Simple SummaryLittle is known about the interdependencies between livestock production and biodiversity. The swine sector is characterized by a diversity of extensive and intensive production practices, which rely on a wide range of natural and manmade activities (e.g., different use of the land) that can reduce its adverse effects on biodiversity. The Nero d’Abruzzo pig is a black domestic pig from the Abruzzo region, Italy, that is reared with extensive practice. This study using a proteomics approach aimed to investigate breed differences between the autochthon Nero d’Abruzzo and commercial-hybrid pigs commonly used by the industry. The comparison of the protein profile of muscle exudate obtained following centrifugation from the diaphragm of the two pig breeds highlight significant differences in the protein expression of a large pool of proteins. Among the proteins that were upregulated or downregulated differently in the two pigs, three—fatty acid synthase, catalase and glutathione peroxidase—may contribute in part to explaining, according to their functions, the phenotypic differences between the pigs. This work has identified a cohort of proteins that can be potentially useful to define new molecular phenotypes for novel applications in pig breeding programs and are of great interest for future work.AbstractCapital-driven animal husbandry systems undertaken in the last century led to the abandoning of many pig breeds that were not profitable. These local pig breeds and their respective production systems have great potential as they are able to respond to the high criteria and needs of modern society concerning some environmental aspects, animal-welfare, healthiness, etc. This is the case of the black pigs of Italy. The Apulo-Calabrese is a breed of black pig, known by many other names such as Nero d’Abruzzo. In order to further understand the biological differences between different types of porcine genetics (Nero d’Abruzzo and commercial-hybrid) we used a label-free LC-MS strategy and Western-blot to characterize the proteomes of muscle-exudate collected from these pigs. This proteomics approach identified 1669 proteins of which 100 changed significantly in abundance between breeds. Bioinformatics functional analysis indicated that differentially expressed proteins were involved in several biological processes related to energy-metabolism and response to oxidative stress, suggesting that these functions might distinguish between these pigs. Fatty-acid synthase, catalase and glutathione-peroxidase, involved in enzymatic activity were found to be more represented in samples obtained from the Nero d’Abruzzo. This biological information can potentially provide new biological factors that could determine the different production performances of these pigs, distinguished by their different genetic backgrounds.