Genome-wide diversity of Pagliarola sheep residual population and its conservation implication

Local breeds represent an underestimated resource in terms not only of their important cultural and economical role in marginal areas, but also because they often own a potential genetic pool well adapted to extreme conditions. This fact is of increasing interest, especially when considering climate global challenges where peculiar and uncommon traits could be advantageous. In this study, we genotyped 24 individuals belonging to the small residual Pagliarola sheep population using the OvineSNP50K array, in order to compare its genomic architecture with other 21 Italian local breeds. Moreover, we performed the fixation index (FST) outlier analysis to identify genes most differentiated between Pagliarola and Merino-derived Italian breeds. All population genetic analyses highlighted that Pagliarola breed represents a distinct genetic unit showing a genetic relationship with Merino-derived breeds underlying the close cultural connection between these breeds related to transhumance. However, Pagliarola breed resulted to be divided into two different sub-populations, named Pagliarola 1 (PAG-1) and Pagliarola 2 (PAG-2). Genetic diversity indices and inbreeding estimated from runs of homozygosity (FROH) indicated that while PAG-1 showed among the highest values, PAG-2 turned out strongly inbred, probably as a consequence of a founder effect. The FST outlier analysis identified the 5 most differentiated single nucleotide polymorphisms, two of which mapping within known genes (MACF1 and GLIS1) reported to be linked to feed efficiency and local adaption. All these information strongly suggest that proper conservation measures should be implemented in order to recover the Pagliarola population and its fundamental local products.HIGHLIGHTS All population genetic analyses highlighted that Pagliarola breed represent a distinct genetic unit, and clusters with the Merino-derived Italian breeds. The breed resulted to be divided into two different sub-populations. For the two Pagliarola sub-populations, the genetic diversity indices suggest a very different genetic makeup. Results from the Bayesian approach identified two know genes (MACF1and GLIS1) related to feed efficiency in livestock species and local adaptation. The information generated in this study strongly suggests that proper conservation measures should be implemented in order to recover the Pagliarola population.