Canine Genetics The tremendous phenotypic diversity of modern dog breeds represents the end point of a >15,000-year experiment. Each breed has undergone strong artificial selection in which dog fanciers selected for many traits including body size, fur color, skull shape, and even behavior, to create novel breeds. As a result, there is strong phenotypic homogeneity within breeds including breed-associated genetic diseases such as cancer. These traits were explored in depth (Ostrander et al., 2017), in a paper which was featured on the cover of Nature Reviews Genetics. Canine Whole Genome Sequence Drs. Bob Wayne and Elaine Ostrander organized a June 2016 meeting in Beijing with 18 other labs to establish a collaboration aimed at generating whole genome sequence (WGS) for 10,000 dogs in the next five years. We assigned participating labs to subcommittees (sampling, processing, QC, analyses, etc.) with a plan to meet again this year. Our goal is to sequence (30x) 10,000 unrelated dogs from each of 300 registered breeds from the U.S., Africa, Europe, and Asia. Dogs from non-breed working populations, as well as free breeding, semi-feral populations from East/Central Asia, South America, the Middle East, and Africa will also be sequenced. This effort is a partnership with the Chinese Academy of Sciences. Our own collection efforts this year have included Mexico, Chile, Italy, and many others. The Ostrander lab has catalogued WGS sequence from over 700 canines thus far. Ostrander lab sequences are uploaded in sort read archive (SRA) and variants are uploaded to Broad-managed browsers. We have used our data, in papers currently under consideration, to identify genes associated with a myriad of morphologic traits, providing insights into human growth and development. Our interest in canine breed morphology continues to have a focus on body size (Plassais et al., 2017). While previous studies focused on the identification of alleles that contribute to small skeletal size, little is known about the underlying genetics controlling large breed size. We therefore performed a genome-wide association study (GWAS) which compared 165 large-breed dogs from 19 breeds (defined as having a Standard Breed Weight (SBW) >41 kg 90 lb) to 690 dogs from 69 small breeds (SBW 41 kg). We identified two loci on the canine X chromosome that were strongly associated with large body size. Analyses of whole genome sequencing (WGS) data from 163 dogs revealed two indels in the Insulin Receptor Substrate 4 (IRS4) gene at 82.2 Mb and two additional 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 and thyroid pathways whose roles include determination of body size. We also found one highly associated SNP in the 5'UTR of Acyl-CoA Synthetase Long-chain family member 4 (ACSL4) at 82.9 Mb, a gene which controls the traits of muscling and back fat thickness. We show by analysis of sequencing data from 26 wolves and 959 dogs representing 102 domestic dog breeds that skeletal size and body mass in large dog breeds are strongly associated with variants within IRS4, ACSL4 and IGSF1. We note that the same genes, when mutated in humans, are associated with disease traits such as insulin resistance and obesity. Thus, this study demonstrates how identification of genes controlling breed traits in dogs can lend new insights into the study of human metabolic disorders. Canine Population Structure Ostrander lab Staff scientist Heidi Parker undertook a large study of canine breed structure (Parker et al., 2017) in order to better inform our disease mapping studies. We assembled the most diverse dataset of dog breeds in existence reflecting extensive phenotypic variation and heritage. Combining genetic distance, migration, and genome-wide haplotype sharing analyses we uncovered geographic patterns of development and independent origins of common traits. Our analyses characterized the complexities of breed development, resolving longstanding questions regarding individual breed origination, the effect of migration on geographically distinct breeds and, by inference, transfer of trait and disease alleles among dog breeds. When applied to the traits of blindness and drug tolerance in a subset of breeds, we show we can track the history of variant alleles, offering predictions as to additional breeds where these diseases may appear next. This work is foundational to all studies in disease mapping in dog breeds, as it informs study design by determining how breeds should be partitioned or grouped for analyses. Dog Origins A natural outgrowth of this work has been our continued collaborations to better understand the process of domestication. Such studies highlight genes and regions of genes that are particularly malleable, providing insights into the genes that are likely most important in understanding human variation (Pilot et al., 2018; Schweizer et al., 2018; Talenti et al., 2018). One important lesson from these studies is that dog breed formation mirrors human migration patterns. Thus, one excellent way to better understand the migration of peoples and disease alleles in early human history is to follow the patterns that define dog breed development. We show this is true, for instance, in a set of Italian breeds, where there is clear evidence of co-development of early dog and human populations (Talenti et al., 2018). Dog Behavior and Human Syndromes In a study led by collaborator Bridget vonHoldt (vonHoldt et al., 2017) we were able to examine the molecular underpinnings of behavioral characteristics associated with domestication. We analyzed a 5Mb genomic region in the dog genome under positive selection in domestication. Deletion of this region is linked to Williams-Beuren syndrome (WBS) in humans, a multi-system congenital disorder characterized by hyper-social behavior. This study associated quantitative data on behavioral phenotypes symptomatic of WBS in humans with structural changes in the WBS locus in dogs, showing that hyper-sociability, a central feature of WBS, is also a core element of domestication that distinguishes dogs from wolves. Structural variants in the GTF2I and GTF2IRD1 genes, previously implicated in the WBS, contribute to extreme sociability in dogs. This finding expands the ever-growing knowledge base between variation in genes controlling behavior in dogs, which are also components of major human syndromes (vonHoldt et al., 2017). This collaboration continues. We also did a whole genome comparison of two types of dog breeds: those that are highly athletic and include the sport-hunting breeds versus the terriers which are known for their hyperactivity (Kim et al., 2018). These are groups at the ends of a continuum in both form and function. We found that genes underlying cardiovascular, muscular, and neuronal functions are under strong selection in sport-hunting breeds, including ADRB1, TRPM3, RYR3, UTRN, ASIC3, and ROBO1 We also identified an allele of TRPM3 that was significantly associated with the speed aspect of performance. Finally, we observed a significant association of ROBO1 with breed-specific accomplishments in competitive obstacle course events and problem solving in athletics. In terms of terriers, in results we are now expanding, we found associations with genes that are associated with human hyperactivity and panic response. These results demonstrate how strong behavioral selection alters physiology to create breeds with distinct capabilities, and further established the dog as a system for identifying behavioral genes of interest to human health and biology. This paper was featured on the cover of PNAS.
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