Genome-wide association studies of 74 plasma metabolites of German shepherd dogs reveal two metabolites associated with genes encoding their enzymes
German shepherd dogs (GSDs) are a popular breed affected by numerous disorders. Few studies have explored genetic variations that influence canine blood metabolite levels.
To investigate genetic variants affecting the natural metabolite variation in GSDs.
A total of 82 healthy GSDs were genotyped on the Illumina CanineHD Beadchip, assaying 173,650 markers. For each dog, 74 metabolites were measured through liquid and gas chromatography mass spectrometry (LC–MS and GC–MS) and were used as phenotypes for genome-wide association analyses (GWAS). Sliding window and homozygosity analyses were conducted to fine-map regions of interest, and to identify haplotypes and gene dosage effects.
Summary statistics for 74 metabolites in this population of GSDs are reported. Forty-one metabolites had significant associations at a false discovery rate of 0.05. Two associations were located around genes which encode for enzymes for the relevant metabolites: 4-hydroxyproline was significantly associated to D-amino acid oxidase (DAO), and threonine to l-threonine 3-dehydrogenase (LOC477365). Three of the top ten haplotypes associated to 4-hydroxyproline included at least one SNP on DAO. These haplotypes occurred only in dogs with the highest 15 measurements of 4-hydroxyproline, ranging in frequency from 16.67 to 20%. None of the dogs were homozygous for these haplotypes. The top two haplotypes associated to threonine included SNPs on LOC477365 and were also overrepresented in dogs with the highest 15 measurements of threonine. These haplotypes occurred at a frequency of 90%, with 80% of these dogs homozygous for the haplotypes. In dogs with the lowest 15 measurements of threonine, the haplotypes occurred at a frequency of 26.67% and 0% homozygosity.
DAO and LOC477365 were identified as candidate genes affecting the natural plasma concentration of 4-hydroxyproline and threonine, respectively. Further investigations are needed to validate the effects of the variants on these genes.
KeywordsCanine Plasma Metabolomics Genetics GWAS
This work was supported by the Canine Research Foundation. This research is supported by an Australian Government Research Training Program (RTP) Scholarship. Metabolites were extracted and analysed from plasma at Metabolomics Australia (School of BioSciences, University of Melbourne, Australia), a National Collaborative Research Infrastructure Strategy (NCRIS) initiative under Bioplatforms Australia, Pty Ltd. The authors would like to thank Himasha Mendis, Nirupama Jayasinghe and Alice Ng from Metabolomics Australia who extracted and analysed metabolites. The authors would also like to thank the owners and dogs that donated samples for this study.
PXYS performed research, analysed the data, and wrote the manuscript. JMMC, CJJ, and SM contributed to performing research, analysis of data, and writing the manuscript. SM, RB, BC and SC collected the samples and data, and conceived the study. MSK contributed in the analysis, interpretations and writing. UR and SN advised on metabolomics analysis and contributed to writing. PW conceived the study, performed research, contributed to the analysis of the data and writing of the manuscript.
Compliance with ethical standards
Conflict of interest
All authors declare that they have no conflicts of interest.
All protocols in this study was conducted in accordance with the guidelines of the Animal Research Act, NSW, Australia, approved by the University of Sydney’s Animal Ethics Committee under protocols 444 and 4949.
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