Conservation status and rates of inbreeding of Italian autochthonous beef breeds

Albeit the success of commercial beef cattle nowadays, local breeds are an important reservoir of traits that might be crucial to meet future challenges. Genetic analysis is a primary step to study populations in order to elaborate conservation measures and handle inbreeding. This study investigates the population structure of six local cattle beef breeds through pedigree data, namely: Calvana (n = 2798), Mucca Pisana (n = 3339), Pontremolese (n = 328), Sarda (n = 97,163), Sardo Bruna (n = 74,981) and Sardo Modicana (n = 25,355). The current population size of the three Tuscan breeds is extremely low counting: 263 Calvana (37 males and 226 females), 346 Mucca Pisana (52 males and 294 females) and 52 Pontremolese (8 males and 44 females) extant animals. These figures classify Calvana and Pisana as endangered breeds, while Pontremolese as critical breed. Genetic analysis was performed by the ENDOG 4.8 software using pedigree information. To overcome pedigree incompleteness, we estimated the effective population size (Ne) based on the equivalent generations calculated as Σ(1/2)n, where n was the number of generations separating the individual from each of the known ancestors. Pontremolese and Sarda had the lowest Ne (14.62 and 16.64, respectively) while Sardo Modicana the highest value (39.79). The others showed similar Ne, around 19. The average inbreeding coefficient for the Tuscan breeds was 7.25, 5.10 and 3.64 % for Mucca Pisana, Calvana and Pontremolese, respectively. Sardinian breeds showed the smallest values ranging between 1.23% (in Sardo Bruna) to 1.90% (in Sarda). The average generation interval in years was rather high for all breeds, with the lowest value observed in Sardo Modicana (7.8 SD =9.75) and the highest in Sardo Bruna (13.3 SD =16.7). Following Ne, the rates of inbreeding per generation (ΔF = 1/2Ne) were ~2.6% for Calvana, Mucca Pisana and Sardo Bruna, 3% and 3.42% for the Sarda and Pontremolese, respectively, and ~1.26% for Sardo Modicana. This preliminary data suggests the urgency of conservation strategies for the three Tuscan breeds. In the next steps, we will further integrate pedigree and genomic information to (i) explore the population structure and genetic diversity within and between breeds, (ii) identify signatures of selection and (iii) plan assortative matings to control the inbreeding.