Genetics overview


The Genes and Markers programme was aimed at providing tools for breeding animals that were more genetically resistant to Johne’s Disease (JD). Evidence suggests that some animals are more resistant to the disease than others. This investment was to develop knowledge of genetics as a a potential method for disease control.

DNA was collected and genotyped from approximately 2000 dairy cows and 1000 deer affected by JD. In dairy cattle researchers identified a set of markers for Johne’s that were developed into a predictive test for Johne's Disease Susceptibility (JDS). The test was commercialised by Livestock Improvement Corporation in 2015. Validation studies have indicated that substantial work would be required to maintain the predictability of the test over time which has reduced its commercial viability. Work continues to develop a similar test for susceptibility in deer.

Deer were used as the target species for the early stage investigation of novel markers for resistance and susceptibility from macrophages and for the purposes of a gene expression study which used DNA sequencing to identify genes whose expression was associated with resistance to JD. In both projects researchers successfully used cutting edge techniques to develop fundamental information about genetic markers.

Dairy DNA collection and genome wide association studies


  • Milestone 1 - Validation of milk ELISA for detection of Johne’s Disease in dairy cows. LIC, March 2009. Download here.
  • Milestones 2 and 3 – Validation of milk ELISA for detection of Johne’s Disease in dairy cows.  LIC, June 2009. Download here.
  • LIC report for the 2011 JDRC Science Review. LIC. 2011. Download here.
  • Effect of Johne’s disease on milk production and estimation of genetic parameters for incidence of Johne’s disease in New Zealand dairy cattle.  PJ Back and N Lopez-Villalobos. 2011. Download here.
  • LIC Report for the JDRC. Ric Sherlock. 2013. Download here.
  • LIC Report for the JDRC. Ric Sherlock. December 2014. Download here.
  • Validation study Report. Ric Sherlock. November 2015. Download here.
  • Identifying the genomic basis of Johne’s disease in the New Zealand dairy population. Sarah Loker, Hinrich Voges, Ric Sherlock and Richard Spelman. Download here, here and here.

Papers/ Proceedings

  • Whole Genome Association Analysis of Susceptibility to Paratuberculosis in New Zealand Dairy Cattle.  Ric Sherlock.  Proceedings of the Association for the Advancement of Animal Breeding and Genetics 20th Conference, 2013. Download here.
  • Predicting Susceptibility to Johne’s Disease in New Zealand Dairy Cattle.  R.G. Sherlock  10th World Congress of Genetics Applied to Livestock Production. Download here.


  • Farmer Update: Johne’s Disease Pilot trial.  LIC 2009. Download here.
  • Bovine DNA Archive – Genomics Study. LIC. 2009. Download here.
  • Johne’s Disease in the New Zealand Dairy Herd - A Decade of Dairy Cow Culling Records. Hinrich Voges, 2009. Download here.
  • Evaluation of a JD bulk milk ELISA as a herd screening tool in NZ dairy herds.  Hinrich Voges, 2009. Download here.
  • Johnes Disease Project Update. Penny Back. May 2011. Download here.

Deer DNA collection and genome wide association studies

  • Developing a DNA Test for Johne’s Resistance in Deer.  Allan Crawford. Science Presentation, Wellington, April, 2011. Download here.
  • Final Report Archive of cervine DNA Milestone # 4.1.1.  Allan Crawford.  March 2011. Download here.

Gene expression study in deer


  • 2011 Milestone report. Colin Mackintosh. 2011. Download here.
  • Final Report for Milestone 4.2. Colin Mackintosh, AgResearch, 2012. Download here.
  • Review of Genetics of host resistance/susceptibility to paratuberculosis.  Colin Mackintosh, AgResearch 2012. Download here.


  • Gene expression in deer resistant or susceptible to Johne’s disease: Preliminary findings, Colin Mackintosh, Proceedings of the Deer Branch of the NZVA, 2011. Read more. 
  • Gene Expression in Red Deer Resistant or Susceptible to Map.  Colin Mackintosh, 11th Colloquium of Paratuberculosis, Australia 2012. Download here.
  • Longitudinal Pathogenesis Study of Young Red Deer (Cervus elaphus ) after Experimental Challenge with Mycobacterium avium subsp. Paratuberculosis (MAP).  Colin Mackintosh Veterinary Medicine International.  Volume 2012, Article ID 931948, 8 pages. Read more.
  • Immunological and pathological responses of red deer resistant or susceptible genotypes to experimental challenge. C.G. Mackintosh Veterinary Immunology and Immunology, 143, 1-2, 131-142, September 2011. Read more.
  • SOLiD SAGE sequencing shows differential gene expression in jejunal lymph node samples of resistant and susceptible red deer (Cervus elaphus) challenged with Mycobacterium avium subsp. Paratuberculosis.  Mackintosh CG, Veterinary Immunology and Immunology. 169, 102-110, January 2016. Read more.


  • SOLiD-SAGE analysis of the Deer Transcriptome. Rudiger Banning, 2012. Download here.
  • Gene Expression in Deer Resistant or Susceptible to Johne’s Disease. Colin Mackintosh, 2012. Download here.
  • Heritable resistance/susceptibility of red deer to challenge with Mycobacterium avium subsp. Paratuberculosis. Colin Mackintosh. Download here.

Novel markers for resistance and susceptibility in deer


  • 2011 Milestone Report for Novel Molecular Markers. Griffin 2011. Download here.


  • Innate immune markers that distinguish red deer (Cervus elaphus) selected for resistant or susceptible genotypes for Johne’s disease. Dobson et al. Veterinary Research 2013, 44:5. Read more.


  • Diagnosis and Intervention to control Paratuberculosis in Farmed Deer.  New technologies for Old diseases.  Frank Griffin, Rory O’Brien, Simon Liggett, Disease Research Laboratory, University of Otago. Download here.
  • Novel Molecular Markers.  Rory O’Brien. Disease Research Laboratory, University of Otago. Download here.