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Utsunomiya Tochigi, Japan

Hauswirth R.,University of Bern | Jude R.,Certagen GmbH | Haase B.,University of Bern | Haase B.,University of Sydney | And 7 more authors.
Animal Genetics | Year: 2013

Variants in the EDNRB, KIT, MITF, PAX3 and TRPM1 genes are known to cause white spotting phenotypes in horses, which can range from the common white markings up to completely white horses. In this study, we investigated these candidate genes in 169 horses with white spotting phenotypes not explained by the previously described variants. We identified a novel missense variant, PAX3:p.Pro32Arg, in Appaloosa horses with a splashed white phenotype in addition to their leopard complex spotting patterns. We also found three novel variants in the KIT gene. The splice site variant c.1346+1G>A occurred in a Swiss Warmblood horse with a pronounced depigmentation phenotype. The missense variant p.Tyr441Cys was present in several part-bred Arabians with sabino-like depigmentation phenotypes. Finally, we provide evidence suggesting that the common and widely distributed KIT:p.Arg682His variant has a very subtle white-increasing effect, which is much less pronounced than the effect of the other described KIT variants. We termed the new KIT variants W18-W20 to provide a simple and unambiguous nomenclature for future genetic testing applications. © 2013 The Authors, Animal Genetics © 2013 Stichting International Foundation for Animal Genetics. Source


Ishii H.,Tohoku University | Ishii H.,Laboratory of Racing Chemistry | Yamaguchi H.,Tohoku University | Mano N.,Tohoku University
Chemical and Pharmaceutical Bulletin | Year: 2016

The goal of this study was to demonstrate the utility of in-source collision-induced dissociation for shifting the linear range in liquid chromatography-electrospray ionization-tandem mass spectrometry (LC/ESI-MS/MS). The linear ranges for uracil, deoxyuridine, and uridine were shifted from 0.3-300, 1-100, and 10-1000 ng/mL to 10-1000, 30-3000, and 100-10000 ng/mL, respectively, by changing the declustering potential controlling in-source collision-induced dissociation. This technique should be considered for control of linear range in simultaneous quantitative measurements of extremely different amounts of compounds, drugs, and metabolites using LC/ESI-MS/MS. © 2016 The Pharmaceutical Society of Japan. Source


McCue M.E.,University of Minnesota | Bannasch D.L.,University of California at Davis | Petersen J.L.,University of Minnesota | Gurr J.,University of Sydney | And 18 more authors.
PLoS Genetics | Year: 2012

An equine SNP genotyping array was developed and evaluated on a panel of samples representing 14 domestic horse breeds and 18 evolutionarily related species. More than 54,000 polymorphic SNPs provided an average inter-SNP spacing of ~43 kb. The mean minor allele frequency across domestic horse breeds was 0.23, and the number of polymorphic SNPs within breeds ranged from 43,287 to 52,085. Genome-wide linkage disequilibrium (LD) in most breeds declined rapidly over the first 50-100 kb and reached background levels within 1-2 Mb. The extent of LD and the level of inbreeding were highest in the Thoroughbred and lowest in the Mongolian and Quarter Horse. Multidimensional scaling (MDS) analyses demonstrated the tight grouping of individuals within most breeds, close proximity of related breeds, and less tight grouping in admixed breeds. The close relationship between the Przewalski's Horse and the domestic horse was demonstrated by pair-wise genetic distance and MDS. Genotyping of other Perissodactyla (zebras, asses, tapirs, and rhinoceros) was variably successful, with call rates and the number of polymorphic loci varying across taxa. Parsimony analysis placed the modern horse as sister taxa to Equus przewalski. The utility of the SNP array in genome-wide association was confirmed by mapping the known recessive chestnut coat color locus (MC1R) and defining a conserved haplotype of ~750 kb across all breeds. These results demonstrate the high quality of this SNP genotyping resource, its usefulness in diverse genome analyses of the horse, and potential use in related species. © 2012 McCue et al. Source


Hauswirth R.,University of Bern | Haase B.,University of Sydney | Blatter M.,Swiss National Stud | Brooks S.A.,Cornell University | And 16 more authors.
PLoS Genetics | Year: 2012

During fetal development neural-crest-derived melanoblasts migrate across the entire body surface and differentiate into melanocytes, the pigment-producing cells. Alterations in this precisely regulated process can lead to white spotting patterns. White spotting patterns in horses are a complex trait with a large phenotypic variance ranging from minimal white markings up to completely white horses. The "splashed white" pattern is primarily characterized by an extremely large blaze, often accompanied by extended white markings at the distal limbs and blue eyes. Some, but not all, splashed white horses are deaf. We analyzed a Quarter Horse family segregating for the splashed white coat color. Genome-wide linkage analysis in 31 horses gave a positive LOD score of 1.6 in a region on chromosome 6 containing the PAX3 gene. However, the linkage data were not in agreement with a monogenic inheritance of a single fully penetrant mutation. We sequenced the PAX3 gene and identified a missense mutation in some, but not all, splashed white Quarter Horses. Genome-wide association analysis indicated a potential second signal near MITF. We therefore sequenced the MITF gene and found a 10 bp insertion in the melanocyte-specific promoter. The MITF promoter variant was present in some splashed white Quarter Horses from the studied family, but also in splashed white horses from other horse breeds. Finally, we identified two additional non-synonymous mutations in the MITF gene in unrelated horses with white spotting phenotypes. Thus, several independent mutations in MITF and PAX3 together with known variants in the EDNRB and KIT genes explain a large proportion of horses with the more extreme white spotting phenotypes. © 2012 Hauswirth et al. Source


Tozaki T.,Laboratory of Racing Chemistry | Miyake T.,Kyoto University | Kakoi H.,Laboratory of Racing Chemistry | Gawahara H.,Laboratory of Racing Chemistry | And 3 more authors.
Journal of Animal Breeding and Genetics | Year: 2012

This study evaluated the differences between linear and non-linear modelled heritability estimates of racing performance based on lifetime earnings (LE) and lifetime ranking (LR) in Japanese Thoroughbred racehorses. The heritability estimate (h2=0.25) obtained from a non-linear model based on formal Japan Racing Association ranking was much higher than that obtained from a linear model based on the original trait phenotype (h2=0.11). The linear models showed slightly higher heritability estimates under the trait categorizations than under the original phenotypes, while the non-linear categorical trait models showed much higher heritability estimates than the linear models, especially for binary trait categorizations (h2=0.34) with non-winning and winning horses. The binary trait categorizations were consistent with the case and control classifications in the previous genome-wide association study (GWAS), which identified possible sequence variants on ECA18 that affect racing performance in Japanese Thoroughbred racehorses. Those findings suggested that the different heritability estimates obtained from several trait categorizations would reflect the possible presence of susceptibility gene segregations in the analyzed population, indicating that heritability estimates from non-linear models are useful for the selection of case and control populations in GWAS. © 2011 Blackwell Verlag GmbH. Source

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