Identification of loci associated with tolerance to Johne's disease in Holstein cattle

Authors: ZANELLA, RICARDO - Washington State University; SETTLES, MATTHEW - Washington State University; MCKAY, STEPHANIE - University Of Missouri; SCHNABEL, ROBERT - University Of Missouri; TAYLOR, JEREMY - University Of Missouri; FYOCK, TERRY - University Of Pennsylvania; WHITLOCK, ROBERT - University Of Pennsylvania; SCHUKKEN, YNTE - Cornell University; Van Kessel, Jo Ann; Karns, Jeffrey; HOVINGH, ERNEST - Pennsylvania State University; SMITH, JULIE - University Of Vermont; NEIBERGS, HOLLY - Washington State University

Submitted to: Animal Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/23/2010
Publication Date: 5/12/2010
Citation: Zanella, R., Settles, M., Mckay, S.D., Schnabel, R.D., Taylor, J.F., Fyock, T., Whitlock, R.H., Schukken, Y., Van Kessel, J.S., Karns, J.S., Hovingh, E., Smith, J., Neibergs, H.L. 2010. Identification of loci associated with tolerance to Johne's disease in Holstein cattle. Animal Genetics. 42(1):28-38.

Interpretive Summary: Johne’s disease is an infectious disease of cattle caused by infection with the bacterium, Mycobacterium avium subsp. paratuberculosis (Map). A large number of U.S. dairy herds are infected with Map and the dairy industry incurs large economic losses as a result of Johne’s disease. There is often a very long lag between the initial infection of a cow with Map and the onset of visible Johne’s disease symptoms and infected cows can harbor Map in their tissues without shedding the organism in their feces. The objective of this study was to identify areas of the cow genome that are associated with tolerance in cows infected with Map. Tolerance was defined as a cow's fitness at a given level of Map infection intensity. Fitness was measured by Map fecal culture results because of its correlation with mortality and reproductive performance. Map infection intensity was measured by Map culture results generated from sampling of intestinal tissue and associated lymph nodes. A genome-wide association analysis was performed to identify if loci (specific areas of DNA) were associated with tolerance. DNA was extracted from tissue from each animal, and using this DNA, each animal was genotyped with the Illumina BovineSNP50 BeadChip that analyzes single base changes across the cow genome. Four points on the genome were identified as being related to tolerance of Map infection in cattle. This is the first genome-wide association study identifying loci (single points on the cow chromosome) associated with tolerance to an infectious disease in cattle. The identification of loci associated with tolerance to Johne's disease is the first step in identifying the genes involved in the host defense to Map. Once the genes are identified, they may be used to select tolerant animals that are less harmed by Map infection, reduce the transmission of Map to other animals in the herd, and improve profitability.

Technical Abstract: Johne's disease is a bacterial illness caused by Mycobacterium avium subspecies paratuberculosis (Map). The objective of this study was to identify loci associated with genetic tolerance in cows infected with Map. Tolerance was defined as a cow's fitness at a given level of Map infection intensity. Fitness, the ability to survive and reproduce, was measured by Map fecal culture results because of its correlation with mortality and reproductive performance. Map infection intensity was measured by Map culture results generated from sampling of the ileum, ileo-cecal valve, and two ileo-cecal lymph nodes. Tolerance was measured as a quantitative and categorical phenotype. The quantitative phenotype consisted of numerical indexes of the fecal and tissue Map peak (peak tolerance or PT) and average (average tolerance or AT) culture results from 245 Holstein cows. The categorical phenotype consisted of cases with Map tissue infection (>100 cfu/g) and fecal shedding (>75 cfu/g) or controls with Map tissue infection (>100 cfu/g) but low or no fecal shedding (<10 cfu/g). A genome-wide association analysis was performed to identify if loci were associated with the quantitative and categorical phenotypes of tolerance using PLINK (version 1.04). Map was identified in one or more tissues in 94 cows, of which 44 demonstrated substantial Map tissue levels (cfu/g greater than 100) and 36 exhibited Map fecal shedding (cfu/g greater than 1). Poorly performing SNPs and samples were removed leaving genotypes of 45,789 SNPs in 90 animals for the quantitative phenotype, and genotypes of 16 cases and 25 controls for the categorical analysis of tolerance. For the quantitative phenotype of tolerance, rs41748405 on BTA15 was strongly associated with PT (P=1.12x10-7, P=0.005 after Bonferroni correction) and moderately (P=2.17x10-6) associated with AT. Adjacent SNPs, ss61512613 and ss61530518 on BTA6 (P<3.0x10-5) were moderately associated with PT and ss86284768 on BTA1 was moderately associated (P=3.3x10-5) with AT. For the categorical phenotype of tolerance, a moderate association (P<5.0x10-5) with ss86326531 on BTA6 was found. Tolerance is a host defense mechanism which is distinct from resistance. The identification of loci associated with tolerance provides new opportunities to exploit this mechanism to reduce the losses incurred from Johne’s disease.