Submitted to: Journal of Animal Breeding and Genetics
Publication Type: Peer reviewed journal
Publication Acceptance Date: 3/8/2011
Publication Date: 6/17/2011
Citation: Uthe, J.J., Qu, L., Couture, O., Bearson, S.M., O'Connor, A., Mckean, J., Rodriguez, T.Y., Dekkers, J.C., Nettleton, D., Tuggle, C.K. 2011. Use of bioinformatic SNP predictions in differentially expressed genes to find SNPs associated with Salmonella colonization in swine. Journal of Animal Breeding and Genetics. 128(5):354-365. Interpretive Summary: Salmonella-contamination of the food chain by food-producing animals extends beyond tainted meat; fruits and vegetables can be contaminated when waterways used for irrigation of crops are contaminated with Salmonella from animal manure applied as crop fertilizer. Furthermore, pigs colonized with Salmonella are a food safety concern since most pigs are asymptomatic carriers of the bacterium and can shed Salmonella upon exposure to stress, thereby contaminating their pen-mates and the environment. Thus, on-farm interventions are a logical control point to improve food safety. One approach to reduce Salmonella in pigs is to identify and breed pigs with decreased colonization and fecal shedding of Salmonella. If genetic differences in pigs can be identified that associate with Salmonella shedding status, diagnostic tests can be developed to screen pig lines for the desired trait. We searched sequence databases for genetic variation in greater than 3,000 porcine genes previously identified by our research team as differentially-expressed during exposure to Salmonella and found 30 single nucleotide polymorphisms (SNPs). Genotype analysis of four independent pig populations revealed that three of the 30 SNPs were associated with tissue colonization or fecal shedding of Salmonella in pigs. These associations may be useful to industry, university and government researchers interested in improving food safety by identifying and breeding pigs with increased resistance to Salmonella colonization.
Technical Abstract: Asymptomatic Salmonella-carrier pigs present a major problem in pre-harvest food safety, with a recent survey indicating greater than 50% of swine herds in the U.S. have Salmonella-positive animals. Salmonella-carrier pigs serve as a reservoir for contamination of neighboring pigs, abattoir pens and pork products. In addition, fresh produce as well as water can be contaminated with Salmonella from manure used as fertilizer. Control of Salmonella at the farm level could be through genetic improvement of porcine disease resistance, a potentially powerful method of addressing pre-harvest pork safety. In this research, we integrate gene expression profiling data and sequence alignment-based prediction of single nucleotide polymorphisms (SNPs) to successfully identify SNPs in functional candidate genes to test for associations with swine response to Salmonella. A list of 3,308 genes were selected, and SNPs were predicted using ANEXdb database by sequence-based assembly of all available porcine sequences downloaded from NCBI. A set of 30 SNPs was selected for genotype analysis of four independent populations (n=750) with Salmonella fecal shedding or tissue colonization phenotypes. Eleven SNPs segregated with minor allele frequency (MAF) greater than or less than 15% in at least two populations. Statistical analysis revealed SNPs potentially associated with Salmonella shedding, such as HP (p=0.001, q=0.01) and NCF2 #2 (p=0.04, q=0.21) and PGD (p=0.066, q=0.21). These associations may be useful in identifying and selecting pigs with improved resistance to this bacterium.