Analysis of Large Versus Small Dogs Reveals Three Genes on the Canine X Chromosome Associated with Body Weight, Muscling Trait and Back Fat Thickness in Dogs

Domestic dog breeds display significant diversity in both body mass and skeletal size, resulting from intensive selective pressure during the formation and maintenance of modern breeds. While previous studies focused on the identification of alleles that contributes to small skeletal size, little is known about the underlying genetics controlling large sizes. We first performed a genome wide association study (GWAS) using the Illumina Canine HD 170,000 SNP array which compared large dog breeds, defined as having a Standard Breed Weight > 41kgs (90 lbs) and which included 165 dogs from 19 breeds to 690 dogs from 69 smaller breed (SBW<41kgs [90 lbs]). We identified two loci on the canine X chromosome that were strongly associated with large body size at 82-84 Mb and 101-104 Mb. Whole genome sequencing (WGS) data from 163 dogs revealed two indels in the Insulin Receptor Substrate 4 (IRS4) at 82.2 Mb and two mutations (one SNP and one deletion of a single codon) in ImmunoGlobulin Superfamily member 1 gene (IGSF1) at 102.3 Mb. IRS4 and IGSF1 are members of the GH/IGF1 pathway whose roles include determination of skeletal size. We also found one SNP in the 5’UTR of Acyl-CoA Synthetase Long-chain family member 4 (ACSL4) as 82.9 Mb, which controls the traits of muscling and back fat thickness. We show by Sanger sequencing of 27 wolves and 977 dogs from 105 breeds of varying body size that strong and ancient contributions to increased mass and skeletal size derive from variants within IRS4, ACSL4 and IGSF1.