Genome-wide identification of selection signatures across altitudinal gradients in dairy sheep breeds

Deciphering the genetic mechanisms of adaptation in livestock species is important in ensuring sustainability of livestock production in the context of climatic change. Here, we aimed to identify signatures of selection within Sarda and Valle del Belice, the two major Italian dairy sheep breeds, as well as between their ecotypes raised at three different altitudinal gradients: plain, hill, and mountain. By joinly analyzing the three ecotypes from each breed, we found strong signatures of selection at the KDM6A gene (X chromosome), a key epigenetic regulator involved in modulating gene expression in response to environmental stress. In both breeds, the mountain ecotype showed a strong selection toward several pleiotropic genes with effects linked to the nervous system, body size, energy balance and muscular function and development. Our study also provides evidence that genes involved in neuroendocrine mechanisms are targets of environmental adaptation in the mountain ecotypes, suggesting their fundamental role in the regulation of several vital physiological adaptive responses to mountainous areas in sheep, including growth, energy expenditure, thermogenesis, sensory perception, and locomotor activity. Through the identification of compelling candidate selection targets, our study illustrates how natural selection has contributed to environmental adaptation of sheep to highlands.