The study, the first of its kind for any United Kingdom (UK) pig breed, has identified unique genetic markers for the Lop breed which has been reduced to an effective breeding population of about 40 to 45 hogs.
While there is genetic diversity within the breed, there is also a high level of genomic inbreeding, the study revealed.
The findings reinforce the need for robust measures to tackle in-breeding and prevent any further decrease in breeding population, the researchers said.
Originating in the West Country, the Lop - a white pig with distinctive lop ears that touch the end of its nose - is one of the rarest native breeds of pig in the UK.
The genome study was commissioned by the Rare Breeds Survival Trust in conjunction with the British Lop Pig Society.