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

Abstract

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.

DNA Markers for the Genetic Diversity in Korean Native Chicken Breeds: A Review

“…또한 방대한 re-sequencing data 를 이용해서 60K, 600K 등의 high-density(HD) SNP chip이 개발되어 많은 유전자 마커의 정보를 획득할 수 있게 되었 다 (Groenen et al, 2011;Kranis et al, 2013 …”

Evaluation of the genome in bird breeding

“…Общедоступными чипами для кур являются чипы средней плотности (SNP60K) или более низкой плотности (Groenen et al, 2011) производства Illumina (США) и чип высокой плотности типа SNP600K (Kranis et al, 2013) производства Affymetrix (США). С использованием чипа SNP60K были просканированы геномы двух линий кур, у которых в процессе 50 поколений отбора получена 9крат-ная разница по массе тела (Johansson et al, 2010).…”

Using the variability of linkage disequilibrium between subpopulations to infer sweeps and epistatic selection in a diverse panel of chickens

“…The panel has been shown to be capable of reconstituting phylogenetic relationships between breeds based on marker data. Chickens were genotyped using an Affymetrix Axiom HD genotyping array (Affymetrix, Santa Clara, CA, USA) (Kranis et al, 2013), for which SNPs were mapped to the Gallus_gallus_4.0 reference genome. The SNPs in this array were selected to have an approximately uniform distribution across the genome in terms of SNPs per cM, leading to a higher physical density (SNPs per kb) on microchromosomes than on macrochromosomes.…”