with each other and/or blend the clusters together. Genotype calls are not provided for multi-allelic SNPs.

*Expert Design Arrays are designed by key opinion leaders in the plant and animal genomics community and made available to the public for the purpose of advancing research and breeding programs. These arrays contain genetic markers and annotations that are provided by the original customer who designed the array and are therefore not updated by Affymetrix in the same manner as other catalog products. Through the program, Affymetrix continually provides agrigenomics researchers access to genotyping arrays that have been utilized by their peers in the research community.

Required Products
Axiom Analysis Suite
GeneChip Command Console Software
GeneTitan Multi-Channel Instrument

Axiom™ Apple Genotyping Array (Applied Biosystems™)

Axiom Apple Genotyping Array (Axiom_Apple480) was designed through the Affymetrix Expert Design Program in collaboration with the FruitBreedomics consortium (www.FruitBreedomics.com). The sequencing and marker selection was conducted by experts from Fondazione Edmund Mach, INRA, Dalhousie University, Wageningen UR, University Di Bologna, and Universita Degli Studi Di Milano.

The 96-format array includes markers identified using whole-genome sequence data from 63 Malus domestica cultivars and two double haploid accessions. Table 1 lists the number of cultivars and corresponding country of origin used in the SNP discovery process.

Axiom Apple Genotyping Array includes 480,000 markers and together with Axiom Analysis Suite software overcomes the genotyping challenges associated with polyploidy, rapid linkage disequilibrium (LD) decay, and high polymorphism observed in the apple genome.

Array highlights
• Very high diversity
• Includes markers discovered in 63 worldwide M. domestica cultivars• High resolution to address rapid decay of LD   - 487,249 markers on the array
   - Bias towards common variants with minor allele frequency (MAF) >0.05
   - Includes 21,463 previously validated markers: 19,990 markers from an existing in-;market 20K Fruitbreedomics apple array and 1,473 markers identified using genotyping-by-sequencing (GBS)
• Absence of paralogous variants through the use of double haploid accessions in SNP discovery

Applications of Axiom Apple Genotyping Array
• Construction of high-resolution genetic maps
• Fine mapping of quantitative trait loci
• Genome-wide association studies

Required Products
GeneChip Command Console Software
GeneTitan Multi-Channel InstrumentAxiom Apple Genotyping Array (Axiom_Apple480) was designed through the Expert Design Program at Affymetrix in collaboration with the FruitBreedomics consortium (www.FruitBreedomics.com). The sequencing and marker selection was conducted by experts from Fondazione Edmund Mach, INRA, Dalhousie University, Wageningen UR, University Di Bologna, and Universita- Degli Studi Di Milano.

The 96-format array includes markers identified using whole-genome sequence data from 63 Malus domestica cultivars and two double haploid accessions. Table 1 lists the number of cultivars and corresponding country of origin used in the SNP discovery process.

Axiom Apple Genotyping Array includes 480,000 markers and together with Axiom™ Analysis Suite software overcomes the genotyping challenges associated with polyploidy, rapid linkage disequilibrium (LD) decay, and high polymorphism observed in the apple genome.

Array highlights
  • Very high diversity
  • Includes markers discovered in 63 worldwide M. domestica cultivars
  • High resolution to address rapid decay of LD
    • 487,249 markers on the array
    • Bias towards common variants with minor allele frequency (MAF) >0.05
    • Includes 21,463 previously validated markers: 19,990 markers from an existing in-market 20K Fruitbreedomics apple array and 1,473 markers identified using genotyping-by-sequencing (GBS)
  • Absence of paralogous variants through the use of double haploid accessions in SNP discovery
Applications of Axiom Apple Genotyping Array
  • Construction of high-resolution genetic maps
  • Fine mapping of quantitative trait loci
  • Genome-wide association studies

Table 1: The country of origin and the number of cultivars used in the SNP discovery process for Axiom Apple Genotyping Array.
Country of origin Number of cultivars
Australia 1
Central Europe 39
Canada 1
Iran 1
Simmental 16
Japan 1
New Zealand 1
Northern Europe 4
Russia 9
Tunisia 1
United States 5
 



Axiom Canine Genotyping Array Set B (Applied Biosystems™)

Axiom™ Canine Genotyping Array Sets A and B were designed as part of the Expert Array Design program. The arrays offer access to approximately 1.1M markers that were discovered by the National Human Genome Research Institute of the National Institutes of Health. The content, distributed over two arrays, offers dense genotyping for validation and discovery of variants associated with specific phenotypes. All of the new content was discovered through high quality sequencing of over 300 dog genomes. The content on the array was aligned with the CanFam3 reference genome.

Canis Familiaris also serves as a model organism in understanding the human disease drug discovery process. Axiom canine genotyping arrays offer dense genotyping for isolating the variants associated with specific phenotypes. Understanding these genotypes allows breeders to anticipate the phenotypes of potential offspring, maximizing the potential to ensure dogs are mated with minimal inbreeding and to screen for possible genetic disorders.

Features of Axiom Canine Genotyping Array Set B
This array contains over 670,000 variants that are equally distributed across the chromosomes.

Learn more about Canine Array Set A ›

Applications of Axiom Canine Genotyping arrays
• Genome-wide association studies
• Veterinary research
• Direct-to-consumer applications
• As a model organism to help us understand complex human diseases such as cancer and diabetes

Data from the Axiom Canine Genotyping arrays are analyzed with Axiom Analysis Suite and Axiom CNV Summary Tools Software. Automated genotyping analysis with Axiom Analysis Software enables accurate genotyping of samples from various breeds including samples that exhibit in-breeding, a common occurrence in canine species.

Axiom™ Trout Genotyping Array (96 format) (Applied Biosystems™)

Axiom Trout Genotyping Array (96 format) was designed under the Affymetrix Expert Design Program in collaboration with the National Center for Cool and Cold Water Aquaculture, USDA-ARS, USA, and AquaGen, Trondheim, Norway. The array includes 57,501 markers and is available in both 96 format and 384 format.

Axiom Trout Genotyping Array offers a standard high-throughput, cost-effective, and robust genotyping technology to conduct genome-wide association studies (GWAS), to study genetic architecture, perform marker-trait association, and to increase accuracy of breeding programs. The high marker density on the array ensures a broad coverage of the trout genome to provide representation of all regions in the genome.

Features of Axiom Trout Genotyping Array
Comprehensive content: The array includes 57,501 markers spaced across the genome as follows:
    - 17,000 markers that are unique to SNPs discovered in a previous USDA study1
    - 20,000 markers unique to an outbred Norwegian commercial population
    - Amino acid shifting SNPs
    - SNPs preferentially located within a gene and with minor allele frequency (MAF) >0.2
    - Y chromosome-specific SNPs near the sdY gene (male-specific in rainbow trout)2

Applications of Axiom Trout Genotyping Array
Complex trait research and molecular breeding
    - GWAS and quantitative trait locus (QTL) mapping
    - Identification of economically important traits
    - Improved accuracy in aquaculture breeding programs through genomic selection

Population and evolutionary genetics
    - Development of new breeding populations
    - Differentiation between fish of different origins
    - Gender determination via sdY chromosome-specific probes
    - Differentiation of farmed and wild populations

Required Products
Axiom Analysis Suite
GeneChip Command Console Software
GeneTitan Multi-Channel Instrument

Axiom™ Canine HD Array (Applied Biosystems™)

The Axiom Canine HD Array was designed as part of the Expert Array Design Program. The array was developed by screening over 2000 samples using the Axiom Canine Genotyping Array Sets A and B. The samples covered over 50 breeds and were carefully selected with appropriate pedigree to maximize polymorphic content. The array offers over 710,000 markers for validation and discovery of variants associated with specific phenotypes. The content on the array was aligned with the CanFam3 reference genome.

Features include:
• Over 710,000 markers with legacy content from in-market arrays including new variants
• Functional variants of biological relevance
• Intergenic variants based on newly available long non-coding RNA (lnc RNA) data
• miRNA variants
• Breed-specific markers
• Over 150 disease and trait specific markers

Applications
• Genome-wide association studies
• Veterinary research
• Direct-to-consumer applications
• A model organism to aid understanding of complex human diseases such as cancer and diabetes

Data from the Axiom Canine HD Array are analyzed using Axiom Analysis Suite and Axiom CNV Summary Tools software. The data can also be exported into long format using the Axiom Long Format Export Tool (AxLE). Automated genotyping analysis with Axiom Analysis Software enables accurate genotyping of samples from various breeds including samples that exhibit in-breeding, a common occurrence in canine species.

Learn more about Canine Array Set A ›
Learn more about Canine Array Set B ›

Required products
GeneChip Command Console Software
GeneTitan Multi-Channel Instrument
Axiom Analysis Suite Software

Axiom™ Wheat HD Genotyping Arrays (Applied Biosystems™)

Axiom Wheat HD Genotyping Arrays were designed through Affymetrix Expert Design Program in a collaboration led by Dr. Keith Edwards, project leader and professor of Cereal Functional Genomics at the School of Biological Sciences and member of the Cabot Institute, University of Bristol.*

This product is part of a two array set. Array Plate B can be accessed at 550492 Axiom™ Wheat HD Genotyping Arrays.

The arrays were designed through a public sector pre-breeding program dedicated to accelerating the genetic improvement of modern wheat varieties. Select from one of two formats:
• Axiom; Wheat HD Genotyping Array, a high-density research tool with 817,000 SNPs in a two-array set in the 96-array plate format
• Axiom; Wheat Breeder's Genotyping Array, which includes 35,000 SNPs for worldwide elite wheat lines in the 384-array plate format

Markers on these arrays can be queried on the CerealsDB website (http://www.cerealsdb.uk.net/). This is a searchable database that was created by the Functional Genomics group at the University of Bristol, UK for the purpose of making SNP information available to the worldwide wheat community. It is updated regularly and contains:

• SNP statistics: Map location or contig code, 120 bp flanking sequences. MAF and PIC score are provided for SNPs on Axiom Wheat Breeder's Genotyping Array
• Variety comparison: Select two or more varieties of wheat to see the SNPs in common or SNPs that are different between them

*Expert Design Arrays are designed by key opinion leaders in the plant and animal genomics community and made available to the public for the purpose of advancing research and breeding programs. These arrays contain genetic markers and annotations that are provided by the original customer who designed the array and are therefore not updated by Affymetrix in the same manner as other catalog products. Through the program, Affymetrix continually provides agrigenomics researchers access to genotyping arrays that have been utilized by their peers in the research community.

Required Products
Axiom Analysis Suite
GeneChip Command Console Software
GeneTitan Multi-Channel Instrument

Axiom™ Rice Genotyping Array (Applied Biosystems™)

Axiom Rice Genotyping Array offers comprehensive genomic coverage, which allows researchers to easily assay the natural variation of rice varieties worldwide to identify genes underlying important phenotypic traits (e.g., high yields), to understand genetic sources of variation, and to differentiate cultivars for fingerprinting and classification purposes.

Axiom Rice Genotyping Array includes 42,961 markers from GeneChip™ Rice 44K Genotyping Arrayand 5,499 markers from a whole-genome SNP array (RICE6K) for genomic breeding in rice.

Highlights:
Content
   - Backwards compatibility with older data based on 44,000 makers from GeneChip Rice 44K SNP Genotyping Array
   - Detection of common genetic variants within and between the major subpopulations of rice, including indica, aus, tropical japonica, temperate japonica, and group V ("aromatic")
   - Efficient progeny screening in rice breeding with markers identified by Yu et al.

Applications:
Complex-trait research
   - Flexible and fast identification and classification of germplasm
   - Identification of high-yield variants
   - Genome-wide association mapping and tracking of disease genes
Molecular breeding
   - Allows for fingerprinting rice germplasm, genotyping bulked segregating pools, checking seed authenticity, and selecting genetic background
   - Enables genetic variation analysis of any O. sativa strain
   - Offers information for polymorphisms between indica and japonica subspecies as well as varieties within indica and japonica groups

Required Products
GeneChip Command Console Software
GeneTitan Multi-Channel Instrument

Axiom™ Equine Genotyping Array (Applied Biosystems™)

Axiom Equine Genotyping Array (Axiom MNEC670) for equine genotyping was designed through the Expert Design Program by Affymetrix in collaboration with the University of Minnesota and members of the Equine Genetic Diversity Consortium.*

Axiom Equine Genotyping Array is a novel array and the only array that can be used for genotyping 20 different breeds. It offers maximum utility for research in equine genetics. It features 670,796 markers that were selected through a screening of 2 million markers for optimal genomic coverage of known genetic diversity among domestic horse breeds.1 Powered by Axiom Genotyping Solution, the array offers the highest data completeness, call rates, and reproducibility of any technology available today.

Features of Axiom® Equine Genotyping Array:
• Expert design: developed by key opinion leaders in the equine community
• High resolution: available in 96 format; supporting a wide range of genotyping applications for equine research

Highlights
Content:
• Axiom Equine Genotyping Array includes a total of 670,796 markers:
   - Approximately 400,000 markers between population tag SNPs
   - Approximately 200,000 markers within population tag SNPs
   - Approximately 70,000 SNPs from legacy arrays
   - Additional SNP density within the equine major histocompatibility complex

Diversity:
Axiom Equine Genotyping Array includes markers that were selected to maximize accuracy of imputation up to 1.8 million markers both within and across 20 breeds(Fig. 1). An emphasis was placed on breeds with high commercial relevance.

Applications of Axiom Equine Genotyping Array:
• Complex trait research
   - Genome-wide analysis and fine mapping
   - Diversity analyses
   - Genomic prediction of disease risk
• Molecular breeding
   - Association mapping
   - Improved efficiency of breeding programs
   - Selection signature analyses

*The Equine Genetic Diversity Consortium (EGDC) led by the University of Minnesota represents a collaborative international community of equine researchers who are working to build a comprehensive understanding of genetic diversity among equine populations across the world. (http://www.cvm.umn.edu/equinegenetics/egdc/)

Required Products
GeneChip Command Console Software
GeneTitan Multi-Channel Instrument

Axiom™ Cotton Genotyping Array (Applied Biosystems™)

Axiom Cotton Genotyping Array was designed through Affymetrix- Expert Design Program, and the markers on the array were selected from public databases in collaboration with the National Botanical Research Institute, India. The array includes 35,550 markers that were discovered in G. hirsutum and G. barbadense.

Axiom Cotton Genotyping Array can be used to analyze samples from different populations by adding up to 380,000 custom markers or by transferring polymorphic markers with 100%; fidelity on to the Axiom 384HT myDesign™ breeders array. The Axiom GT1 algorithm can automatically cluster, assign genotypes, and classify the markers into six different categories for easy visualization.

Features of Axiom Cotton Genotyping Array
Comprehensive content:
The Axiom Cotton genotyping array includes a total of 35,550 markers:
• 28,158 intra-specific markers identified using gene-enriched genomic sequences of G. hirsutum.
• 7,392 markers discovered using genome reduction methodology that is based on restriction site conservation (GR-RSC).
   - 5,286 markers were discovered in an inter-specific assembly of G. hirsutum and G. barbadense.
   - 2,106 markers are intra-specific to G. hirsutum.

Applications of Axiom Cotton Genotyping Array
Complex trait research and molecular breeding:
• GWAS and QTL mapping
• Identification of economically-important traits
• Improved accuracy marker-assisted selection programs through genomic selection

Required Products
GeneChip Command Console Software
GeneTitan Multi-Channel Instrument

Axiom™ Buffalo Genotyping Array (Applied Biosystems™)

Axiom Buffalo Genotyping Array was designed by the Affymetrix Expert Design Program.* The array was developed in collaboration with the International Buffalo Genome Consortia, which included Fondazione Parco Tecnologico Padano in Italy, Iowa State University, and the Agricultural Research Service, United States Department of Agriculture (USDA).

Axiom Buffalo Genotyping Array provides the highest genome-wide coverage of polymorphic SNPs across multiple species and breeds of the water buffalo (Bubalus bubalis bubalis and Bubalus bubalis carabanensis), one of the most important beef and dairy animals in Italy, Brazil, and South Asia.

This array is the only commercially available high-density buffalo genotyping tool.

Features of Axiom Buffalo Genotyping Array:
Comprehensive content – 90,000 common and rare markers selected from sequencing initiatives of the water buffalo (B. bubalis bubalis)
Multiple breeds represented – Mediterranean, Murrah, Jaffarabadi, and Nili-Ravi
Robust assay performance – SNPs demonstrate a ≥99%; call rate and ≥80% conversion rate on Murrah and Mediterranean samples

Applications of Axiom Buffalo Genotyping Array:
Molecular breeding:
   - Genomic biomarker discovery
   - Marker-assisted selection
   - Routine screening
   - DNA fingerprinting for animal tracking

Complex trait research:
   - High-resolution mapping of genetic loci in complex traits such as milk production, percentage of milk fat, and feed conversion efficiency
   - Discovery of genes and pathways underlying simple and complex traits

Conservation and biodiversity:
   - Population diversity studies in river and swamp buffalo
   - Genomic marker-assisted conservation strategies

*Expert Design Arrays are designed by key opinion leaders in the plant and animal genomics community and made available to the public for the purpose of advancing research and breeding programs. These arrays contain genetic markers and annotations that are provided by the original customer who designed the array and are therefore not updated in the same manner as other catalog products. Through the program, we continually provides agrigenomics researchers access to genotyping arrays that have been utilized by their peers in the research community.

Required Products
Axiom Analysis Suite
GeneChip Command Console Software
GeneTitan Multi-Channel Instrument

Axiom™ Genome-Wide Chicken Array Kit (Applied Biosystems™)

Axiom Chicken Genotyping Array was developed in collaboration with leading academic institutions and commercial poultry companies including the Roslin Institute, Aviagen Ltd, Hy-Line International under BBSRC LINK funding and the German Synbreed project funded by the BMBF.

This genotyping array detects genetic variants in white egg layers, brown egg layers, broilers and outbred non-commercial breeds. The parental high-density information from the array is useful for poultry breeding while markers associated with wild out-bred lines are useful for analysis of genetic diversity among indigenous chicken populations.

Features and benefits of Axiom Chicken Genotyping Array:
Comprehensive content: Over 580,000 common and rare markers selected from 1.8M tested variants
Genome-wide coverage: Well-annotated markers uniformly distributed across the genome in layers and broilers
Designed for your breed: Over 24 breeds represented including commercial layers and broilers and non-commercial outbred lines
Affordable: High return on investment and lowest available cost per marker
Robust assay performance: Includes genotype-tested SNPs that are highly polymorphic and demonstrate a >99% call rate

Applications of Axiom Chicken Genotyping Array:
Genome-wide association studies
High-resolution genetic mapping
Mendelian trait mapping
Diversity analysis in indigenous chickens
Selection signature analysis
Required Products
Axiom Analysis Suite
GeneChip Command Console Software
GeneTitan Multi-Channel Instrument

Axiom™ Porcine Breeders Array, mini-96 format (Applied Biosystems™)

The Applied Biosystems Axiom Porcine Breeders Array includes markers focused on genomic selection of commercial porcine breeds, including Large White, Landrace, Duroc, and Pietrain. Core markers for the array were selected from markers on the Axiom Porcine High-Density Array that were evaluated using samples from multiple commercial and domestic breeds, including European wild boars. The inclusion of the most informative and well-performing markers from existing porcine arrays ensures that this array can be used for comparison with data generated by previous studies. With the availability of the Axiom Long Format Export Tool, which converts Axiom array data into long format, the array also provides the ability to continue existing projects with no change to the current bioinformatics infrastructure and pipeline.

Features include:
• 55,150 markers for genomic and trait selection
• 42 trait-specific markers selected by United States Department of Agriculture
• 64 parentage markers, including ISAG core markers
• Evenly distributed SNPs across the porcine genome
• Marker annotations aligned to Sscrofa10.2/susScr3 genome and dbSNP 148
• Targeted for commercial breeds including Large White, Landrace, Duroc, and Pietrain

Applications
• Parentage analysis
• Identification of economically important traits
• Genetic improvement of pure lines

Required products
GeneChip Command Console Software
GeneTitan Multi-Channel Instrument
Axiom Analysis Suite Software

Axiom™ Ovine Genotyping Array (50K) (Applied Biosystems™)

The Applied Biosystems Axiom Ovine Genotyping Array (50K) provides the power and resolution to enable a wide range of applications in sheep breeding, including breed assignment, parentage verification and discovery, and traceability and monitoring of polymorphisms of known large effect. The Axiom Ovine Genotyping Array includes markers that were selected by the International Sheep Genomics Consortium, with markers derived from three separate sequencing experiments. The array content is augmented with additional markers for parentage testing and traceability in globally diverse breeds of sheep. These include 163 highly informative parentage markers (MAF ≥0.3) in 48 +5 breed groups that enable accurate parentage testing and traceability in many of the world’s sheep breeds.

Features include:
• Expert design—developed in collaboration with Donagh Berry at Teagasc, Animal and Grassland Research and Innovation Center, Ireland
• Exceptionally high quality SNPs with excellent call and concordance rates across platforms and laboratories
• Includes SNPs for parentage as well as other traits including scrapie
• Compatible with Sheep Consortium 15K arrays and thus with previous studies

Applications
• Parentage verification and discovery
• Accurate genomic evaluations
• Genome-wide associations following accurate imputation to higher density panel
• Breed assignment
• Monitoring of major genes
• Aneuploidy detection—early detection of such abnormalities enables identification of animals that are not suitable parents for the next generation
• Measurement of genetic diversity including calculation of genomic inbreeding statistics
• Mating designs
• Traceability

Data from the Axiom Ovine Genotyping Array are analyzed using Axiom Analysis Suite and Axiom CNV Summary Tools software. The data can also be exported into long format using the Axiom Long Format Export Tool (AxLE).

Required products
GeneChip Command Console Software
GeneTitan Multi-Channel Instrument
Axiom Analysis Suite Software