A Label-Free Quantitative Analysis for the Search of Proteomic Differences between Goat Breeds

Simple Summary Biodiversity conservation is one of the most relevant current issues. The safeguarding of genetic resources of autochthon farm animals at risk of extinction, such as the Teramana goat, reflects the enhancement of the relative animal productions, in order to highlight the peculiarities that can induce breeders to devote themselves to a specific type of breeding and that can attract the interests of potential consumers. Recent advances in proteomics and bioinformatics tools offer the potential to investigate breed differences at the level of proteins (proteome) and consequently in terms of the biological processes and molecular functions of the specific breed under study. However, there is a lack of information on the potentiality of autochthonous breeds such as the Teramana goat. Therefore, in this study, a global differential proteomic experiment was carried out with the purpose of identifying variations in the expression of muscle proteins between the autochthon Teramana goat and the breed commonly used by the industry, Saanen. The results showed a difference in the expression pattern of 41 proteins that clearly separate the two breeds (underlying genetic differences), highlighting biological features that could influence the productivity, resilience and other traits of these animals. The intensification and standardization of livestock farming are causing a decline in the number of animal breeds in many species, such as the goat. The availability of more studies on the potentiality of goat breeds could raise awareness of their importance, conservation and productive possibilities. Label-free quantitative analysis was applied in this study to investigate the proteomic differences between the autochthon Teramana and Saanen goats that could be useful for defining peculiar features of these breeds. A total of 2093 proteins were characterized in the muscle exudate proteome of the Teramana and Saanen breeds. A total of 41 proteins clearly separated the two breeds. Eukaryotic initiation factor proteins and aldehyde-dehydrogenase 7 family-member A1 were up-regulated in the autochthon breed and associated with its resilience, whereas catalase was down-regulated and associated with lower muscular mass. This study is the most detailed report of goat muscle proteome. Several differentially regulated proteins between the two breeds were identified, providing insights into functional pathways that define this organism and its biology.