PT  - JOURNAL ARTICLE
AU  - Maria Chiara Fabbri
AU  - Christos Dadousis
AU  - Francesco Tiezzi
AU  - Christian Maltecca
AU  - Emmanuel Lozada-Soto
AU  - Stefano Biffani
AU  - Riccardo Bozzi
TI  - Genetic diversity and population history of eight Italian beef cattle breeds using measures of autozygosity
AID  - 10.1101/2021.02.22.432240
DP  - 2021 Jan 01
TA  - bioRxiv
PG  - 2021.02.22.432240
4099  - http://biorxiv.org/content/early/2021/02/22/2021.02.22.432240.short
4100  - http://biorxiv.org/content/early/2021/02/22/2021.02.22.432240.full
AB  - In the present study, GeneSeek GGP-LDv4 33k single nucleotide polymorphism chip was used to detect runs of homozygosity (ROH) in eight Italian beef cattle breeds; six breeds with distribution limited to Tuscany (Calvana, Mucca Pisana, Pontremolese) or Sardinia (Sarda, Sardo Bruna and Sardo Modicana) and two cosmopolitan breeds (Charolais and Limousine). ROH detection analyses were used to estimate autozygosity and inbreeding and to identify genomic regions with high frequency of ROH, which might reflect selection signatures. Comparative analysis among breeds revealed differences in length and distribution of ROH and inbreeding levels. The Charolais, Limousine, Sarda, and Sardo Bruna breeds were found to have a high frequency of short ROH (30.000); Calvana and Mucca Pisana presented also runs longer than 16 Mbp. The highest level of average genomic inbreeding was observed in Tuscan breeds, around 0.3, while Sardinian and cosmopolitan breeds showed values around 0.2. The population structure and genetic distances were analyzed through principal component analysis and multidimensional scaling analysis, and resulted in a clear separation among the breeds, with clusters related to productive purposes and sample sizes. The frequency of ROH occurrence revealed eight breed-specific genomic regions where genes of potential selective and conservative interest are located (e.g. MYOG, Chitinases (BTA16), TIMELESS, APOF, Olfactory receptors, CACNG2 (BTA5) and Collagens (BTA2)). In all breeds, we found the largest proportion of homozygous by descent segments to be those that represent inbreeding events that occurred around 32 generations ago; with Tuscan breeds also having a significant proportion of segments relating to more recent inbreeding.