BOVITA: a first overview on genome-wide genetic diversity of Italian autochthonous cattle breeds

Analysis of genomic data is increasingly becoming part of the livestock industry and is an invaluable resource for effective management of breeding programs in small populations. The recent availability of genome-wide SNP panels allows providing background information concerning genome structure in domestic animals, opening new perspectives to livestock genetics. BOVITA was established to join local efforts and resources for the genomic characterization of Italian local cattle breeds. Despite the growing diffusion of some cosmopolite specialized breeds, several autochthonous breeds are still bred in Italy. The main aim of the BOVITA is to investigate the genomic structure of Italian local cattle breeds, to provide information on their genetic status that will be useful for the management of the genetic variability, as a contribution to biodiversity conservation and prioritization actions. A total of about 800 animals (20-32 per breed) belonging to thirty Italian cattle breeds (Agerolese, Bar\ue0-Pustertaler, Burlina, Cabannina, Calvana, Chianina, Cinisara, Garfagnina, Italian Brown, Italian Holstein, Italian Simmental, Marchigiana, Maremmana, Modenese, Modicana, Mucca Pisana, Pezzata Rossa d\u2019Oropa, Piedmontese, Pinzgau, Podolica, Pontremolese, Pustertaler, Reggiana, Rendena, Romagnola, Rossa Siciliana, Sarda, Sardo-Bruna, Sardo-Modicana and Ottonese-Varzese) and two cosmopolitan breeds (Charolaise and Limousine) genotyped with the Illumina BovineSNP50 v2 BeadChip array were collected for the analysis. The genotypes of several breeds were detected in the frame of the project, whereas for some breeds these data are derived by previous studies. The dataset will be analyzed to: study several aspects of population genetic diversity, multi-dimensional scaling plot, population structure, linkage disequilibrium, and runs of homozygosity. In addition, comparative analysis of conserved haplotypes will be conducted to identify genomic segments under selection pressure. Such information also provides important insights into the mechanisms of evolution and is useful for the annotation of significant functional genomics regions. Data analysis will also be useful to select SNPs suitable for parentage test and breed genetic traceability. The analysis of the data will pinpoint the genetic distinctiveness of Italian breeds. Moreover, the obtained results contribute to a better characterization of history and genetic structure of Italian cattle breeds

Relationship between lactation curve function and phenotypic variance in random regression Test Day models

In Random Regression models (RRM), the most updated version of Test Day (TD) models, the lactation curve is split into a fixed average curve and a random animal specific part (deviation from the average curve) (Schaeffer, 2004). The variance component of the RR coefficients determines the (co) variance function of each pair of days in milk (DIM) (Pool and Meuwissen, 2000)

Fit of different linear models to the lactation curve of Italian water buffalo

Mathematical modelling of lactation curve by suitable functions of time, widely used in the dairy cattle industry, can represent also for buffaloes a fundamental tool for management and breeding decision, where average curves are considered, and for genetic evaluation by random regression models, where individual patterns are fitted

Individual dairy curd production and association analysis with 14 candidate genes in Italian buffalo

The genetic merit of Italian buffaloes is mainly related to theability of producing mozzarella cheese. This trait is measured by the estimated mozzarella production (PK M index) according to Altiero et al. (1989). Several studies have shown that PKM based only on milk yield, fat (FP) and protein percentage (PP) may over-or under- estimate the real mozzarella yield. The individual curd production (ICP) is proposed as index of the mozzarella making ability. Values were compared with estimated PKM. Associations between ICP and 14 loci related to milk traits (ACACA, BLG, CSN1S1, CSN1S2, CSN2, CSN3, LEP, LPL, LTF, OXT, OXTR, PRL, PRLRand SCD) were tested. Idividual milk samples of 233 Italian river buffaloes were collected monthly along the whole lactation. A total o f36 variable swere measured: Fat(FP),protein(PP) and lactose % (LP), milk coagulation properties (r,clottingtime;k20,curd firming time; a30, curd firmness at 30min), SH, pH, Individual Curd Production at 24h (ICP24), etc. Cows were genotyped for published and new SNPs found in the explored genes. Associations between phenotypes and candidate gene polymorphisms were tested using a mixed linear model. Two out of 16 markers in 2 out of 14 investigated genes gave significant associations with ICP24 and FP: OXTR (g.129C>T) and SCD (g.-461A>C). The genotype AC at SCD showed an over-dominance effect with a higher increase vs AA of 13.15 g/kg milk (p=0.015) for ICP24 and + 0.54 FP (p=0.010). The estimated PKM/ICP ratio showed that the PKM under-estimates the prediction of mozzarella yield ( on average 0.929).These data confirm the findings of Parlato and Zicarelli (2015) on the necessity of a new prediction model, and offer useful indication for the application of MAS programs in buffalo

Issues and perspective in dairy sheep breeding

The present review consists of two parts. In the first part, the authors briefly describe the state of the art of breeding programmes for Italian dairy sheep; then they report new models for genetic evaluation and consider the problem of genotype x environment interaction and the impact of farming systems on the genetic merit of animals. In the second part new breeding goals regarding the evolution of milk quality concept and the increasing importance of functional traits are reported. Regarding milk quality, the authors especially focus on the traits related to cheese-making ability and on the nutraceutical aspects of milk. Among functional traits, resistance to diseases (mastitis and Scrapie) has been highlighted for its great importance in livestock species. Finally, the perspectives of marker-assisted selection have also been reported