Comparative analysis of heterozygosity-enriched regions in Reggiana and Modenese genomes providesinformation on local cattle breed specific variabilit.

Reggiana and Modenese are dual-purpose cattle breeds mainly reared in the North of Italy and linked to the production of monobreed branded Parmigiano-Reggiano cheese, which provides the economic income to the farmers that is needed for the sustainable conservation of these autochthonous breeds. The population size of these breeds experienced a drastic reduction in the 1980’ and a subsequent slow recovery. Inbreeding is an important parameter that should be monitored to define appropriate conservation programs of local genetic resources. We therefore already evaluated inbreeding in these breeds using pedigree and genomic information based on runs of homozygosity (ROH). Hotspot regions of heterozygosity may be useful to define other relevant population genomic information. Runs of Heterozygosity (ROHet) are regions of continuous single nucleotide polymorphisms (SNPs) with heterozygous genotype. In this study, we obtained a genomic landscape picture of ROHet in Reggiana and Modenese cattle breeds and identified ROHet islands. A total of 2730 Reggiana cows and 564 Modenese cattle (almost two thirds of the actual population for both breeds) were genotyped with the GGP Bovine 150K SNPchip. Quality filters were applied with PLINK1.9. ROHet were identified with detectRuns R package. In total, 38942 and 7289 ROHet were identified in Reggiana and Modenese cattle populations, respectively. The average number of ROHet per animal in Reggiana was 14.24±3.8, with a minimum of 1 ROHet and a maximum of 30. In Modenese breed, the average number of ROHet per animal was 12.91±3.3, with a minimum of 1 and a maximum of 23. For Reggiana, the longest ROHet was on chromosome BTA10, with a length of 1029 kb, while for Modenese the longest ROHet was on BTA21 and measured 1228 kb. The total average size of the genome covered by ROHet for each animal was 2532.38±858 and 2291.26±781 kb in Reggiana and Modenese, respectively. These regions included many genes involved in fecundity, survival, and fitness-related traits that might be involved in defining breed genetic features. 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).