Evaluation of single nucleotide polymorphism markers on four pig chromosomes for potential associations with halothane sensitivity phenotypes in a population of Yorkshire-Landrace pigs

Wednesday, July 23, 2014
Exhibit Hall AB (Kansas City Convention Center)
Kaitlyn R. Perry , Michigan State University, East Lansing, MI
Catherine W. Ernst , Michigan State University, East Lansing, MI
Juan P. Steibel , Michigan State University, East Lansing, MI
Ronald O. Bates , Michigan State University, East Lansing, MI
Abstract Text:

We have previously reported that a proportion of pigs homozygous normal for the RYR1 g. 1843 C>T polymorphism were halothane sensitive and had lower post-mortem Longissimus dorsi pH. Pigs from this project (n = 363), which were progeny of Landrace sires and Yorkshire-Landrace F1 dams, were subsequently genotyped for 67 SNPs across four chromosomes (SSC6, SSC10, SSC12, and SSC14).  These SNPs were located in or near genes responsible for malignant hyperthermia or myopathies in humans (CACNA1S, CPT2, SCN4 and RYR2) that may influence the stress response in pigs, including multiple SNPs within RYR1. The objective of this study was to determine the association of these SNPs with the halothane sensitivity phenotypes recorded in this population.  Pigs were evaluated for limb rigidity (RIGID), limb tremors (TREM), and abdominal discoloration (AD) observed after halothane challenge. Halothane sensitivity was assessed after 60 sec exposure to 5% halothane gas in a closed system delivered at 2 L/min.  Pigs were considered to be either sensitive (1) to halothane or not sensitive (0) for each trait. Assays were multiplexed and SNP genotypes collected using Sequenom MassArray. Twelve SNPs were discarded from analysis due to low genotyping call rate (< 90%). Twenty-nine of the remaining 55 SNPs were not in Hardy-Weinberg equilibrium (p < 0.05). The three halothane response variables were fit to a generalized linear model that included the fixed effects of sex and SNP, and the random effects of replication and litter. False discovery rate (FDR) was used to determine significance. For the 55 SNPs tested for each halothane sensitivity variable, generally there were few SNPs with p-values less than 0.05. Three SNPs for TREMOR, 1 for RIGID and 1 for AD had p-values less than 0.05.  The FDR for all SNPs was greater than 0.25 and therefore it was determined that no SNP significantly associated with any of the three halothane response variables. These results indicate that halothane sensitivity in this population is not controlled by variation in these regions of the swine genome, and other genomic regions should be investigated to determine the genetic control of halothane sensitivity.


pig, halothane sensitivity, SNP