TY - JOUR T1 - Development of a high-density, 2M SNP genotyping array and 670k SNP imputation array for the domestic horse JF - bioRxiv DO - 10.1101/112979 SP - 112979 AU - Robert J Schaefer AU - Mikkel Schubert AU - Ernest Bailey AU - Danika L. Bannasch AU - Eric Barrey AU - Gila Kahila Bar-Gal AU - Gottfried Brem AU - Samantha A. Brooks AU - Ottmar Distl AU - Ruedi Fries AU - Carrie J. Finno AU - Vinzenz Gerber AU - Bianca Haase AU - Vidhya Jagannathan AU - Ted Kalbfleisch AU - Tosso Leeb AU - Gabriella Lindgren AU - Maria Susana Lopes AU - Nuria Mach AU - Artur da Câmara Machado AU - James N. MacLeod AU - Annette McCoy AU - Julia Metzger AU - Cecilia Penedo AU - Sagi Polani AU - Stefan Rieder AU - Imke Tammen AU - Jens Tetens AU - Georg Thaller AU - Andrea Verini-Supplizi AU - Claire M. Wade AU - Barbara Wallner AU - Ludovic Orlando AU - James R. Mickelson AU - Molly E. McCue Y1 - 2017/01/01 UR - http://biorxiv.org/content/early/2017/03/02/112979.abstract N2 - Background To date, genome-scale analyses in the domestic horse have been limited by suboptimal single nucleotide polymorphism (SNP) density and uneven genomic coverage of the current SNP genotyping arrays. The recent availability of whole genome sequences has created the opportunity to develop a next generation, high-density equine SNP array.Results Using whole genome sequence from 153 individuals representing 24 distinct breeds collated by the equine genomics community, we cataloged over 23 million de novo discovered genetic variants. Leveraging genotype data from individuals with both whole genome sequence, and genotypes from lower-density, legacy SNP arrays, a subset of ~5 million high-quality, high-density array candidate SNPs were selected based on breed representation and uniform spacing across the genome. Considering probe design recommendations from a commercial vendor (Affymetrix) a set of ~2 million SNPs were selected for a next-generation high-density SNP chip (MNEc2M). Genotype data were generated using the MNEc2M array from a cohort of 332 horses from 20 breeds and a lower-density array, consisting of ~670 thousand SNPs (MNEc670k), was designed for genotype imputation.Conclusions Here, we document the steps taken to design both the MNEc2M and MNEc670k arrays, report genomic and technical properties of these genotyping platforms, and demonstrate the imputation capabilities of these tools for the domestic horse.SNPSingle Nucleotide PolymorphismMNEc2Mthe 2 million SNP array developed hereMNEc670kthe 670 thousand SNP array developed hereWGSwhole genome sequencingbpbase pairGATKgenome analysis tool kitQUALgeneric quality score output by GATK and SAMtoolsMORthe Morgan horse breedSTDthe Standardbred horse breedVQSLODvariant quality score log-oddsGbgiga-basesMHCmajor histocompatibility complexECAEquus caballus chromosomeVIPvery important probeMAFminor allele frequencyALTalternate alleleKDEkernel density estimationLDlinkage disequilibriumChrUn1Equus calballus unknown chromosome ER -