This is thought to be a world-first for any species or breed of livestock.
University of Otago immunologist Prof Frank Griffin said the term resilient was chosen carefully.
Unlike resistance, which was the ability to remain free from infection, resilience was the ability to stay healthy and productive following exposure to a specific infectious pathogen.
Johnes is widespread in dairy herds and sheep flocks around the world and is a problem in many New Zealand deer herds, where it can cause major losses in young stock.
There is no effective treatment.
Control has normally only been by culling affected animals.
Prof Griffin, who has spent a lifetime working on the management of Tb and Johnes disease in deer, said culling of susceptible animals and the selection of resilient bloodlines offered the best long-term prospects for the control of the disease.
After Peel Forest diagnosed Johnes disease in 2000, owner Graham Carr approached Prof Griffin.
He had a number of valuable bloodlines that would be lost to the industry unless he could assure potential buyers that they were free from the disease.
He said Peel Forests' comprehensive pedigree database helped his group identify susceptible and resilient bloodlines, assisted by postmortem data from culled animals.
The stud had been involved in embryo transfer programmes and had eight extremely pure bloodlines, providing an opportunity for genetic study that Prof Griffin believed was unprecedented for domestic livestock.
It had produced some of the most useful information Prof Griffin had seen in 40 years of research.
The study found resilience to the disease had a genetic basis and was linked to certain bloodlines.
For example, a bloodline called B11 was extremely resilient and by chance was also associated with high breeding values for weight gain.
Prof Griffin believed resilient animals posed either no risk or a significantly lower risk for the spread of the disease.
But he said he could not be definitive, because he did not have the proof, and that would be extremely costly and time-consuming to obtain.
Graham Carr sells all his stags as 3 year-olds, and while no test was perfect, stags were given three consecutive annual blood-tests showing them to be free of the disease.
He said getting to this point had cost Peel Forest a small fortune in the culling of apparently healthy animals because they did not have the genetics for resilience, and the inability to sell stags and breeding hinds, the stud's core business.
But, as with any farm that got Johnes, the issue had to be confronted and a strategy adopted to get on top of it.
Now, the point had been reached where he said Peel Forest could help other farmers who were trying to live with the disease in their herds.
Mr Carr could not claim he had reached the ultimate goal of breeding 100% resilient animals, but said he was well down the track.
Farmers who had Johnes disease on their properties now could get stags from Mr Carr that would help, he said.
The stags would cope with exposure to the disease and their progeny would help build heritable resilience in their herd.
Mr Carr said Peel Forest Estate was one of the first deer studs to adopt deer breeding values (DBVs) as a basis for the selection of highly productive animals and this remained very important.
But having had exposure to Johnes disease, he was now treating resilience as equally important.
DBVs were important but whether they were breeding for finishing or replacements, farmers needed high performance animals that were fit for their farming environment and unfortunately for many of them, that environment included Johnes disease.