Insights into Genetic Diversity, Runs of Homozygosity and Heterozygosity-Rich Regions in Maremmana Semi-Feral Cattle Using Pedigree and Genomic Data

SIMPLE SUMMARY: In this study, we estimated genetic diversity in semi-feral Maremmana cattle using both pedigree- and genomic-based approaches, and detected regions of homozygosity (ROH) and heterozygosity (ROHet) in the genome, which are still poorly characterized in the Maremmana breed. A sensitivity analysis on the parameters used to detect ROH and ROHet provided information which can be useful to guide studies on the detection of genomic runs in general, and in semi-feral cattle populations in particular. The average observed and expected heterozygosity were estimated at [Formula: see text] and [Formula: see text] , respectively. Pedigree-based average inbreeding (F) was estimated at [Formula: see text]. A total of [Formula: see text] ROH and [Formula: see text] ROHet were detected in the genomes of the 149 animals included in the study. Genes found to be within the identified ROH and ROHet islands (e.g., KCTD8, GNPDA2) point to phenotypic characteristics related to environmental adaptation and robustness of Maremmana cattle. These results are of important because they will help design and implement breeding and conservation strategies for Maremmana cattle, and provide guidelines for other local cattle breeds. ABSTRACT: Semi-feral local livestock populations, like Maremmana cattle, are the object of renewed interest for the conservation of biological diversity and the preservation and exploitation of unique and potentially relevant genetic material. The aim of this study was to estimate genetic diversity parameters in semi-feral Maremmana cattle using both pedigree- and genomic-based approaches ([Formula: see text] and [Formula: see text]), and to detect regions of homozygosity (ROH) and heterozygosity (ROHet) in the genome. The average heterozygosity estimates were in the range reported for other cattle breeds ([Formula: see text] , [Formula: see text]). Pedigree-based average inbreeding (F) was estimated at [Formula: see text]. The correlation was low between F and genomic-based approaches ([Formula: see text] with [Formula: see text] , [Formula: see text] with [Formula: see text]), while it was higher between [Formula: see text] and [Formula: see text] ([Formula: see text]). The low correlation between F and [Formula: see text] coefficients may be the result of the limited pedigree depth available for the animals involved in this study. The ROH islands identified in Maremmana cattle included candidate genes associated with climate adaptation, carcass traits or the regulation of body weight, fat and energy metabolism. The ROHet islands contained candidate genes associated with nematode resistance and reproduction traits in livestock. The results of this study confirm that genome-based measures like [Formula: see text] may be useful estimators of individual autozygosity, and may provide insights on pedigree-based inbreeding estimates in cases when animals’ pedigree data are unavailable, thus providing a more detailed picture of the genetic diversity.