Building the LD Chip and an Update on the Sheep Genomes Database

The LD chip is a new addition to the family of ovine SNP ships. Here we present its final design. The major driver was a low cost chip for genomic selection in industry. We designed and tested it for imputation. In addition to imputation SNPs the chip also has parentage and key functional SNPs and has backwards compatibility with earlier versions of ovine LD chips. It is the first LD chip to fully utilise version 3.1 of the genome as well as results derived from the HD ovine chip.

The SheepGenomesDB is an electronic warehouse containing sequence variants called from the expanding collection of sheep genomes being generated across our research community. Through the application of a single harmonised pipeline for read QC, mapping, variant detection and annotation, SheepGenomesDB makes available variant collections derived in a standardised manner supported by the European Variation Archive. The first analysis run has been completed, with read mapping and variant calling performed for more than 250 sheep genomes from over 50 breeds. This identified in excess of 25 million SNP. The creators view SheepGenomesDB as an essential resource for researchers interested in gene mutation discovery, imputation as it relates to genome-wide association and genomic prediction as well as investigations into genome evolution, domestication and the consequences of selection.