Genome - wide search of distinctiveness selection signatures in Maremmana cattle compared to Italian Podolian-derived breeds

Several Italian breeds such as Marchigiana, Romagnola, Chianina, Calvana, Podolica, Cinisara, Modicana and Maremmana belong to the so-called ‘Podolian’ group. The Maremmana is one of the most distinctive cattle breeds because it is raised in semi-feral conditions and it still displays many ancestral features such as horn shape and size, sexual dimorphism and longevity. The aim of this study was to map genomic regions that might explain the phenotypic distinctiveness observed in Maremmana cattle compared to the other Podolian-derived Italian breeds. Putative selection signatures in Maremmana were investigated using genotypes generated for 146 Maremmana and 174 individuals belonging to Podolian-derived Italian breeds using the Bovine SNP50K v2 BeadChip and combining three statistical approaches designed to quantify the excess of haplotype homozygosity either within (iHS) or among pairs of populations (Rsb and XP-EHH). We used−log10(p-value)=2.5 as a threshold to define significant iHS, Rsb and XP-EHH candidate regions. Multidimensional scaling and neighbor-joining tree revealed a clear separation between Maremmana and the other Podolian-derived breeds. Overall, the three haplotype-based analyses revealed selection signatures distributed over 19 genomic regions. Of these, six regions spanning 87 known genes, were identified by at least two approaches. Within these regions, we found genomic signatures of selective sweeps spanning genes related to muscle development, growth and meat traits (SCIN, THSD7A, ETV1, UCHL1 and MYOD1) which reflects the different breeding schemes between Maremmana and the other Podolian-derived breeds. We also identified several genes possibly linked to Maremmana adaptation to the environment of the western central part of Italy, known to be hyperendemic for malaria and other tick-borne diseases. These include several chemokine (C–C motif) ligand genes crucially involved in both innate and adaptive immune responses to intracellular parasite infections and other genes playing key roles in pulmonary disease (HEATR9, MMP28, ASIC2) or strongly associated with malaria resistance/susceptibility (AP2B1). Information about the location of these regions can be used to detect variants that may underlie important traits of practical interest for the beef industry as well as to enhance our understanding of the genomic basis of the millenarian environmental adaptation of Maremmana to the semi-wild conditions of its rearing cradle.