Diverse dog breeds genotyped on Affymetrix Canine v2 Arrays
Ontology highlight
ABSTRACT:
ORGANISM(S): Canis lupus familiaris Canis lupus
PROVIDER: GSE63439 | GEO | 2014/11/20
SECONDARY ACCESSION(S): PRJNA268030
REPOSITORIES: GEO
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Project description:Diverse dataset of 1247 dogs from many breeds and wolves used to investigate the origins of dog domestication DNA for 1228 dogs from 35 breeds and 19 wolves was extracted from whole blood samples and genotyped on the Affymetrix Canine v2 Arrays. Genotypes were called using Affymetrix's snp5-probeset-genotype software and the BRLMM-P calling algorithm. The included breed designations are owner reported.
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Project description:Through thousands of years of breeding and strong human selection, the dog (Canis lupus familiaris) exists today within hundreds of closed populations throughout the world, each with defined phenotypes. A singular geographic region with broad diversity in dog breeds presents an interesting opportunity to observe potential mechanisms of breed formation. Italy claims 14 internationally recognized dog breeds, with numerous additional local varieties. To determine the relationship among Italian dog populations, we integrated genetic data from 263 dogs representing 23 closed dog populations from Italy, seven Apennine gray wolves. Using 142,840 genome-wide SNPs, this dataset was used in the identification of breed development routes for the Italian breeds that included divergence from common populations for a specific purpose, admixture of regional stock with that from other regions, and isolated selection of local stock with specific attributes.
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Project description:Diverse dog breeds genotyped on Affymetrix Canine v2 Arrays
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Project description:The inherent diversity of canines is closely intertwined with the unique color patterns of each dog population. These variations in color patterns are believed to have originated through mutations and selective breeding practices that occurred during and after the domestication of dogs from wolves. To address the significant gaps that persist in comprehending the evolutionary processes that underlie the development of these patterns, we generated and analyzed deep-sequenced genomes of 113 Korean indigenous Jindo dogs that represent five distinct color patterns to identify the associated mutations in CBD103, ASIP, and MC1R. The degree of linkage disequilibrium and estimated allelic ages consistently indicate that the black-and-tan dogs descend from the first major founding population on Jindo island, compatible with the documented literature. We additionally demonstrate that black-and-tan dogs, in contrast to other color variations within the breed, exhibit a closer genetic affinity to ancient wolves from western Eurasia than those from eastern Eurasia. Lastly, population-specific genetic variants with moderate effects were identified, particularly in loci associated with traits underlying body size and behavioral variations, potentially explaining the observed phenotypic diversity based on coat colors. Overall, comparisons of whole genome sequences of each coat color population diverged from the same breed provided an unprecedented glimpse into the properties of evolutionary processes maintaining variation in Korean Jindo dog populations that were previously inaccessible.
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Project description:Osteosarcoma in dogs is a spontaneously occurring disease with a global tumor gene expression signature indistinguishable from human pediatric tumors and clinical progression is remarkably similar. Unlike human OS, canine OS is a highly heritable disease with some large and giant dog breeds at >10x increased risk. We did a genome wide association study of osteosarcoma using the Illumina CanineHD genotyping array in three breeds: greyhound (mortality from OS = 26%), rottweiler (17%) and Irish wolfhound (IWH, 21%) and identified 33 inherited risk loci explaining 55 to 85% of phenotype variance in each breed. Data created for a genome-wide association studio of heritable osteosarcoma risk factors in dogs, including 267 racing greyhounds (153 affected (A) + 114 unaffected (U)), 135 rottweilers (80 A + 55 U), 141 IWH (76 A + 65 U) and 19 AKC greyhounds using the Illumina CanineHD array (~170,000 SNPs genomewide)
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Project description:Osteosarcoma in dogs is a spontaneously occurring disease with a global tumor gene expression signature indistinguishable from human pediatric tumors and clinical progression is remarkably similar. Unlike human OS, canine OS is a highly heritable disease with some large and giant dog breeds at >10x increased risk. We did a genome wide association study of osteosarcoma using the Illumina CanineHD genotyping array in three breeds: greyhound (mortality from OS = 26%), rottweiler (17%) and Irish wolfhound (IWH, 21%) and identified 33 inherited risk loci explaining 55 to 85% of phenotype variance in each breed. Data created for a genome-wide association studio of heritable osteosarcoma risk factors in dogs, including 267 racing greyhounds (153 affected (A) + 114 unaffected (U)), 135 rottweilers (80 A + 55 U), 141 IWH (76 A + 65 U) and 19 AKC greyhounds using the Illumina CanineHD array (~170,000 SNPs genomewide)
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Project description:Osteosarcoma in dogs is a spontaneously occurring disease with a global tumor gene expression signature indistinguishable from human pediatric tumors and clinical progression is remarkably similar. Unlike human OS, canine OS is a highly heritable disease with some large and giant dog breeds at >10x increased risk. We did a genome wide association study of osteosarcoma using the Illumina CanineHD genotyping array in three breeds: greyhound (mortality from OS = 26%), rottweiler (17%) and Irish wolfhound (IWH, 21%) and identified 33 inherited risk loci explaining 55 to 85% of phenotype variance in each breed. Data created for a genome-wide association studio of heritable osteosarcoma risk factors in dogs, including 267 racing greyhounds (153 affected (A) + 114 unaffected (U)), 135 rottweilers (80 A + 55 U), 141 IWH (76 A + 65 U) and 19 AKC greyhounds using the Illumina CanineHD array (~170,000 SNPs genomewide)
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