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Infinium Assay for Large-scale SNP Genotyping Applications
Published on: November 19, 2013
Development of a high density 600K SNP genotyping array for chicken.
Andreas Kranis1, Almas A Gheyas, Clarissa Boschiero
1Aviagen Ltd, Midlothian, UK. akranis@aviagen.com
BMC Genomics
|January 30, 2013
Summary
A new high-density SNP genotyping array for chickens has been developed, enabling high-resolution genetic analysis in diverse chicken populations. This tool supports research in genomic selection and disease association studies.
Area of Science:
- Animal Genetics
- Genomics
- Avian Biology
Background:
- High-density (HD) SNP genotyping arrays are crucial for genetic analysis in animals and plants.
- Despite the economic importance of chickens, a HD array for high-resolution genetic analysis was previously unavailable.
Purpose of the Study:
- To develop and validate a novel 600K Affymetrix® Axiom® HD genotyping array for chickens.
- To provide a high-density tool for advanced genetic studies in diverse chicken populations.
Main Methods:
- Re-sequencing of 243 chickens from 24 diverse lines to identify segregating SNPs.
- Bioinformatic analysis to detect and filter millions of putative SNPs based on quality and design scores.
- Validation of selected SNPs through genotyping on an independent sample set (n=282).
Main Results:
- Developed a 580,954 SNP array, including 21,534 coding variants, with uniform genomic distribution.
- The array demonstrated high call rates (>98%) and stable Mendelian inheritance for validated SNPs.
- The array successfully genotyped diverse chicken samples (broilers and layers), revealing population structure.
Conclusions:
- The Affymetrix® Axiom® array is the first commercially available HD SNP genotyping array for chickens.
- This array is expected to facilitate widespread applications in genomic selection, GWAS, and fine mapping.
