In the last 50 years, the diversity of cattle breeds has experienced a severe contraction. However, in spite of the growing diffusion of cosmopolite specialized breeds, several local cattle breeds are still farmed in Italy. Genetic characterization of breeds represents an essential step to guide decisions in the management of farm animal genetic resources. The aim of this work was to provide a high-resolution representation of the genome-wide diversity and population structure of Italian local cattle breeds using a medium-density single nucleotide polymorphism (SNP) array. After quality control filtering, the dataset included 31,013 SNPs for 800 samples from 32 breeds. Our results on the genetic diversity of these breeds agree largely with their recorded history. We observed a low level of genetic diversity, which together with the small size of the effective populations, confirmed that several breeds are threatened with extinction. According to the analysis of runs of homozygosity, evidence of recent inbreeding was strong in some local breeds, such as Garfagnina, Mucca Pisana and Pontremolese. Patterns of genetic differentiation, shared ancestry, admixture events, and the phylogenetic tree, all suggest the presence of gene flow, in particular among breeds that originate from the same geographical area, such as the Sicilian breeds. In spite of the complex admixture events that most Italian cattle breeds have experienced, they have preserved distinctive characteristics and can be clearly discriminated, which is probably due to differences in genetic origin, environment, genetic isolation and inbreeding. This study is the first exhaustive genome-wide analysis of the diversity of Italian cattle breeds. The results are of significant importance because they will help design and implement conservation strategies. Indeed, efforts to maintain genetic diversity in these breeds are needed. Improvement of systems to record and monitor inbreeding in these breeds may contribute to their in situ conservation and, in view of this, the availability of genomic data is a fundamental resource.

The Maremmano horse is considered one of the most important Italian warmblood breeds which originated from an ancient population. In 1980, the National Association of Maremmano Breeders established the first Studbook that recorded 440 dams and four sire founders. In this study, we selected the most significant maternal lines in terms of offspring (for a total of 74 lineages and 92 Maremmano horses) and analyzed their mitochondrial DNA control regions. We found a high variability, reflecting the importance of this local breed as a genetic resource to be preserved. Through multiple sampling, we then verified the pedigree information for 12 dam lines by matching genealogical data with mitochondrial haplotypes. A complete concordance was demonstrated in nine lineages, while for the other we highlighted a different number of haplotypes for each line (three in Fiorella, two in Nizza I, and two in Pomposina), thus suggesting that the information recorded in the Studbook could be wrong and the samples do not descend from the same maternal founder. Our combined analysis provides the opportunity to confirm the ancestry of animals and could be employed to prevent errors in pedigree data also for other breeds and species.

The purpose of this study was to estimate the heritability and genetic correlations of four biometric measurements and an overall score (OS) in the Sardinian Anglo-Arab horse (SAA); moreover, the effect of inbreeding on these traits was investigated. A dataset with 43,624 horses (27,052 females and 16,572 males) was provided by the Agricultural Research Agency of Sardinia (AGRIS). Cannon bone circumference (BC), chest girth (CG), shoulder length (SL), and withers height (WH) were measured on 6033 SAA horses born in Sardinia between 1967 and 2005; beside the measurements, an overall score (OS) was taken comparing the morphology of each horse to an “ideal type” that is scored out of 100. The mean value is 20.5 cm for BC, 185.9 cm for CG, 67.6 cm for SL, 160.8 cm for WH, and 73.2 for the OS. The heritability estimates ranged from 0.78 to 0.23. The results allow to foresee high genetic progress through the breeding programs. The most affected trait by the inbreeding rate seems to only be the withers height.

The availability of a large amount of SNP markers throughout the genome of different livestock species offers the opportunity to estimate genomic breeding values (GEBVs). However, the estimation of many effects in a data set of limited size represent a severe statistical problem. A pre-selection of SNPS based on single regression may provide a reasonable compromise between accuracy of results, number of independent variables to be considered and computing requirements. A total of 595 and 618 SNPS were pre-selected using a simple linear regression for each SNP, based on phenotypes or polygenic EBVs, respectively, with an average distance of 9–10 cM between them. Chromosome four had the largest frequency of selected SNPS. Average correlations between GEBVs and TBVs were about 0.82 and 0.73 for the TRAINING generations when phenotypes or polygenic EBVs were considered as dependent variable, whereas they tend to decrease to 0.66 and 0.54 for the PREDICTION generations. The pre-selection of SNPs using the phenotypes as dependent variable together with a BLUP estimation of marker genotype effects using a variance contribution of each marker equal to σ2a/nsnps resulted in a remarkable accuracy of GEBV estimation (0.77) in the PREDICTION generations.

The Sella Italiano stallions are selected by 100-day perfomance test, but many breeders organisations use station test of shorter length. In twelve editions, 17,394 ten-point scores both for character and gaits, and 6291 scores for jumping were assigned to 314 candidate stallions. By means of the comparison of univariate EBVs, calculated from the complete dataset or from the reduced subsets, a dataset lasting only from 33rd day to 78th day of the training period was selected: it included less than 70% of the original data. The subset was validated by 3-trait AM BLUP: there were no evident effects on the estimates of variance component or ratio, and the aggregated selection index for the three traits showed a 99% rank correlation with the official index. These findings demonstrate that the training period could be reduced without affecting the genetic progress in the Sella Italiano breed.