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Agrigenomics Research Community

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Featured articles

Can genomics boost productivity of orphan crops?
In Nat. Biotechnol., Rajeev K. Varshney and colleagues review different breeding methods and argue that molecular breeding can improve orphan crops as it has for temperate cereal crops.

The 9 billion-people question
John Parker outlines in The Economist some of the challenges and strategies that must be considered to feed the growing world population.

Array and NGS integration in genomics

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The root hair infectome of Medicago truncatula: secrets of hair removal

The root hair 'infectome' of Medicago truncatula: secrets of hair removal

Andy Breakspear, John Innes Center, UK
Medicago truncatula is a legume native to the Mediterranean. It has symbiotic relationships with two microbes that provide nitrogen and phosphorus in exchange for sugars via the root. Rhizobial infection interferes with this symbiosis. Dr. Andrew Breakspear discusses the the use of Affymetrix' Medicago truncatula genome array to study infection transcripts in the root hair and better understand Rhizobial infection.

Microarray resources for genetic and genomic studies in chicken: A review

Microarray resources for genetic and genomic studies in chicken: A review

Geyas A. A., et al. Genesis DOI: 10.1002/dvg.22387 (2013).
This review discusses how the relative strengths of microarray and NGS technologies are best applied in genomics of livestock animals and experimental models.

de novo marker selection strategies

Development and evaluation of a high-density genotyping array for Soybean

Development and evaluation of a high-density genotyping array for Soybean

Song Q., et al. PLoS ONE 8(1):e54985. doi:10.1371/journal.pone.0054985 (2013).
If de novo markers are not validated, marker failure can be high. Here, 22% of 60,800 SNPs are monomorphs or fail on the array due to manufacturing or poor clustering.

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Robust marker validation and selection – example from chicken genomics

Robust marker validation and selection – example from chicken genomics

Prof. Dave Burt, Roslin Institute, UK.
Incomplete data, errors and marker redundancy can be managed by validating de novo SNPs after NGS. This method, first used in animals, is now used in plants.

De novo assembly of the pepper transcriptome (Capsicum annuum): a benchmark for in silico discovery of SNPs, SSRs, and candidate genes

De novo assembly of the pepper transcriptome (Capsicum annuum): a benchmark for in silico discovery of SNPs, SSRs, and candidate genes

Ashrafi H., et al. BMC Genomics 13:571 (2012).
A strategy for developing a marker panel without a complete reference genome.

Robust marker validation and selection – example from cattle genomics

Robust marker validation and selection – example from cattle genomics

Ali Pirani, Bioinformatics, Affymetrix.
Our bioinformatics team first developed a workflow for validating de novo SNPs in animals. They have since applied this successfully in multiple plant species.

Marker selection from NGS data: avoiding errors, monomorphs, and redundancy

Marker selection from NGS data: avoiding errors, monomorphs, and redundancy

Affymetrix Genomics Scientists
A marker panel with optimized coverage ensures maximum power for any downstream genotyping application. Our bioinformaticians share their expertise.

Axiom genotyping of markers with nearby secondary polymorphisms

Axiom® genotyping of markers with nearby secondary polymorphisms

Laurent Bellon, Product Development, Affymetrix.
Axiom® Genotyping Solution is uniquely suited to genotyping of highly polymorphic genomes as it is permissive to secondary variants as close as 10 bp from the target variant.

Learn more about Axiom myDesign Arrays

Learn more about Axiom myDesign™ Arrays

Custom Axiom myDesign™ Arrays enable de novo marker validation and downstream genotyping for whole-genome or focused panels.

Automation and best practice for polyploid genotype calling

Automated analysis of complex genomes with Axiom Genotyping

Automated analysis of complex genomes with Axiom® Genotyping

Laurent Bellon, Product Development, Affymetrix.
Manual genotype clustering for polyploid species is very time consuming. Learn how the Axiom® automated genotyping software enables polyploid analysis in ~1 hour.

Best practices for genotyping analysis of plant and animal genomes

Best practices for genotyping analysis of plant and animal genomes

Ali Pirani, Bioinformatics, Affymetrix.
Overview of the best workflow to get from data to results in the shortest time.

Allopolyploid genotyping algorithm on Affymetrix Axiom Arrays

Allopolyploid genotyping algorithm on Affymetrix Axiom® Arrays

Hong Gao, Bioinformatics, Affymetrix.
An automated algorithm that reduces genotype analysis to ~1 hour is described and applied to hexaploid wheat data.

Statistical methods for off-target variant genotyping on Axiom Arrays

Statistical methods for off-target variant genotyping on Axiom® Arrays

Teresa Webster, Bioinformatics, Affymetrix.
Automated clustering and calling of "Off-Target Variants," atypical cluster patterns caused by secondary variants in the probe hybridization region.

High throughput and low cost for routine genotyping applications

High throughput and low cost for routine genotyping applications

Michael Shapero, Product Development, Affymetrix.
Outline of the development and performance of the new Axiom® 384 high-throughput format for low-cost genotyping of up to 50,000 SNPs.

High throughput and low cost for routine genotyping applications

High throughput and low cost for routine genotyping applications

Shantanu Kaushikkar, Genotyping Business Unit, Affymetrix.
For high-throughput processing, the new Axiom® 384 high-throughput format enables low-cost processing of up to 50,000 SNPs in 3,000+ samples per week.

Learn more about Affymetrix genomics solutions

Axiom Genotyping Solution for agrigenomics

Axiom® Genotyping Solution for agrigenomics

Download an overview to see how you can use the Axiom® platform.

Axiom Genotyping Solution for agrigenomics

Axiom® Genotyping Solution for agrigenomics

Visit the web page to learn about the arrays available and the custom flexibility and scalability that make the Axiom® platform ideal for research and commercial uses.

Axiom myDesign™ Arrays for custom agrigenomics

Axiom myDesign™ Arrays for custom agrigenomics

The Axiom myDesign™ platform enables high-density de novo marker validation and scalable whole-genome or focused panels for downstream genotyping.

"For Research Use Only. Not for use in diagnostic procedures."

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Archived Webinars +

Plant Genomics Webinar

Validating Complex Biology Webinar

Translating Genetic Biomarkers to the Clinic Webinar

Clinical Validation of Cancer Biomarker Signatures using Array Technology Webinar

Cancer Genomics Webinar

Circulating Tumor Cells Webinar

Warning! The earliest signals for cancer - miRNA regulation

The Hunt for Missing Heritability