Stage of lactation, parity, breed, milk composition, and minerals affect the nonenzymatic antioxidant activity of sheep milk.

The aims of this study were to (1) characterize sheep milk for nonenzymatic antioxidant activity via 2 different assays, namely the ferric reducing antioxidant power (FRAP) and the 2,2-diphenyl-1-picryl-hydrazyl-hydrate (DPPH), and (2) investigate the effect of milk composition and animal-related parameters on these 2 assays by using the generalized additive mixed model (GAMM) approach. A total of 740 ewes belonging to the Massese and Comisana breeds were sampled once during the morning milking across 11 sampling sessions. All milk samples were analyzed for fat, protein, CN, and lactose, SCS, and minerals (Ca, Mg, Na, and Cl).

Microsatellite imputation using SNP data for parentage verification in four Italian sheep breeds.

Microsatellite markers (MS) have been widely used for parentage verification in most of the livestock species over the past decades mainly due to their high polymorphic information content. In the genomic era, the spread of genotype information as single-nucleotide polymorphism (SNP) has raised the question to effectively use SNPs also for parentage testing. Despite the clear advantages of SNP panels in terms of cost, accuracy, and automation, the transition from MS to SNP markers for parentage verification is still very slow and, so far, only routinely applied in cattle.

Genetic evaluation of gestation length in Italian Holstein breed.

Gestation length (GL) can potentially affect health and performance of both the dam and the newborn calf, and it is controlled by two genetic components, direct and maternal. This means that both the calf (direct effect) and the cow (maternal effect) genotypes contribute to determine GL and its variability. The aims of the present study were to estimate direct and maternal variance components of GL, develop a routine genetic evaluation of GL in Italian Holstein and evaluate potential (un)favourable associations with traits for which selection is undertaken in this population.

Integration of beef cattle international pedigree and genomic estimated breeding values into national evaluations, with an application to the Italian Limousin population.

Background: International evaluations combine data from different countries allowing breeders to have access to larger panels of elite bulls and to increase the accuracy of estimated breeding values (EBV). However, international and national evaluations can use different sources of information to compute EBV (EBV and EBV, respectively), leading to differences between them. Choosing one of these EBV results in losing the information that is contained only in the discarded EBV.

Using Pedigree and Genomic Data toward Better Management of Inbreeding in Italian Dairy Sheep and Goat Breeds.

The inbreeding coefficient is an important parameter for livestock management. Small ruminant breeders and associations mainly rely on pedigree information, but genomic tools are gaining relevance, overcoming possible pedigree inconsistencies. This study investigates the relationship between pedigree-based and genomic inbreeding in two goat and four sheep dairy breeds.

Machine Learning Algorithms Highlight tRNA Information Content and Chargaff's Second Parity Rule Score as Important Features in Discriminating Probiotics from Non-Probiotics.

Probiotic bacteria are microorganisms with beneficial effects on human health and are currently used in numerous food supplements. However, no selection process is able to effectively distinguish probiotics from non-probiotic organisms on the basis of their genomic characteristics. In the current study, four Machine Learning algorithms were employed to accurately identify probiotic bacteria based on their DNA characteristics.

Relationship among Milk Conductivity, Production Traits, and Somatic Cell Score in the Italian Mediterranean Buffalo.

The measurement of milk electrical conductivity (EC) is a relatively simple and inexpensive technique that has been evaluated as a routine method for the diagnosis of mastitis in dairy farms. The aim of this study was to obtain further knowledge on relationships between EC, production traits and somatic cell count (SCC) in Italian Mediterranean Buffalo. The original dataset included 5411 records collected from 808 buffalo cows.

Automated image analysis to assess hygienic behaviour of honeybees.

Focus of this study is to design an automated image processing pipeline for handling uncontrolled acquisition conditions of images acquired in the field. The pipeline has been tested on the automated identification and count of uncapped brood cells in honeybee (Apis Mellifera) comb images to reduce the workload of beekeepers during the study of the hygienic behavior of honeybee colonies. The images used to develop and test the model were acquired by beekeepers on different days and hours in summer 2020 and under uncontrolled conditions.

Genetic diversity and population history of eight Italian beef cattle breeds using measures of autozygosity.

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.

Effects of Heated Drinking Water on the Growth Performance and Rumen Functionality of Fattening Charolaise Beef Cattle in Winter.

The effects of heated drinking water on growth performance and rumen functionality in fattening beef cattle during winter were evaluated. Newly received Charolaise bulls ( = 224) were allocated to two experimental groups: (i) water at room temperature (RTW) (weight 408 ± 34 kg); (ii) constantly heated water (25 °C) (HW) (weight 405 ± 38 kg). Growth performances, feed intake, feed conversion rate, water intake and carcass characteristics were evaluated.

Effect of Weeping Teats on Intramammary Infection and Somatic Cell Score in Dairy Goats.

Mastitis is the most common disease affecting dairy goats and causing economic losses. Although it is accepted that increased somatic cell count (SCC) is mainly a response to infection, its reliability for subclinical mastitis detection in goats is controversial. Indeed, many physiological and extrinsic variables can increase SCC, including breed, parity, age, stage of lactation, seasonal variations, and milking methods.

Comparison of machine learning methods to predict udder health status based on somatic cell counts in dairy cows.

Bovine mastitis is one of the most important economic and health issues in dairy farms. Data collection during routine recording procedures and access to large datasets have shed the light on the possibility to use trained machine learning algorithms to predict the udder health status of cows. In this study, we compared eight different machine learning methods (Linear Discriminant Analysis, Generalized Linear Model with logit link function, Naïve Bayes, Classification and Regression Trees, k-Nearest Neighbors, Support Vector Machines, Random Forest and Neural Network) to predict udder health status of cows based on somatic cell counts.

Accounting for Genetic Differences Among Unknown Parents in : A Case Study From the Italian Mediterranean Buffalo.

The use of genetic evaluations in the Water Buffalo by means of a Best Linear Unbiased Prediction (BLUP) animal model has been increased over the last two-decades across several countries. However, natural mating is still a common reproductive strategy that can increase the proportion of missing pedigree information. The inclusion of genetic groups in variance component (VC) and breeding value (EBV) estimation is a possible solution.

'Meta-analysis of dry matter intake and neutral detergent fiber intake of hair sheep raised in tropical areas'.

Inadequate estimates of fiber and dry matter intake of sheep raised in tropical conditions may explain part of the inefficiency of those production systems. Therefore, we aimed to estimate dry matter intake (DMI) and neutral detergent fiber intake (NDFI) of hair sheep raised under tropical conditions. A meta-analysis of 61 independent performance experiments, comprising a total of 413 experimental units (treatment means or animals), was performed.

Heritability of Teat Condition in Italian Holstein Friesian and Its Relationship with Milk Production and Somatic Cell Score.

In spite of the impressive advancements observed on both management and genetic factors, udder health still represents one of most demanding objectives to be attained in the dairy cattle industry. Udder morphology and especially teat condition might represent the first physical barrier to pathogens' access. The objectives of this study were to investigate the genetic component of teat condition and to elucidate its relationship with both milk yield and somatic cell scores in dairy cattle.

Genetic parameters of weeping teats in Italian Saanen and Alpine dairy goats and their relationship with milk production and somatic cell score.

This paper reports a quantitative genetics analysis of weeping teats (WT), an abnormality of the mammary gland in goats. Weeping teats are characterized by milk oozing out of the teat or by the presence of multiple cysts near its base. This abnormality has been routinely recorded in Italian Alpine and Saanen goats since 2000 using a score of 0 or 1 (0 = defect not present, 1 = defect present).

Population Structure and Genetic Diversity of Italian Beef Breeds as a Tool for Planning Conservation and Selection Strategies.

The aim was to investigate the population structure of eight beef breeds: three local Tuscan breeds under extinction, Calvana (CAL), Mucca Pisana (MUP), and Pontremolese (PON); three local unselected breeds reared in Sardinia, Sarda (SAR), Sardo Bruna (SAB), and Sardo Modicana (SAM); and two cosmopolitan breeds, Charolais (CHA) and Limousine (LIM), reared in the same regions. An effective population size ranges between 14.62 (PON) to 39.

Rumination time as a potential predictor of common diseases in high-productive Holstein dairy cows.

We examined the hypothesis that rumination time (RT) could serve as a useful predictor of various common diseases of high producing dairy cows and hence improve herd management and animal wellbeing. We measured the changes in rumination time (RT) in the days before the recording of diseases (specifically: mastitis, reproductive system diseases, locomotor system issues, and gastroenteric diseases). We built predictive models to assess the association between RT and these diseases, using the former as the outcome variable, and to study the effects of the latter on the former.

Design and validation of a 90K SNP genotyping assay for the water buffalo (Bubalus bubalis).

Background: The availability of the bovine genome sequence and SNP panels has improved various genomic analyses, from exploring genetic diversity to aiding genetic selection. However, few of the SNP on the bovine chips are polymorphic in buffalo, therefore a panel of single nucleotide DNA markers exclusive for buffalo was necessary for molecular genetic analyses and to develop genomic selection approaches for water buffalo. The creation of a 90K SNP panel for river buffalo and testing in a genome wide association study for milk production is described here.

The effect of mislabeled phenotypic status on the identification of mutation-carriers from SNP genotypes in dairy cattle.

Background: Statistical and machine learning applications are increasingly popular in animal breeding and genetics, especially to compute genomic predictions for phenotypes of interest. Noise (errors) in the data may have a negative impact on the accuracy of predictions. The effects of noisy data have been investigated in genome-wide association studies for case-control experiments, and in genomic predictions for binary traits in plants.

Virulence Genes of S. aureus from Dairy Cow Mastitis and Contagiousness Risk.

() is a major agent of dairy cow intramammary infections: the different prevalences of mastitis reported might be related to a combination of virulence factors beyond host factors. The present study considered 169 isolates from different Italian dairy herds that were classified into four groups based on the prevalence of infection at the first testing: low prevalence (LP), medium-low (MLP), medium-high (MHP) and high (HP). We aimed to correlate the presence of virulence genes with the prevalence of intramammary infections in order to develop new strategies for the control of mastitis.

Identification of candidate genes for paratuberculosis resistance in the native Italian Garfagnina goat breed.

Paratuberculosis disease is a chronic bacterial disease infection of ruminants of global relevance, caused by MAP (Mycobacterium avium subsp. paratuberculosis). The present study was conducted on the Garfagnina goat breed that is an Italian native goat population registered on the Tuscan regional repertory of genetic resources at risk of extinction.

Use of SNP genotypes to identify carriers of harmful recessive mutations in cattle populations.

Background: SNP (single nucleotide polymorphisms) genotype data are increasingly available in cattle populations and, among other things, can be used to predict carriers of specific mutations. It is therefore convenient to have a practical statistical method for the accurate classification of individuals into carriers and non-carriers. In this paper, we compared - through cross-validation- five classification models (Lasso-penalized logistic regression -Lasso, Support Vector Machines with either linear or radial kernel -SVML and SVMR, k-nearest neighbors -KNN, and multi-allelic gene prediction -MAG), for the identification of carriers of the TUBD1 recessive mutation on BTA19 (Bos taurus autosome 19), known to be associated with high calf mortality.