The development and characterization of a 60K SNP chip for chicken

Abstract

BackgroundIn livestock species like the chicken, high throughput single nucleotide polymorphism (SNP) genotyping assays are increasingly being used for whole genome association studies and as a tool in breeding (referred to as genomic selection). To be of value in a wide variety of breeds and populations, the success rate of the SNP genotyping assay, the distribution of the SNP across the genome and the minor allele frequencies (MAF) of the SNPs used are extremely important.ResultsWe describe the design of a moderate density (60k) Illumina SNP BeadChip in chicken consisting of SNPs known to be segregating at high to medium minor allele frequencies (MAF) in the two major types of commercial chicken (broilers and layers). This was achieved by the identification of 352,303 SNPs with moderate to high MAF in 2 broilers and 2 layer lines using Illumina sequencing on reduced representation libraries. To further increase the utility of the chip, we also identified SNPs on sequences currently not covered by the chicken genome assembly (Gallus_gallus-2.1). This was achieved by 454 sequencing of the chicken genome at a depth of 12x and the identification of SNPs on 454-derived contigs not covered by the current chicken genome assembly. In total we added 790 SNPs that mapped to 454-derived contigs as well as 421 SNPs with a position on Chr_random of the current assembly. The SNP chip contains 57,636 SNPs of which 54,293 could be genotyped and were shown to be segregating in chicken populations. Our SNP identification procedure appeared to be highly reliable and the overall validation rate of the SNPs on the chip was 94%. We were able to map 328 SNPs derived from the 454 sequence contigs on the chicken genome. The majority of these SNPs map to chromosomes that are already represented in genome build Gallus_gallus-2.1.0. Twenty-eight SNPs were used to construct two new linkage groups most likely representing two micro-chromosomes not covered by the current genome assembly.ConclusionsThe high success rate of the SNPs on the Illumina chicken 60K Beadchip emphasizes the power of Next generation sequence (NGS) technology for the SNP identification and selection step. The identification of SNPs from sequence contigs derived from NGS sequencing resulted in improved coverage of the chicken genome and the construction of two new linkage groups most likely representing two chicken micro-chromosomes.

Analysis of genome-wide structure, diversity and fine mapping of Mendelian traits in traditional and village chickens

“…A major caveat of current 'genome-wide' studies in chicken using the 60K SNP chip (Groenen et al, 2011) is that they are not entirely genome-wide. Chickens have 38 pairs of autosomes, and of the B1.05 Gb reference genome only 95% has been anchored to some but not all chromosomes (Gga 1-28, Gga 32, Gga Z and Gga W).…”

“…We characterised here at the genome-wide level using the 60K chicken SNP chip (Groenen et al, 2011) the diversity, haplotype blocks and LD structure of traditional and village chicken genomes, addressing the usefulness of non-pedigree chicken populations for mapping Mendelian traits. The use of a high-density SNP chip allows us first to investigate the genetic make-up of the breeds/populations studied.…”

“…This approach has been particularly successful in dogs (Karlsson et al, 2007;Chase et al, 2009;Akey et al, 2010). The recent development and characterisation of a 60K single-nucleotide polymorphism (SNP) chip for domestic chicken (Groenen et al, 2011) provides an opportunity to demonstrate this approach using traditional chicken breeds. Moreover, the presence of a diversity of phenotypes in village chicken also provides the opportunity to apply the same approach in village chicken, with the expectation that these older chicken populations may provide enhanced mapping resolutions compared with the traditional chicken breeds of more recent origins.…”

Genomic Variation between Genetic Lines of White Leghorns Differed in Resistance to Marek’s Disease

“…The DNA samples were quantified with a Quant-iT PicoGreen dsDNA Assay (Life Technologies, Grand Island, NY). SNP typing was done with a chicken 60K SNP array [45] at DNA LandMarks Inc. (Quebec, Canada).…”

Prediction of heterosis using genome-wide SNP-marker data: application to egg production traits in white Leghorn crosses

“…The Illumina chicken 60 K SNP BeadChip was used (Groenen et al, 2011). The same array was used for all genotyping.…”