College of Veterinary Medicine
This work involves searching for genes and alleles responsible for genetic traits in dogs and horses, particularly those that affect the neuromuscular and nervous systems, metabolism, health, or performance. The researchers use a combination of approaches that include genome scanning with SNP markers to map gene loci, whole genome sequencing to identify variants, and transcriptome sequencing to examine possible cellular effects. They are currently using MSI for five projects:
- Assessment of genotype imputation resource for the domestic dog: The development of 50,000 and 175,000 (50K and 1755K) SNP genotyping arrays for the dog has led to successful mapping of genetic loci responsible for or contributing to many health and performance traits using genome-wide association and/or identification of genomic signatures of selection. Despite these successes, the SNP density of the first-generation arrays has proven inadequate for mapping complex traits and for mapping in breeds with high diversity and rapid decay of linkage disequilibrium. One method for increasing marker density is through genotype imputation, which utilizes dense SNP genotype and haplotype information from a reference population to computationally infer unknown genotypes in a more sparsely genotyped test population. The researchers are assessing the ability of soon to be released Affymetrix Canine 670K and 1.3 M SNP chips from which 50K and 175K SNP data can be imputed to much higher levels in several breeds which are the subjects of GWAS projects.
- GWAS to investigate the genetic basis of neurological and neuromuscular diseases in dogs: The group's long-term goals have been to identify the genes and alleles that underlie susceptibility to genetic diseases in dogs and horses. Many of the neurological and neuromuscular diseases they study are likely complex traits, thus the genetic risk for disease within an individual is the result of that individual’s unique combination of genetic alleles, in concert with environmental influences. Conditions currently being pursued include inherited polyneuropathies in Leonbergers, idiopathic epilepsies in Australian shepherds and vizlas, and exercise-induced collapse in border collies, Australian shepherds, and whippets.
- Use of WGS to discover variants associated with GWAS regions of interest: The researchers are collecting 6 – 12 fold genome coverage sequences from eight Leonbergersfour Australian shepherds, and four border collies, as well as sequences from up to eight other dogs in small projects.
- Transcriptomics of Equine Tissues: The researchers will be collecting samples from 24 different tissues from each of six horses to analyze their expression patterns of mRNA, lnNCRNA and miRNA.