Detection and characterisation of genetic associations with canine skull shape and disease
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Date
29/06/2019Author
Marchant, Thomas William
Metadata
Abstract
The brachycephalic head conformation is a morphological trait under human
selection across many popular breeds such as the Pug. The conformation is
characterised by the concurrent rostrocaudal shortening and mediolateral widening
of the skull. Overwhelming evidence suggests this skull conformation predisposes
breeds to a respiratory morbidity, Brachycephalic Obstructive Airway Syndrome
(BOAS) which restricts airflow. This is a major welfare concern.
To date, very little is known regarding the genetic factors underpinning canine
craniofacial variation or how such factors may influence BOAS aetiology. This project
utilised computer tomography scans of 560 dogs to generate high resolution three-dimensional
reconstructions of the skull. Geometric morphometric analysis
permitted the separation of the confounding influence of size on shape (allometry)
at an individual-level – a study design never previously utilised in dogs. Genome-wide
association studies (GWAS) using viscerocranial shape changes identified a QTL on
chromosome 1 associated with canine brachycephaly. Haplotype mapping refined
the critical interval to encompass the SPARC-related modular calcium-binding protein
2 (SMOC2) gene. Leveraging haplotype mapping and whole-genome sequencing, a
long interspersed nuclear element (LINE-1) was discovered within intron eight of
SMOC2. Transcriptomic analysis revealed the presence of alternative SMOC2
transcripts containing premature stop codons and a downregulation of the gene
among brachycephalic carriers of the LINE-1. Models of phenotypic effect predicted
that this structural variant explains up to 36% of the total craniofacial variation in the
dog.
Despite many brachycephalic dogs being fixed for the SMOC2 LINE-1 mutation,
heterogeneity in BOAS presentation suggests additional genetic factors contribute to
disease risk and presentation. To address this, a respiratory distress syndrome with
remarkable similarities to BOAS was assessed in the Norwich Terrier. Endoscopic
examinations of 233 Norwich Terriers graded and characterised the respiratory
syndrome for the use in a GWAS. A single QTL on chromosome 13 was associated
with changes in the structure of the laryngeal saccules and cartilage of affected dogs.
The underlying disease-associated haplotype encompassed the disintegrin and
metalloproteinase with thrombospondin motifs 3 (ADAMTS3) gene which was
observed to harbour a missense mutation in severely affected dogs. Screening for the
variant across 89 diverse dog breeds revealed it was enriched in brachycephalic
breeds, suggesting that the brachycephalic conformation alone does not completely
explain the presentation of BOAS in these breeds. Together, these results provide the
opportunity to improve animal welfare by offering genetic screening tests and further
our understanding of the condition which is driven by both skeletal and non-skeletal
factors.