Comparative analysis of heterozygosity-enriched regions in two autochthonous Italian cattle breeds.

Reggiana and Modenese are autochthonous cattle breeds mainly reared in Emilia Romagna region, in the North of Italy. The production of two breed-branded Parmigiano-Reggiano cheeses assures the sustainable conservation of these cattle genetic resources. Both breeds experienced a reduction in population size in the 1980’, followed by a slow recovery. Therefore, the monitoring of inbreeding and the definition of proper conservation programs are fundamental. Information derived from pedigree and from genomic regions based on runs of homozygosity had previously been evaluated for both breeds. Here, we explored Runs of Heterozygosity (ROHet), defined as regions of continuous single nucleotide polymorphisms (SNPs) with heterozygous genotype. In this work, almost two thirds of the actual population for both breeds have been genotyped with the GGP Bovine 150k SNP chip panel. ROHet were identified with the R package ‘detectRuns’ and ROHet islands were defined by analysing the proportion of SNPs occurring in ROHet over all genotyped cattle. The average number of ROHet in Reggiana and Modenese cattle was 14.24±3.8 and 12.91±3.3, respectively. The average length of the genome covered by ROHet was 2,532.38±858 kb in Reggiana cattle and 2,291.26±781 kb in Modenese cattle. According to the functional annotation of the ROHet islands, these regions might have an impact on reproduction and other fitness-related traits. Results will be useful to dissect genetic mechanisms affecting breed-specific traits and define breeding and conservation programmes to further exploit these animal genetic resources. Acknowledgements: The research was funded by the PSRN (Programma di Sviluppo Rurale Nazionale) Dual Breeding 2 (co-funded by the European Agricultural Fund for Rural Development of the European Union and by the MASAF).