Relationships between European carcass evaluation and Meat Standards Australia grading scheme applied to young beef cattle.

The European carcass grading scheme (EUROP) places large emphasis on meat yield and therefore on quantitative traits such as carcass conformation and superficial fat coverage. However, it falls short in considering sensory properties and consumer satisfaction. In contrast, the Meat Standards Australia (MSA) grading scheme considers, among others, animals' ossification, marbling, and ultimate pH as primary indicators of beef eating quality. This study aims to characterize MSA carcass grading scheme applied to the Italian beef production system, considering its significant role in European beef market. The study involved 3204 Charolais, Limousin, and crossbred young bulls and heifers slaughtered in a commercial Italian abattoir. Data collection spanned a broad range of variables, including animal characteristics, MSA traits, and EUROP carcass grading traits. Regardless of the sex of the animal, no significant relationship was observed between MSA traits and EUROP carcass grading scores. Factors such as sex, age, and arrival season at the fattening unit significantly affected most of MSA traits. Females had significantly higher marbling score, and lower ossification score and hump height than males. Animals imported in autumn and winter had significantly lower marbling score, but similar ossification score compared to those imported in spring and summer. Older females had the highest marbling scores. While further research is needed to assess whether the MSA grading scheme can be adapted to all different European rearing systems, results of this study are a prelude to the potential benefits that the MSA grading scheme can bring to the European beef industry.

Presence of pathogen DNA in milk harvested from quarters is associated to changes in cows' milk yield and composition.

BACKGROUND: Intramammary infection is the result of invasion and multiplication of microorganisms in the mammary gland and commonly leads to mastitis in dairy animals. Although much has been done to improve cows' udder health, mastitis remains a significant and costly health issue for dairy farmers, especially if subclinical. In this study, quarter milk samples from clinically healthy cows were harvested to detect pathogens via quantitative PCR (qPCR) and evaluate changes in individual milk traits according to the number of quarters infected and the type of microorganism(s). A commercial qPCR kit was used for detection of Mycoplasma bovis, Mycoplasma spp., Staphylococcus aureus, coagulase-negative staphylococci (CNS), Streptococcus agalactiae, Streptococcus dysgalactiae, Streptococcus uberis, Prototheca spp., Escherichia coli, Klebsiella spp., Enterococcus spp. and Lactococcus lactis ssp. lactis. Quarter and pooled milk information of 383 Holstein, 132 Simmental, 129 Rendena, and 112 Jersey cows in 9 Italian single-breed herds was available. RESULTS: Among the cows with pathogen(s) present in at least 1 quarter, CNS was the most commonly detected DNA, followed by Streptococcus uberis, Mycoplasma bovis, and Streptococcus agalactiae. Cows negative to qPCR were 206 and had the lowest milk somatic cell count. Viceversa, cows with DNA isolated in ≥ 3 quarters were those with the highest somatic cell count. Moreover, when major pathogens were isolated in ≥ 3 quarters, milk had the lowest casein index and lactose content. In animals with pathogen(s) DNA isolated, the extent with whom milk yield and major solids were impaired did not significantly differ between major and minor pathogens. CONCLUSIONS: The effect of the number of affected quarters on the pool milk quality traits was investigated in clinically healthy cows using a commercial kit. Results remark the important negative effect of subclinical udder inflammations on milk yield and quality, but more efforts should be made to investigate the presence of untargeted microorganisms, as they may be potentially dangerous for cows. For a smarter use of antimicrobials, analysis of milk via qPCR is advisable - especially in cows at dry off - to identify quarters at high risk of inflammation and thus apply a targeted/tailored treatment.

The Meat Standards Australia carcass grading site affects assessment of marbling and prediction of meat-eating quality in growing European beef cattle.

The lack of consumer feedback on beef eating quality contributes to reduced beef consumption in Europe. The Meat Standards Australia (MSA) grading scheme can assess the palatability of beef carcasses usually graded at the 10th thoracic vertebrae. However, the European beef industry relies on late-maturing breeds usually cut at the 5th vertebrae due to commercial reasons. Data from 55 young bulls and heifers of late-maturing breeds were collected in an Italian slaughterhouse following the MSA guidelines at both carcass grading sites and sides. Intramuscular fat levels were assessed through two scores and used with other variables to feed the MSA model, which predicts the MSA index, the meat-eating quality scores (MQ4) for 5 muscles and for each carcass grading site × side combination. The scores were analyzed using a mixed linear model. A correlation analysis was conducted to predict the variables measured at the 10th site using their correspondent at the 5th carcass grading site. A stepwise regression was conducted to understand the weight of each measured variable on marbling and MQ4 scores measured both at 5th and 10th carcass grading sites. Results showed significantly higher value for the studied traits at the 5th carcass grading site, while carcass side had no significant impact. The equations had high predictive capability and MSA marbling score played a key role in explaining the variability across carcass grading sites. The differences in marbling and MQ4 scores between the carcass grading sites suggest considering this factor if the MSA grading system will be applied to Europe.

Genomic insights into shank and eggshell color in Italian local chickens.

Eggshell and shank color in poultry is an intriguing topic of research due to the roles in selection, breed recognition, and environmental adaptation. This study delves into the genomics foundations of shank and eggshell pigmentation in Italian local chickens through genome-wide association studies analysis to uncover the mechanisms governing these phenotypes. To this purpose, 483 animals from 20 local breeds (n = 466) and 2 commercial lines (n = 17) were considered and evaluated for shank and eggshell color. All animals were genotyped using the Affymetrix Axiom 600 K Chicken Genotyping Array. As regards shank color, the most interesting locus was detected on chromosome Z, close to the TYRP1 gene, known to play a key role in avian pigmentation. Additionally, several novel loci and genes associated with shank pigmentation, skin pigmentation, UV protection, and melanocyte regulation were identified (e.g., MTAP, CDKN2A, CDKN2B). In eggshell, fewer significant loci were identified, including SLC7A11 and MITF on chromosomes 4 and 12, respectively, associated with melanocyte processes and pigment synthesis. This comprehensive study shed light on the genetic architecture underlying shank and eggshell color in Italian native chicken breeds, contributing to a better understanding of this phenomenon which plays a role in breed identification and conservation, and has ecological and economic implications.

Genome-wide analysis of the Siboney de Cuba cattle breed: genetic characterization and framing with cattle breeds worldwide.

Crossbreeding has been employed to address environmental challenges. One successful example is the Siboney de Cuba, developed in response to economic challenges in the 1960s. The aim of this study was to perform the first genomic characterization of the Siboney de Cuba breed, a successful hybrid breed resulting from the crossbreeding of Cuban Zebu and Holstein, using SNP array chip. For this purpose, 48 Siboney de Cuba cattle samples were collected and genotyped with the GGP Bovine 100k BeadChip, resulting in 83,314 SNPs after quality control. The genetic diversity was investigated using observed and expected heterozygosity, inbreeding coefficient, and minor allele frequency. Runs of homozygosity (ROH) analysis provided insights into molecular inbreeding. Additionally, the study investigated copy number variants (CNV), identifying CNV regions and their distribution. The genetic relationship and population structure of Siboney de Cuba were analyzed in comparison with worldwide cattle populations using ADMIXTURE, multidimensional scaling, and phylogenetic analysis. Six ROH islands containing a total of 50 genes were discovered, some of which were uncharacterized loci. Furthermore, 792 CNV with higher occurrence of genetic material loss were observed. The overall genome coverage for CNV regions was 2.16%. The Siboney de Cuba exhibited a good level of genetic variability with high heterozygosity and low inbreeding when compared with other cattle breeds worldwide. Also, the breed shared genetic similarity to hybrids from America and Bos indicus from Africa and highlighted a moderate level of genetic isolation with some overlaps with Bos taurus from America. The breed showed a complex genetic composition, influenced by historical factors. Overall, findings of the present study contribute to the understanding of genomic structure of Siboney de Cuba cattle breed.

Effects of vaccination timing and target pathogens on performances and antimicrobial use in long-transported Charolais beef cattle from France to Italy - A retrospective study.

Antimicrobial use (AMU) in the livestock sector is a major driver of antimicrobial resistance. Italian beef industry strongly relies on the import of young cattle from France, which are commingled in sorting facilities before transportation to Italy. Both commingling and transportation are stressors for animals and lead to higher risk of bovine respiratory disease (BRD), which in turn increases the risk of AMU. This study aimed to investigate how the timing of first BRD vaccination and the different vaccination target pathogens affect AMU and performance of young Charolais beef cattle imported from France to Italy. Information on animal performance, antimicrobial treatments, and vaccinations was available for 60,726 Charolais cattle belonging to 1449 batches in 33 Italian specialised fattening farms between January 2016 and December 2021. Antimicrobial use was estimated using the treatment incidence 100 adapted for Italy (TI100it). A mixed linear model was used to quantify the effects of the vaccination and the time of first administration on slaughter age, carcase weight, and average daily carcase gain. Similarly, a generalised linear mixed model was used to analyse the TI100it. The vaccination programme was usually applied the first day after the animals' arrival to the Italian fattening farms. Most animals were vaccinated with a polyvalent vaccine against infectious bovine rhinotracheitis (IBR), bovine parainfluenza type 3 virus (PI-3), bovine viral diarrhoea virus type 1 and 2 (BVDV), and bovine respiratory syncytial virus (BRSV). The most used class of antimicrobials to treat BRD were the macrolides, followed by aminoglycosides, amphenicols, tetracyclines, aminopenicillins, and fluoroquinolones. Animals that got vaccinated against any of the considered BRD pathogens upon arrival had significantly lower TI100it, greater average daily carcase gain, and reached slaughter age earlier than animals that got vaccinated later. Animals that received the vaccination against BVDV had lower TI100it and greater average daily carcase gain, and animals that received the vaccination against BRSV were younger at slaughter than unvaccinated animals. The vaccination against Mannheimia haemolytica significantly decreased the slaughter age and increased the carcase weight and average daily carcase gain, and the vaccination against PI-3 and Histophilus somni significantly increased the slaughter age. Thus, even if the vaccination programme is essential to tackle BRD, this practice is questionable if applied at arrival to the Italian fattening farms and it is advisable that the vaccination programme is planned before the commingling procedure in France.

Genome-wide investigation to assess copy number variants in the Italian local chicken population.

BACKGROUND: Copy number variants (CNV) hold significant functional and evolutionary importance. Numerous ongoing CNV studies aim to elucidate the etiology of human diseases and gain insights into the population structure of livestock. High-density chips have enabled the detection of CNV with increased resolution, leading to the identification of even small CNV. This study aimed to identify CNV in local Italian chicken breeds and investigate their distribution across the genome. RESULTS: Copy number variants were mainly distributed across the first six chromosomes and primarily associated with loss type CNV. The majority of CNV in the investigated breeds were of types 0 and 1, and the minimum length of CNV was significantly larger than that reported in previous studies. Interestingly, a high proportion of the length of chromosome 16 was covered by copy number variation regions (CNVR), with the major histocompatibility complex being the likely cause. Among the genes identified within CNVR, only those present in at least five animals across breeds (n = 95) were discussed to reduce the focus on redundant CNV. Some of these genes have been associated to functional traits in chickens. Notably, several CNVR on different chromosomes harbor genes related to muscle development, tissue-specific biological processes, heat stress resistance, and immune response. Quantitative trait loci (QTL) were also analyzed to investigate potential overlapping with the identified CNVR: 54 out of the 95 gene-containing regions overlapped with 428 QTL associated to body weight and size, carcass characteristics, egg production, egg components, fat deposition, and feed intake. CONCLUSIONS: The genomic phenomena reported in this study that can cause changes in the distribution of CNV within the genome over time and the comparison of these differences in CNVR of the local chicken breeds could help in preserving these genetic resources.

Pathogen Detection via Quantitative PCR in Milk of Healthy Cows Collected Using Different Sampling Protocols.

In this study we evaluated the prevalence of pathogens detected via quantitative PCR (qPCR) in milk from apparently healthy cows to identify the most common etiological agents present in Italian dairy farms. Milk samples were collected using a sterile protocol at quarter-level (3239 samples, 822 cows) and a conventional protocol at udder level as composite milk from the functional quarters of each cow (5464 samples, 5464 cows). The qPCR commercial kit detected Mycoplasma bovis, Mycoplasma spp., Staphylococcus aureus, coagulase-negative staphylococci (CNS), Streptococcus agalactiae, Streptococcus dysgalactiae, Streptococcus uberis, Prototheca spp., Escherichia coli, Klebsiella spp., Enterococcus spp. and Lactococcus lactis ssp. lactis as well as DNA from the penicillin resistance ß-lactamase gene from staphylococci. The prevalence of specific DNA was calculated based on its presence or absence in the samples, factoring in both the sampling protocols and herds. Regardless of the sampling protocol used, the most frequently detected pathogens were CNS (26.6% in sterile and 13.9% in conventional protocol) and Streptococcus uberis (9.6% and 16.5%, respectively). These results underscore the necessity for pathogen-specific interventions at the farm level to enhance the udder health of dairy cows via management recommendations.

ß-Casein A1 and A2: Effects of polymorphism on the cheese-making process.

Of late, "A2 milk" has gained prominence in the dairy sector due to its potential implications in human health. Consequently, the frequency of A2 homozygous animals has considerably increased in many countries. To elucidate the potential implications that beta casein (ß-CN) A1 and A2 may have on cheese-making traits, it is fundamental to investigate the relationships between the genetic polymorphisms and cheese-making traits at the dairy plant level. Thus, the aim of the present study was to evaluate the relevance of the ß-CN A1/A2 polymorphism on detailed protein profile and cheese-making process in bulk milk. Based on the ß-CN genotype of individual cows, 5 milk pools diverging for presence of the 2 ß-CN variants were obtained: (1) 100% A1; (2) 75% A1 and 25% A2; (3) 50% A1 and 50% A2; (4) 25% A1 and 75% A2; and (5) 100% A2. For each cheese-making day (n = 6), 25 L of milk (divided into 5 pools, 5 L each) were processed, for a total of 30 cheese-making processes. Cheese yield, curd nutrient recovery, whey composition, and cheese composition were assessed. For every cheese-making process, detailed milk protein fractions were determined through reversed-phase HPLC. Data were analyzed by fitting a mixed model, which included the fixed effects of the 5 different pools, the protein and fat content as a covariate, and the random effect of the cheese-making sessions. Results showed that the percentage of κ-CN significantly decreased up to 2% when the proportion of ß-CN A2 in the pool was ≥25%. An increase in the relative content of ß-CN A2 (≥50% of total milk processed) was also associated with a significantly lower cheese yield both 1 and 48 h after cheese production, whereas no effects were observed after 7 d of ripening. Concordantly, recovery of nutrients reflected a more efficient process when the inclusion of ß-CN A2 was ≤75%. Finally, no differences in the final cheese composition obtained by the different ß-CN pools were observed.

Genomics of Dwarfism in Italian Local Chicken Breeds.

The identification of the dwarf phenotype in chicken is based on body weight, height, and shank length, leaving the differentiation between dwarf and small breeds ambiguous. The aims of the present study were to characterize the sequence variations associated with the dwarf phenotype in three Italian chicken breeds and to investigate the genes associated with their phenotype. Five hundred and forty-one chickens from 23 local breeds (from 20 to 24 animals per breed) were sampled. All animals were genotyped with the 600 K chicken SNP array. Three breeds were described as "dwarf", namely, Mericanel della Brianza (MERI), Mugellese (MUG), and Pepoi (PPP). We compared MERI, MUG, and PPP with the four heaviest breeds in the dataset by performing genome-wide association studies. Results showed significant SNPs associated with dwarfism in the MERI and MUG breeds, which shared a candidate genomic region on chromosome 1. Due to this similarity, MERI and MUG were analyzed together as a meta-population, observing significant SNPs in the LEMD3 and HMGA2 genes, which were previously reported as being responsible for dwarfism in different species. In conclusion, MERI and MUG breeds seem to share a genetic basis of dwarfism, which differentiates them from the small PPP breed.

Genome-wide mapping of signatures of selection using a high-density array identified candidate genes for growth traits and local adaptation in chickens.

BACKGROUND: Availability of single nucleotide polymorphism (SNP) genotyping arrays and progress in statistical analyses have allowed the identification of genomic regions and genes under selection in chicken. In this study, SNP data from the 600 K Affymetrix chicken array were used to detect signatures of selection in 23 local Italian chicken populations. The populations were categorized into four groups for comparative analysis based on live weight (heavy vs light) and geographical area (Northern vs Southern Italy). Putative signatures of selection were investigated by combining three extended haplotype homozygosity (EHH) statistical approaches to quantify excess of haplotype homozygosity within (iHS) and between (Rsb and XP-EHH) groups. Presence of runs of homozygosity (ROH) islands was also analysed for each group. RESULTS: After editing, 541 animals and 313,508 SNPs were available for statistical analyses. In total, 15 candidate genomic regions that are potentially under selection were detected among the four groups: eight within a group by iHS and seven by combining the results of Rsb and XP-EHH, which revealed divergent selection between the groups. The largest overlap between genomic regions identified to be under selection by the three approaches was on chicken chromosome 8. Twenty-one genomic regions were identified with the ROH approach but none of these overlapped with regions identified with the three EHH-derived statistics. Some of the identified regions under selection contained candidate genes with biological functions related to environmental stress, immune responses, and disease resistance, which indicate local adaptation of these chicken populations. CONCLUSIONS: Compared to commercial lines, local populations are predominantly reared as backyard chickens, and thus, may have developed stronger resistance to environmental challenges. Our results indicate that selection can play an important role in shaping signatures of selection in local chicken populations and can be a starting point to identify gene mutations that could have a useful role with respect to climate change.

Genetic characteristics of colostrum refractive index and its use as a proxy for the concentration of immunoglobulins in Holstein cattle.

BACKGROUND: Colostral concentration of immunoglobulins (Ig) is crucial for the passive transfer of antibodies from the cow to the new-born calf. Direct determination of Ig by the gold standard radial immunodiffusion method is demanding in terms of time and costs. For this reason, a refractometer is commonly used at the farm level for an indirect estimation of colostrum quality, which is given as the Ig concentration. In this study, colostrum samples were collected from 548 Italian Holstein cows within 6 h of calving. The refractive index (BRIX, %) of these samples was assessed using a portable optical refractometer, as well as the concentration of total protein, IgG, IgA, and IgM by radial immunodiffusion. A four-trait animal model was used to estimate genetic parameters for BRIX and the different immunoglobulin isotypes. A receiver operating characteristic analysis was carried out to evaluate the BRIX diagnostic accuracy. RESULTS: Colostral BRIX was moderately heritable (0.26) and its genetic and phenotypic correlations with IgG (0.91, 0.78), IgA (0.57, 0.57), and IgM (0.71, 0.61) were all positive and of similar order, although the genetic correlations were generally higher than the phenotypic correlations. Low-quality colostrum samples, defined as those with an IgG concentration lower than 50 g/L, were accurately identified by the refractive index on the BRIX scale, with an area under the curve of 0.90. CONCLUSIONS: The use of a refractometer is recommended on dairy farms to produce a proxy for colostral Ig concentration. BRIX is a useful phenotyping tool that can be used in cattle to improve the quality of colostrum for first feeding of calves through both traditional genetic and genomic strategies. Improving colostrum quality will reduce the incidence of failure of passive transfer of immunity in young stock.

The Role of Quarantine on Post-Mortem Performances of Charolaise Young Bulls.

Biosecurity is essential to prevent the spread of diseases in livestock animals such as the bovine respiratory disease which can lead to negative effects on growth performance, and carcass and meat quality, as well as to an increase of antimicrobial use. The aim of this study was to investigate the effects of the quarantine on post-mortem performances (hot carcass weight, dressing percentage, pH 60 min after slaughtering, carcass SEUROP conformation, and fat cover) of 576 Charolaise young bulls imported from France and fattened in specialized Italian farms. Approximately half of the animals followed a standard fattening procedure without initial quarantine upon arrival to Italy (NO-QUA) and the other half underwent a 30-day period of quarantine (QUA) since their arrival to the farm. Post-mortem performances and parenteral administration of antimicrobial use were recorded. NO-QUA animals had lower average daily gain and slaughter weight but scored higher for carcass SEUROP evaluation and pH than QUA animals (p < 0.05). NO-QUA received more than double the number of parenteral antimicrobial treatments than QUA animals for respiratory diseases (139 vs. 56). Overall, quarantine applied on-farm contributes to improve post-mortem performances while reducing antimicrobial use in beef production.

Promoting Judicious Antimicrobial Use in Beef Production: The Role of Quarantine.

Judicious antimicrobial stewardship in livestock industry is needed to reduce the use of antimicrobials (AMU) and the associated risk of antimicrobial resistance. Biosecurity measures are acknowledged for their role against the spread of diseases and the importance in reducing AMU in different species. However, their effectiveness in beef production has been scarcely considered. The aim of this study was to investigate the effect of the quarantine strategy on AMU in beef cattle. A total of 1206 Charolaise animals in five farms were included in the trial. Roughly half of the animals followed the standard procedure of the fattening cycle (no-quarantine; NO-QUA group) and half followed a 30-day period of quarantine (QUA group) since their arrival. Performance and antimicrobial data were recorded and a treatment incidence 100 (TI100it) per animal was calculated. Penicillins was the most used class of antimicrobials. Differences between groups were significant for males only, with NO-QUA group having greater TI100it (3.76 vs. 3.24; p < 0.05) and lower body weight at slaughter (713.4 vs. 723.7 kg; p < 0.05) than QUA group. Results suggest that quarantine strategy can reduce AMU in males without compromising their performance, whereas further investigation is needed for females.

Egg Quality of Italian Local Chicken Breeds: II. Composition and Predictive Ability of VIS-Near-InfraRed Spectroscopy.

The aims of the present study were to characterize egg composition and develop VIS-Near-infrared spectroscopy (VIS-NIR) models for its predictions in Italian local chicken breeds, namely Padovana Camosciata, Padovana Dorata, Polverara Bianca, Polverara Nera, Pepoi, Ermellinata di Rovigo, Robusta Maculata and Robusta Lionata. Hens were reared in a single conservation center under the same environmental and management conditions. A total of 200 samples (25 samples per breed, two eggs/sample) were analyzed for the composition of albumen and yolk. Prediction models for these traits were developed on both fresh and freeze-dried samples. Eggs of Polverara Nera and Polverara Bianca differed from eggs of the other breeds (p < 0.05) in terms of the greatest moisture content (90.06 ± 1.23% and 89.57 ± 1.31%, respectively) and the lowest protein content (8.34 ± 1.27% and 8.81 ± 1.27%) in the albumen on wet basis. As regards the yolk, Robusta Maculata and Robusta Lionata differed (p < 0.05) from the other breeds, having lower protein content (15.62 ± 1.13% and 15.21 ± 0.63%, respectively) and greater lipid content (34.11 ± 1.12% and 35.30 ± 0.98%) on wet basis. Eggs of Pepoi had greater cholesterol content (1406.39 ± 82.34 mg/100 g) on wet basis compared with Padovana Camosciata, Polverara Bianca and Robusta Maculata (p < 0.05). Spectral data were collected in reflectance mode in the VIS-NIR range (400 to 2500 nm) using DS2500 (Foss, Hillerød, Denmark) on fresh and freeze-dried samples. Models were developed through partial least-squares regression on untreated and pre-treated spectra independently for yolk and albumen, and using several combinations of scattering corrections and mathematical treatments. The predictive ability of the models developed for each compound was evaluated through the coefficient of determination (R2cv), standard error of prediction (SEcv) and the ratio of performance to deviation (RPDcv) in cross-validation. Prediction models performed better for freeze-dried than fresh albumen and yolk. In particular, for the albumen the performance of models using freeze-dried eggs was excellent (R2cv ≥ 0.91), and for yolk it was suitable for the prediction of protein content and dry matter. Good performances of prediction were observed in yolk for dry matter (R2cv = 0.85), lipids and cholesterol (R2cv = 0.74). Overall, the results support the potential of infrared technology to predict the composition of eggs from local hens. Prediction models for proteins, dry matter and lipids of freeze-dried yolk could be used for labelling purposes to promote local breeds through the valorization of nutritional aspects.

Egg Quality of Italian Local Chicken Breeds: I. Yield Performance and Physical Characteristics.

The aim of this study was to compare yield performance (from 39 to 50 weeks of age) and egg physical characteristics (at 50 weeks of age) of eight autochthonous chicken breeds of the Veneto region (Italy). Four white eggshell breeds, namely Padovana Camosciata (PA-C, chamois plumage), Padovana Dorata (PA-G, golden plumage), Polverara Bianca (PO-W, white plumage), and Polverara Nera (PO-B, black plumage), and four tinted eggshell breeds, namely Pepoi (PP), Ermellinata di Rovigo (ER), Robusta Maculata (RM), and Robusta Lionata (RL) from a conservation centre were considered in the trial. Significant differences (p < 0.05) among breeds were observed for yield performance and egg quality. From 39 to 50 weeks of age, the hen-day egg production was higher in PA-C and RM than in RL, and PO-W and ER were intermediate; PA-G, PO-B, and PP were the lowest. The hen-day egg production changed according to the age of the hens. From 39 to 42 weeks of age, ER showed the highest hen-day egg production and PA-G the lowest; from 47 to 50 weeks, PA-C, PO-W, and RM were the highest and PP the lowest. The tinted eggshell breeds, with the exception of PP, had higher egg weights than white eggshell breeds. PP egg weight was similar to PO-B. As regards the tinted eggshell breeds, RM eggs had the highest eggshell a* and b*, and PP the lowest. PA-C had the most spherical eggs, and PO-B and ER had the most ovoid eggs. PO-W and RM had the highest eggshell thickness and ER had the lowest. The highest eggshell ratio was observed for PO-W and PO-B, and the lowest for ER. The yolk-to-albumen ratio was higher in the white eggshell breeds than in PP, ER, and RL. ER had the highest Haugh units and PA-G the lowest. PO-W, PO-B, PA-C, PA-G, and ER had the lowest egg inclusions, and RL and RM the highest. Tinted eggshell eggs differed from white eggshell eggs by having higher meat spots. Results indicated that the eggs produced by the eight local chicken breeds differed according to the laying rate and a wide range of physical external and internal characteristics which allow the consumer to distinguish them for their genetic origin by the eggshell shape and colour, and to use them for different purposes to valorise poultry biodiversity.

The concentrations of immunoglobulins in bovine colostrum determined by the gold standard method are genetically correlated with their near-infrared prediction.

BACKGROUND: The quality of colostrum administered to calves is based on its concentration in immunoglobulins G (IgG, g/L). Immunoglobulins A (IgA) and M (IgM) are also present but at a lower level. The gold standard reference analysis for these traits, radial immunodiffusion, is time-consuming and expensive. In order to define breeding strategies that are aimed at improving colostrum quality in dairy cattle, a large amount of data is needed, and the use of indicator traits would be beneficial. In the study presented here, we explored the heritabilities of reference (radial immunodiffusion) and near infrared-predicted IgG, IgA, and IgM concentrations and estimated their genetic correlations. First, the colostrum of 765 Holstein cows from nine herds was sampled to perform a reference analysis and the near-infrared spectra (400-2500 nm) were stored. We used a calibration set (28% of the initial samples) that was representative of the herds and cow parity orders to develop prediction equations for IgG, IgA, and IgM concentrations. Finally, these traits were predicted in the validation set (72% of the initial samples) to estimate genetic parameters for the predictions. Genetic correlations between reference and predicted values of each trait were estimated through bivariate linear animal models. RESULTS: The three near-infrared-predicted immunoglobulin fractions were genetically correlated with their reference value. In particular, the reference and predicted IgG concentrations were strongly correlated at both the genetic (0.854 ± 0.314) and phenotypic level (0.767 ± 0.019). Weaker associations were observed for IgA and IgM concentrations, which were predicted with lower accuracy compared to IgG. Simulation analyses suggested that improving colostrum quality by selective breeding in Holstein cattle based on near-infrared predicted colostrum immunoglobulins concentrations is feasible. In addition, less than 10 mL of colostrum are needed for spectra acquisition and thus implementation of such analyses is possible in the near future. CONCLUSIONS: The concentrations of colostrum immunoglobulins can be predicted from near-infrared spectra and the genetic correlation between the reference and the predicted traits is positive and favourable, in spite of the large standard errors of the estimates. Near-infrared spectroscopy can be exploited in selective breeding of dairy cattle to improve colostral immunoglobulins concentration.

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. Prediction accuracies of all methods were above 75%. According to different metrics, Neural Network, Random Forest and linear methods had the best performance in predicting udder health classes at a given test-day (healthy or mastitic according to somatic cell count below or above a predefined threshold of 200,000 cells/mL) based on the cow's milk traits recorded at previous test-day. Our findings suggest machine learning algorithms as a promising tool to improve decision making for farmers. Machine learning analysis would improve the surveillance methods and help farmers to identify in advance those cows that would possibly have high somatic cell count in the subsequent test-day.

Dairy Cows' Health during Alpine Summer Grazing as Assessed by Milk Traits, Including Differential Somatic Cell Count: A Case Study from Italy.

Extensive summer grazing is a dairy herd management practice frequently adopted in mountainous areas. Nowadays, this activity is threatened by its high labour demand, but it is fundamental for environmental, touristic and economic implications, as well as for the preservation of social and cultural traditions. Scarce information on the effects of such low-input farming systems on cattle health is available. Therefore, the present case study aimed at investigating how grazing may affect the health status of dairy cows by using milk traits routinely available from the national milk recording scheme. The research involved a dairy herd of 52 Simmental and 19 Holstein × Simmental crossbred cows. The herd had access to the pasture according to a rotational grazing scheme from late spring up to the end of summer. A total of 616 test day records collected immediately before and during the grazing season were used. Individual milk yield was registered during the milking procedure. Milk samples were analysed for composition (fat, protein, casein and lactose contents) and health-related milk indicators (electrical conductivity, urea and ß-hydroxybutyrate) using mid-infrared spectroscopy. Somatic cell count (SCC) and differential SCC were also determined. Data were analysed with a linear mixed model, which included the fixed effects of the period of sampling, cow breed, stage of lactation and parity, and the random effects of cow nested within breed and the residual. The transition from barn farming to pasture had a negative effect on milk yield, together with a small deterioration of fat and protein percentages. Health-related milk indicators showed a minor deterioration of the fat to protein ratio, differential SCC and electrical conductivity, particularly towards the end of the grazing season, whereas the somatic cell score and ß-hydroxybutyrate were relatively constant. Overall, the study showed that, when properly managed, pasture grazing does not have detrimental effects on dairy cows in terms of udder health and efficiency. Therefore, the proper management of cows on pasture can be a valuable solution to preserve the economic, social and environmental sustainability of small dairy farms in the alpine regions, without impairing cows' health.

Genetic Parameters of Bovine Milk Fatty Acid Profile, Yield, Composition, Total and Differential Somatic Cell Count.

The growing interest of consumers for milk and dairy products of high nutritional value has pushed researchers to evaluate the feasibility of including fatty acids (FA) in selection programs to modify milk fat profile and improve its nutritional quality. Therefore, the aim of this study was to estimate genetic parameters of FA profile predicted by mid-infrared spectroscopy, milk yield, composition, and total and differential somatic cell count. Edited data included 35,331 test-day records of 25,407 Italian Holstein cows from 652 herds. Variance components and heritability were estimated using single-trait repeatability animal models, whereas bivariate repeatability animal models were used to estimate genetic and phenotypic correlations between traits, including the fixed effects of stage of lactation, parity, and herd-test-date, and the random effects of additive genetic animal, cow permanent environment and the residual. Heritabilities and genetic correlations obtained in the present study reflected both the origins of FA (extracted from the blood or synthesized de novo by the mammary gland) and their grouping according to saturation or chain length. In addition, correlations among FA groups were in line with correlation among individual FA. Moderate negative genetic correlations between FA and milk yield and moderate to strong positive correlations with fat, protein, and casein percentages suggest that actual selection programs are currently affecting all FA groups, not only the desired ones (e.g., polyunsaturated FA). The absence of association with differential somatic cell count and the weak association with somatic cell score indicate that selection on FA profile would not affect selection on resistance to mastitis and vice versa. In conclusion, our findings suggest that genetic selection on FA content is feasible, as FA are variable and moderately heritable. Nevertheless, in the light of correlations with other milk traits estimated in this study, a clear breeding goal should first be established.