我要吃瓜

Citation

Kranis A, Gheyas AA, Boschiero C, Turner F, Yu L, Smith S, Talbot R, Pirani A, Brew F, Kaiser P, Hocking PM, Fife M, Salmon N, Fulton J, Strom TM, Haberer G, Weigend S, Preisinger R, Gholami M, Qanbari S, Simianer H, Watson KA, Woolliams JA & Burt DW (2013) Development of a high density 600K SNP genotyping array for chicken. BMC Genomics, 14 (1), Art. No.: 59. https://doi.org/10.1186/1471-2164-14-59

Abstract
Background High 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. Results We 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. 我要吃瓜 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). 我要吃瓜 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?

Keywords
Genotyping array; Chicken; SNP

Notes
Additional co-authors: Georg Haberer, Steffen Weigend, Rudolf Preisinger, Mahmood Gholami, Saber Qanbari, Henner Simianer, Kellie A Watson, John A Woolliams & David W Burt

Journal
BMC Genomics: Volume 14, Issue 1

• Published version