Development of a high density 600K SNP genotyping array for chicken

BMC Genomics

Research Article

Fiona Brew¹  Ali Pirani¹  Mahmood Gholami²  Saber Qanbari²  Henner Simianer²  Andreas Kranis³  Kellie A Watson³  Janet Fulton⁴  Georg Haberer⁵  Steffen Weigend⁶  Tim M Strom⁷  Rudolf Preisinger⁸  Nigel Salmon⁹  Mark Fife⁹  David W Burt^1,10  Le Yu^1,10  Almas A Gheyas^1,10  Paul M Hocking^1,10  Frances Turner^1,10  John A Woolliams^1,10  Pete Kaiser^1,10  Sarah Smith^1,10  Clarissa Boschiero^1,10  Richard Talbot^1,10 

[1] Affymetrix, Santa Clara, CA, USA;Animal Breeding and Genetics Group, Georg-August-University Goettingen, Goettingen, Germany;Aviagen Ltd, Midlothian, UK;Hy-Line International, Dallas Center, IA, USA;Institute of Bioinformatics and System Biology, Helmholtz Zentrum München, 85764, Neuherberg, Germany;Institute of Farm Animal Genetics, Friedrich Loeffler Institut, Neustadt-Mariensee, Germany;Institute of Human Genetics, Helmholtz Zentrum, 85764, Neuherberg, Germany;Lohmann Tierzucht GmbH, Cuxhaven, Germany;The Pirbright Institute, Compton Laboratory, Compton, UK;The Roslin Institute, University of Edinburgh, Midlothian, UK;

关键词: Genotyping array;    Chicken;    SNP;   

DOI  :  10.1186/1471-2164-14-59

 received in 2012-10-10, accepted in 2013-01-15,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundHigh density (HD) SNP genotyping arrays are an important tool for genetic analyses of animals and plants. Although the chicken is one of the most important farm animals, no HD array is yet available for high resolution genetic analysis of this species.ResultsWe report here the development of a 600 K Affymetrix® Axiom® HD genotyping array designed using SNPs segregating in a wide variety of chicken populations. In order to generate a large catalogue of segregating SNPs, we re-sequenced 243 chickens from 24 chicken lines derived from diverse sources (experimental, commercial broiler and layer lines) by pooling 10–15 samples within each line. About 139 million (M) putative SNPs were detected by mapping sequence reads to the new reference genome (Gallus_gallus_4.0) of which ~78 M appeared to be segregating in different lines. Using criteria such as high SNP-quality score, acceptable design scores predicting high conversion performance in the final array and uniformity of distribution across the genome, we selected ~1.8 M SNPs for validation through genotyping on an independent set of samples (n = 282). About 64% of the SNPs were polymorphic with high call rates (>98%), good cluster separation and stable Mendelian inheritance. Polymorphic SNPs were further analysed for their population characteristics and genomic effects. SNPs with extreme breach of Hardy-Weinberg equilibrium (P < 0.00001) were excluded from the panel. The final array, designed on the basis of these analyses, consists of 580,954 SNPs and includes 21,534 coding variants. SNPs were selected to achieve an essentially uniform distribution based on genetic map distance for both broiler and layer lines. Due to a lower extent of LD in broilers compared to layers, as reported in previous studies, the ratio of broiler and layer SNPs in the array was kept as 3:2. The final panel was shown to genotype a wide range of samples including broilers and layers with over 100 K to 450 K informative SNPs per line. A principal component analysis was used to demonstrate the ability of the array to detect the expected population structure which is an important pre-investigation step for many genome-wide analyses.ConclusionsThis Affymetrix® Axiom® array is the first SNP genotyping array for chicken that has been made commercially available to the public as a product. This array is expected to find widespread usage both in research and commercial application such as in genomic selection, genome-wide association studies, selection signature analyses, fine mapping of QTLs and detection of copy number variants.

【 授权许可】

CC BY   
© Kranis et al.; licensee BioMed Central Ltd. 2013