Design and Characterization of a 52K SNP Chip for Goats

Abstract

The success of Genome Wide Association Studies in the discovery of sequence variation linked to complex traits in humans has increased interest in high throughput SNP genotyping assays in livestock species. Primary goals are QTL detection and genomic selection. The purpose here was design of a 50–60,000 SNP chip for goats. The success of a moderate density SNP assay depends on reliable bioinformatic SNP detection procedures, the technological success rate of the SNP design, even spacing of SNPs on the genome and selection of Minor Allele Frequencies (MAF) suitable to use in diverse breeds. Through the federation of three SNP discovery projects consolidated as the International Goat Genome Consortium, we have identified approximately twelve million high quality SNP variants in the goat genome stored in a database together with their biological and technical characteristics. These SNPs were identified within and between six breeds (meat, milk and mixed): Alpine, Boer, Creole, Katjang, Saanen and Savanna, comprising a total of 97 animals. Whole genome and Reduced Representation Library sequences were aligned on >10 kb scaffolds of the de novo goat genome assembly. The 60,000 selected SNPs, evenly spaced on the goat genome, were submitted for oligo manufacturing (Illumina, Inc) and published in dbSNP along with flanking sequences and map position on goat assemblies (i.e. scaffolds and pseudo-chromosomes), sheep genome V2 and cattle UMD3.1 assembly. Ten breeds were then used to validate the SNP content and 52,295 loci could be successfully genotyped and used to generate a final cluster file. The combined strategy of using mainly whole genome Next Generation Sequencing and mapping on a contig genome assembly, complemented with Illumina design tools proved to be efficient in producing this GoatSNP50 chip. Advances in use of molecular markers are expected to accelerate goat genomic studies in coming years.

Multiple genomic signatures of selection in goats and sheep indigenous to a hot arid environment

“…We doubt that ascertainment bias influenced our results because athough the exotic breeds showed almost similar levels of diversity as the indigenous breeds, especially for goats, as we had expected their Ne and private allele richness values were lower and their inbreeding levels were higher. The strategy used in the development of the chips included divergent breeds in the discovery panel, and prior to their release, they were tested and validated on a large panel of divergent breeds and populations Tosser-Klopp et al, 2014). Ascertainment bias has also not been reported as an issue in studies that have used the two chips (for example, Kijas et al, 2009;Lv et al, 2014;Lashmar et al, 2015), and results from these studies and ours show that the two chips are highly polymorphic.…”

The Application of Genomic Technologies to Investigate the Inheritance of Economically Important Traits in Goats

“…The design, by the International Goat Genome Consortium, of a 52K SNP chip for the high throughput genotyping of caprine DNA samples should be envisaged as a major scientific achievement in the field of goat genomics [138]. Polymorphism discovery was achieved by next-generation sequencing of dairy (16 individuals from the Alpine, Creole, and Saanen breeds sequenced in a Hiseq2000 platform with 13-26-fold coverage) and meat (pool 1: 20 Boer goats, pool 2: 20 Savanna goats and 24 Katjang goats, both sequenced in an Illumina Genome Analyzer IIx machine with 35-fold coverage) goat DNAs.…”

“…The recent construction of a 52K SNP chip [138] is expected to accelerate the speed at which discoveries are made, facilitating the performance of GWAS with an unprecedented resolution. Importantly, the 52K SNP chip produces data that can be easily standardized amongst labs at an affordable cost (at least if compared with microsatellites).…”

Non-Coding RNA Roles in Ruminant Mammary Gland Development and Lactation

“…The endocrine regulation and physiological processes as well as the signalling pathways involved in these processes are fairly understood [1,2]. Facilitated by the release of the whole genome sequences of cattle, sheep and goat [3][4][5][6] as well as availability of single nucleotide polymorphism (SNP) genotyping chips [7][8][9][10][11], the genetic mechanisms of ruminant lactation have been extensively explored ( Figure 1). As a consequence, many quantitative trait loci (QTL) and genetic markers for lactationrelated traits (for instance, milk yield, milk components, lactation persistency, etc.)…”