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This research communication reports concentrations of two sialic acids (SA), N-acetylneuraminic (Neu5Ac) and N-glycolylneuraminic (Neu5Gc), in fresh milk from different cow breeds throughout lactation. According to published studies, the two SA types found in animal-derived products have diverse and conflicting effects on human health, but SA content is not routinely analysed in individual milk cows samples. We measured the content of Neu5Ac and Neu5Gc in milk from Holstein Friesian (HO), Simmental (SM), Simmental × Holstein crossbred (SM×HO), and Podolica (POD) cows at 60 and 120 d following calving. HO, SM and SM×HO were reared in an intensive production while POD were raised in an extensive system. Results showed that total Neu5Ac was overall thirty times more abundant than Neu5Gc, and their concentrations were higher at 120 d than at 60 d (P < 0.001). Neu5Gc values were greater in HO, SM, and SM × HO than in POD (P < 0.001), while HO had a higher Neu5Ac value than the other three breeds (P < 0.001). These findings shed light on the differences in SA content among cow breeds and lay the groundwork for future research to select animals that produce milk with desirable characteristics for human health.

This research communication reports concentrations of two sialic acids (SA)

BackgroundBovine mastitis, an inflammatory disease of the mammary gland, is classified as subclinical or clinical. Circulating neutrophils are recruited to the udder to combat infection. We compared the transcriptomic profiles in circulating leukocytes between healthy cows and those with naturally occurring subclinical or clinical mastitis.Methods and ResultsHolstein Friesian dairy cows from six farms in EU countries were recruited. Based on milk somatic cell count and clinical records, cows were classified as healthy (n = 144), subclinically (n = 48) or clinically mastitic (n = 22). Circulating leukocyte RNA was sequenced with Illumina NextSeq single end reads (30 M). Differentially expressed genes (DEGs) between the groups were identified using a DESeq2 package, followed by GO enrichment analysis. Both subclinical and clinical mastitis caused significant changes in the leukocyte transcriptome, with more intensive changes attributed to clinical mastitis. We detected 491 DEGs between clinical and healthy groups, 350 DEGs between subclinical and healthy groups and 170 DEGs between clinical and subclinical groups. Most DEGs were associated with cell killing and immune processes. Many upregulated DEGs in clinical mastitis encoded antimicrobial peptides (AZU1, CAMP, CATHL1, CATHL2, CATHL4, CATHL5, CATHL6, DEFB1, DEFB10, DEFB4A, DEFB7, LCN2, PGLYRP1, S100A9, TF and LTF) which were not upregulated in subclinical mastitis. This suggests that the leukocytes may have greater killing capacity in cows with clinical mastitis.ConclusionWe have, for the first time, described circulating leukocyte transcriptomic profiles in naturally occurring subclinical mastitis and assessed their differences from healthy cows and those with clinical mastitis.

Sialyloligosaccharides (SOS) are bioactive molecules that play an important role in brain development and the increase in immunity in infants. In adults, they act as prebiotics, enhancing protection against microbial pathogens. In the present work, we aimed to analyze the levels of SOS in mature milk, at days 60 and 120 after calving in four cow breeds: Holstein (HO), Simmental × Holstein (SM × HO), Simmental (SM), all fed with total mixed ration (TMR) in intensive production, and Podolica (POD) raised on pasture in an extensive system. The concentrations of SOS (3′-sialyllactose = 3′-SL, 6′-sialyllactose = 6′-SL, 6′-Sialyl-N-acetyllactosamine = 6′-SLN, disialyllactose = DSL, expressed in mg/L) were determined using HPAEC-PAD, a high-performance anion-exchange chromatography with pulsed amperometric detection. Results showed both breed and lactation effects. The contents of 3′-SL, 6′-SL, 6′-SLN, and DSL were higher at 60 than 120 days (p < 0.001), as well as in POD, as compared to the other breeds (p < 0.001). Furthermore, SM showed a significantly greater level of 3′-SL than HO (p < 0.001), as well as a significantly higher level of 6′-SLN in SM than HO (p < 0.001) and SM × HO (p < 0.001). Our findings may have implications for several areas of sustainability that might be used in the cattle management system.

Milk fat depression (MFD) syndrome, a consistent decrease in milk fat content, is related to important changes in fatty acid composition due to feed imbalances and the consequent ruminal metabolism alteration. Milk produced in two different farming systems was compared: Holstein Friesian fed with unified in intensive production and Podolica raised on a pasture in an extensive system. Milk chemical characteristics and fatty acid composition were determined comparing milk with a normal fat level (>3.8%) to milk with a low fat level (trans-11 and increase in trans-10 C18:1 (shift from trans-11 to trans-10 C18:1) in low fat with respect to normal fat milk with a consequent decrease in the trans-11/trans-10 C18:1 ratio. Even conjugated linoleic acid (CLA), C18:2 cis-9, trans-11, was lower while CLA trans-10, cis-12 was higher in low fat milk than in normal fat milk from Holstein Friesian. These changes, that are indicators of MFD syndrome, were not found in Podolica milk between fat levels. Holstein Friesian milk showed less short-chain fatty acids (9.48 % vs. 11.05%, p < 0.001), trans vaccenic acid (C18:1 trans-11, 0.51% vs. 3.39%, p < 0.001), rumenic acid (CLA C18:2 cis-9, trans-11, 0.32% vs. 1.45%, p < 0.001) and total CLA (0.53% vs. 1.91%, p < 0.001) contents than Podolica milk. Further losses of these human healthy nutrients in low fat Friesian milk reduced the nutritional quality of the milk, while the milk from animals raised on the pasture was of better quality even when the level of fat was low.

Local adaptation of animals to the environment can abruptly become a burden when faced with rapid climatic changes such as those foreseen for the Italian peninsula over the next 70 years. Our study investigates the genetic structure of the Italian goat populations and links it with the environment and how genetics might evolve over the next 50 years. We used one of the largest national datasets including 1000 goats from 33 populations across the Italian peninsula collected by the Italian Goat Consortium and genotyped with over 50 k markers. Our results showed that Italian goats can be discriminated in three groups reflective of the Italian geography and its geo-political situation preceding the country unification around two centuries ago. We leveraged the remarkable genetic and geographical diversity of the Italian goat populations and performed landscape genomics analysis to disentangle the relationship between genotype and environment, finding 64 SNPs intercepting genomic regions linked to growth, circadian rhythm, fertility, and inflammatory response. Lastly, we calculated the hypothetical future genotypic frequencies of the most relevant SNPs identified through landscape genomics to evaluate their long-term effect on the genetic structure of the Italian goat populations. Our results provide an insight into the past and the future of the Italian local goat populations, helping the institutions in defining new conservation strategy plans that could preserve their diversity and their link to local realities challenged by climate change.

After calving, lipid mobilization caused by increased nutrient demands for lactation leads to elevated circulating concentrations of nonesterified fatty acids (NEFA). Excessive NEFA levels have previously been identified as a major risk factor for postpartum immunosuppression. The aim of this study was to investigate changes in global transcriptomic gene expression of peripheral blood mononuclear cells (PBMC) in dairy cows offered different early lactation diets (high concentrate, n = 7; medium, n = 8; or low, n = 9) and with differing circulating levels of NEFA. Cows were classified as having NEFA concentrations of either 750 µM (high, n = 10) at 14 d in milk. Plasma urea concentrations were greater for cows on the high concentrate diet but β-hydroxybutyrate and glucose concentrations did not differ significantly between either dietary treatments or NEFA groups. Cows with high NEFA weighed more at drying off and suffered greater body condition score loss after calving. The PBMC were isolated at 14 d in milk, and RNA was extracted for RNA sequencing. Differential gene expression was analyzed with DESeq2 with q-value for false discovery rate control followed by Gene Ontology Enrichment. Although there were no differentially expressed genes associated with lactation diet, 304 differentially expressed genes were identified between cows with high and low circulating NEFA, with 118 upregulated and 186 downregulated. Gene Ontology enrichment analysis demonstrated that biological adhesion and immune system process were foremost among various PBMC functions which were altered relating to body defenses and immunity. High NEFA concentrations were associated with inhibited cellular adhesion function by downregulating 20 out of 26 genes (by up to 17-fold) related to this process. Medium NEFA concentrations altered a similar set of functions as high NEFA, but with smaller enrichment scores. Localization and immune system process were most significant, with biological adhesion ranking only eleventh. Our results demonstrated that increased circulating NEFA concentrations, but not diet, were associated with immune system processes in PBMC in early lactation cows. Leukocyte cell-to-cell adhesion was inhibited when the NEFA concentration exceeded 750 µM, which would reduce the efficiency of diapedesis and so contribute to decreased body defense mechanisms and predispose animals to infection.

The aim of the research reported in this paper was to evaluate plasma concentrations of energy, oxidative and inflammatory biomarkers of Simmental (sire) × Holstein (dam) crossbred cows, in comparison with the two parental breeds during the peripartal and early lactation periods and to estimate the effects of heterosis for these traits. Thirty-three animals, managed under the same conditions, 8 Simmental (SI), 9 Holstein (HO) and 16 crossbred (CR) cows were enrolled in this study. Glucose, non-esterified fatty acids (NEFA), β-hydroxybutyrate (BHB), total bilirubin, aspartate aminotransferase (AST), alanine aminotransferase (ALT), alkaline phosphatase (ALP), creatine kinase (CK), total protein, albumin, creatinine and urea were determined in blood sampled at six different time points (30 ± 3 and 15 ± 3 d before the expected calving date, at calving and 15, 30 and 60 d after calving). Furthermore, derived reactive oxygen metabolites (d-ROMs), biological antioxidant potential (BAP), interleukin-6 (IL-6), haptoglobin (Hp) and serum amyloid A protein (SAA) were determined to evaluate inflammatory and oxidative status. Results showed that the CR group had significantly lower average values of glucose and NEFA when compared to HO group; signifcantly lower values of urea than SI group and significantly higher values of creatinine than HO. Furthermore, CR cows showed the lowest average value of d-ROMs with respect to SI and HO parental breeds. Finally, the average value of haptoglobin was significantly lower in CR and HO groups, when compared to SI group. As for the heterosis we found the highest (positive) percentage for CK (98%) and BAP (47%) and the lowest (negative) percentage for OSi (−75%) and d-ROMs (−39%). A negative percentage was also found for the glucose (−11%) and NEFA (−20%) toward the Simmental parental breed. Our results suggest a different response among the three genetic groups during the peripartal and early lactation periods. In particular, CR and SI cows seem more adaptable regarding energy metabolism and oxidative status. Heterosis led to a positive effect on those parameters in Simmental (sire) × Holstein (dam) crossbred cows F1 population (50% Simmental and 50% Holstein).

Simple Summary First, the current work consisted of validating the feasibility of large-scale dairy cow bodyweight prediction from models involving the day in milk, milk yield, parity, and milk mid-infrared spectrum. Second, it aimed to improve the accuracy of predictive models by using feature selection algorithms to decrease the number of predictors to limit overfitting. The models, using accessible and low-cost measurements, provided highly reproducible predictions. These could be easily obtained on an individual basis throughout a cow’s productive life by dairy herd improvement organizations, thus providing potentially relevant information for the dairy farmer at three levels: economics (reproductive performance), animal welfare (disease detection), and environment (methane production). Abstract Knowing the body weight (BW) of a cow at a specific moment or measuring its changes through time is of interest for management purposes. The current work aimed to validate the feasibility of predicting BW using the day in milk, parity, milk yield, and milk mid-infrared (MIR) spectrum from a multiple-country dataset and reduce the number of predictors to limit the risk of over-fitting and potentially improve its accuracy. The BW modeling procedure involved feature selections and herd-independent validation in identifying the most interesting subsets of predictors and then external validation of the models. From 1849 records collected in 9 herds from 360 Holstein cows, the best performing models achieved a root mean square error (RMSE) for the herd-independent validation between 52 ± 2.34 kg to 56 ± 3.16 kg, including from 5 to 62 predictors. Among these models, three performed remarkably well in external validation using an independent dataset (N = 4067), resulting in RMSE ranging from 52 to 56 kg. The results suggest that multiple optimal BW predictive models coexist due to the high correlations between adjacent spectral points.

The identification of genes involved in phenotypes related to milk quality is important for both economic and health aspects in livestock production. The aim of this study was to assess the level of gelsolin gene expression in two breeds of dairy sheep – Sarda and Gentile – with pronounced differences in quantitative and qualitative milk traits. Gelsolin, a type of actin-modulating proteins is involved in the processes of actin remodeling during cell growth and apoptosis; therefore a role of this protein in mammary changes during lactation was here hypothesized. Individual milk samples were collected three times during lactation from 26 ewes of the two breeds. The differential gene expression of gelsolin in the two breeds and the three lactation times was estimated by quantitative PCR on RNA extracted from milk somatic cells. Correlations of gelsolin gene expression with milk yield and quality and days of lactation were also estimated. The results showed that gelsolin gene expression was significantly higher in the Sarda compared to the Gentile at each lactation stage, in agreement with the longer lactation duration and the higher daily milk yield of the first breed. Significant correlations of gelsolin gene expression were found with milk fat content in Sarda breed (−0.46, P

Interleukin 8 (IL8) is a major mediator of the innate immune response. Polymorphisms in this gene are associated with susceptibility to inflammatory disease in humans. Two major promoter polymorphic haplotypes (IL8-h1 and IL8-h2) segregating in cattle populations have shown a significant effect on the immune response profile in calves but their implications for transition cow immunity have not been established. The aims of this study were to assess functional relevance of the IL8 haplotypes on the immunological traits of periparturient cows (n = 32) belonging to three genetic groups: Holstein (HO), Simmental (SI) and their crosses (CR) and to evaluate the frequency of IL8 haplotypes in the HO (dairy) and SI (dual purpose) pure breeds. IL8 haplotypes showed a significant effect on circulating number of both T helper lymphocytes (P = 0.0133) and T cytotoxic lymphocytes (P = 0.0024). Differences in percentage of CD14+ monocytes and T lymphocyte subsets were found between haplotype groups at different time points. Plasma concentrations of Serum Amyloid A (SAA) and Haptoglobin (Hp) were enhanced at calving in IL8-h2 (P = 0.0019, P = 0.0029) and IL8-het (P = 0.050 and P = 0.052) respectively, compared with IL8-h1 cows. In contrast, significantly lower levels of reactive oxygen metabolites (d-ROMs) activation were identified in IL8-h2 and IL8-het cows after calving compared with IL8-h1 cows. Furthermore, genotyping results showed that SI cows have a high frequency of the homozygous IL8-h2 haplotype compared to the HO cows (87.5 % vs 40 %) which reflects the different selective pressure between the two pure breeds. In conclusion, our preliminary data suggests that IL8 promoter haplotype is associated with significant and dynamic changes in immunological traits during peripartum and early lactation period. Future work will focus on a more comprehensive assessment of immune changes in additional cows.

Microbial RNA is detectable in host samples by aligning unmapped reads from RNA\ud sequencing against taxon reference sequences, generating a score proportional to the microbial load.\ud An RNA-Seq data analysis showed that 83.5% of leukocyte samples from six dairy herds in different\ud EU countries contained bovine herpes virus-6 (BoHV-6). Phenotypic data on milk production,\ud metabolic function, and disease collected during their first 50 days in milk (DIM) were compared\ud between cows with low (1–200 and n = 114) or high (201–1175 and n = 24) BoHV-6 scores. There were\ud no differences in milk production parameters, but high score cows had numerically fewer\ud incidences of clinical mastitis (4.2% vs. 12.2%) and uterine disease (54.5% vs. 62.7%). Their metabolic\ud status was worse, based on measurements of IGF-1 and various metabolites in blood and milk. A\ud comparison of the global leukocyte transcriptome between high and low BoHV-6 score cows at\ud around 14 DIM yielded 485 differentially expressed genes (DEGs). The top pathway from Gene\ud Ontology (GO) enrichment analysis was the immune system process. Down-regulated genes in the\ud high BoHV-6 cows included those encoding proteins involved in viral detection (DDX6 and\ud DDX58), interferon response, and E3 ubiquitin ligase activity. This suggested that BoHV-6 may\ud largely evade viral detection and that it does not cause clinical disease in dairy cows.

Simple Summary Reproductive performance is an important factor, which determines productive life and drives culling decisions in dairy herds. There are strong motives for including reproductive performance in genetic selection programs of dairy cows; however, low heritability estimates reported for reproductive performance measures limit the genetic selection efficiency. More effective genetic selection could be achieved using genomic information. The aim of this study was to identify genomic region(s) associated with the length of the calving interval in Holstein cows. The accuracies of genomic estimated breeding values (GEBVs) with single-step genomic BLUP (ssGBLUP) and the pedigree-based BLUP were compared as well. The results showed that the accuracies of GEBVs using the single-step genomic BLUP were much higher than those estimated using the pedigree-based BLUP. We identified three genomic regions (BTA3, BTA6, and BTA7) associated with the length of the calving interval in Holstein dairy cows. Abstract The aim of the present study was to identify genomic region(s) associated with the length of the calving interval in primiparous (n = 6866) and multiparous (n = 5071) Holstein cows. The single nucleotide polymorphism (SNP) solutions were estimated using a weighted single-step genomic best linear unbiased prediction (WssGBLUP) approach and imputed high-density panel (777 k) genotypes. The effects of markers and the genomic estimated breeding values (GEBV) of the animals were obtained by five iterations of WssGBLUP. The results showed that the accuracies of GEBVs with WssGBLUP improved by +5.4 to +5.7, (primiparous cows) and +9.4 to +9.7 (multiparous cows) percent points over accuracies from the pedigree-based BLUP. The most accurate genomic evaluation was provided at the second iteration of WssGBLUP, which was used to identify associated genomic regions using a windows-based GWAS procedure. The proportion of additive genetic variance explained by windows of 50 consecutive SNPs (with an average of 165 Kb) was calculated and the region(s) that accounted for equal to or more than 0.20% of the total additive genetic variance were used to search for candidate genes. Three windows of 50 consecutive SNPs (BTA3, BTA6, and BTA7) were identified to be associated with the length of the calving interval in primi- and multiparous cows, while the window with the highest percentage of explained genetic variance was located on BTA3 position 49.42 to 49.52 Mb. There were five genes including ARHGAP29, SEC24D, METTL14, SLC36A2, and SLC36A3 inside the windows associated with the length of the calving interval. The biological process terms including alanine transport, L-alanine transport, proline transport, and glycine transport were identified as the most important terms enriched by the genes inside the identified windows.

The main objective of this study was to test the efficiency of a management system combining metabolic clustering of cows based on Fourier-transform mid-infrared (FT-MIR) spectra of milk and targeted treatment of metabolically imbalanced cows with propylene glycol drench. We hypothesized that cows identified in a metabolically imbalanced status during early lactation were associated with subsequent impaired health, reproduction, and production, and that treatment with propylene glycol treatment would improve health, reproduction, and production relatively more in these cows than in control cows. We completed a prospective, randomized controlled trial with 356 early-lactation cows in 2 private dairy herds in Denmark from December 2017 to April 2018. Milk samples of cows were collected before treatment, from 4 to 9 d in milk, and after treatment, from 22 to 27 d in milk. Milk samples were analyzed using FT-MIR spectroscopy. We also measured 4 milk metabolites (β-hydroxybutyrate, isocitrate, malate, and glutamate) and fat and protein contents. Based on FT-MIR spectra and cluster analyses, cows were clustered into groups of metabolically imbalanced and healthy cows. Within each group, cows were allocated randomly to treatment with propylene glycol (500 mL for 5 d) or no treatment. We analyzed the effect of the treatment on cow-level variables: metabolic cluster, milk metabolites, fat and protein contents, and fat-to-protein ratio at a milk sampling after the treatment. Furthermore, we analyzed daily milk yield, calving to first service interval, and disease occurrence. Results showed only a few effects of propylene glycol treatment and few interactions between treatment and metabolic clusters. We found no significant main effects of propylene glycol treatment in any of these analyses. A negative effect of the imbalanced metabolic cluster was found for the outcome of calving to first service interval for multiparous cows. In conclusion, we found a longer calving to first service interval in metabolically imbalanced cows, but we were not able to demonstrate overall benefits from the applied detection of cows in imbalanced metabolic status in early lactation and follow-up by treatment with propylene glycol.

Background Previous studies have identified many immune pathways which are consistently altered in humans and model organisms as they age. Dairy cows are often culled at quite young ages due to an inability to cope adequately with metabolic and infectious diseases, resulting in reduced milk production and infertility. Improved longevity is therefore a desirable trait which would benefit both farmers and their cows. This study analysed the transcriptome derived from RNA-seq data of leukocytes obtained from Holstein cows in early lactation with respect to lactation number. Results Samples were divided into three lactation groups for analysis: i) primiparous (PP, n = 53), ii) multiparous in lactations 2–3 (MP 2–3, n = 121), and iii) MP in lactations 4–7 (MP > 3, n = 55). Leukocyte expression was compared between PP vs MP > 3 cows with MP 2–3 as background using DESeq2 followed by weighted gene co-expression network analysis (WGCNA). Seven modules were significantly correlated (r ≥ 0.25) to the trait lactation number. Genes from the modules which were more highly expressed in either the PP or MP > 3 cows were pooled, and the gene lists subjected to David functional annotation cluster analysis. The top three clusters from modules more highly expressed in the PP cows all involved regulation of gene transcription, particularly zinc fingers. Another cluster included genes encoding enzymes in the mitochondrial beta-oxidation pathway. Top clusters up-regulated in MP > 3 cows included the terms Glycolysis/Gluconeogenesis, C-type lectin, and Immunity. Differentially expressed candidate genes for ageing previously identified in the human blood transcriptome up-regulated in PP cows were mainly associated with T-cell function (CCR7, CD27, IL7R, CAMK4, CD28), mitochondrial ribosomal proteins (MRPS27, MRPS9, MRPS31), and DNA replication and repair (WRN). Those up-regulated in MP > 3 cows encoded immune defence proteins (LYZ, CTSZ, SREBF1, GRN, ANXA5, ADARB1). Conclusions Genes and pathways associated with lactation number in cows were identified for the first time to date, and we found that many were comparable to those known to be associated with ageing in humans and model organisms. We also detected changes in energy utilization and immune responses in leukocytes from older cows.

The aim was to estimate genetic parameters for milk urea (MU) concentration and its relationship with milk yield and compositions in Holstein dairy Cows. Edited data were 90,594 test-day records of milk yield and composition collected during 2015 to 2018 on 13,737 lactations obtained from 7,850 Holstein cows in 50 herds. Random regression test-day model was used to estimate genetic parameters. (Co)variance components were estimated with the Bayesian Gibbs sampling method using a single chain of 400,000 iterates. The first 50,000 iterates of each chain were regarded as a burn-in period. Mean (SD) of MU was 23.03 (5.99) and 22.41 (5.74) mg/dl in primiparous and multiparous cows, respectively. Average heritability estimates for daily MU was 0.33 (SD = 0.02) ranged 0.29 to 0.36 and 0.32 (SD = 0.03) ranged 0.27 to 0.34, respectively, for primiparous and multiparous cows. The mean (SD) genetic correlation between MU and milk yield, fat yield, protein yield, lactose yield, fat percentage, protein percentage, lactose percentage, and somatic cell score was, respectively, -0.02 (0.03), -0.02 (0.01), 0.01 (0.04), 0.01 (0.03), 0.00 (0.07), -0.03 (0.04), 0.00 (0.01), -0.11 (0.06) in primiparous cows. The corresponding values in multiparous cows were -0.01 (0.02), -0.01 (0.03), -0.04 (0.04), -0.04 (0.04), 0.04 (0.04), 0.04 (0.07), -0.03 (0.09), 0.06 (0.11), respectively. The results indicate that selection on MU is possible with no effect on milk yield or compositions, however, relationships between MU and other important traits such as longevity, metabolic diseases, and fertility are needed.

The objective of this study was to develop a generic risk management system based on the Hazard Analysis and Critical Control Point (HACCP) principles for the prevention of critical negative energy balance (NEB) in dairy herds using an expert panel approach. In addition, we discuss the advantages and limitations of the system in terms of implementation in the individual dairy herd. For the expert panel, we invited 30 researchers and advisors with expertise in the field of dairy cow feeding and/or health management from eight European regions. They were invited to a Delphi-based set-up that included three inter-correlated questionnaires in which they were asked to suggest risk factors for critical NEB and to score these based on ‘effect’ and ‘probability’. Finally, the experts were asked to suggest critical control points (CCPs) specified by alarm values, monitoring frequency and corrective actions related to the most relevant risk factors in an operational farm setting. A total of 12 experts (40 %) completed all three questionnaires. Of these 12 experts, seven were researchers and five were advisors and in total they represented seven out of the eight European regions addressed in the questionnaire study. When asking for suggestions on risk factors and CCPs, these were formulated as ‘open questions’, and the experts’ suggestions were numerous and overlapping. The suggestions were merged via a process of linguistic editing in order to eliminate doublets. The editing process revealed that the experts provided a total of 34 CCPs for the 11 risk factors they scored as most important. The consensus among experts was relatively high when scoring the most important risk factors, while there were more diverse suggestions of CCPs with specification of alarm values and corrective actions. We therefore concluded that the expert panel approach only partly succeeded in developing a generic HACCP for critical NEB in dairy cows. We recommend that the output of this paper is used to inform key areas for implementation on the individual dairy farm by local farm teams including farmers and their advisors, who together can conduct herd-specific risk factor profiling, organise the ongoing monitoring of herd-specific CCPs, as well as implement corrective actions when CCP alarm values are exceeded.

Physiological imbalance is an abnormal physiological condition that cannot be directly observed but is assumed to precede subclinical and clinical diseases in the beginning of lactation. Alert systems to detect the physiological imbalance in a cow using Fourier transform mid-infrared spectroscopy in milk have been developed. The objective of this study was to estimate the value of information provided from such system with different indicator accuracies, herd prevalence and prices. A decision tree was created to model the probabilities of detection and associated costs of test outcome, intervention and occurrence of disease. We assumed that the negative effect of physiological imbalance was the development of subclinical ketosis and that this negative effect was prevented by drenching the cows with propylene glycol for 5 days. We simulated the economic impact of subclinical ketosis mediated through physiological imbalance to be $194 per case. The results showed that if the alert system was highly accurate (Se = 0.99/Sp = 0.99), and the prevalence of physiological imbalance was 30 %, the value of information provided from the system is $19 per cow-year. In case the prevalence is 5 % or 50 %, the value of information is $3 and $13, respectively. These estimates for the value do not cover the capital costs and operational costs of the alert system. This study furthermore clearly demonstrated that in order to estimate the value of information correctly, it is important to consider that drenching all cows and not drenching any of the cows are the two relevant alternative options in the absence of the alert system. In conclusion, the decision tree and sensitivity analysis developed in this study show that final economic results are highly variable to the prevalence of physiological imbalance and highest at an intermediate prevalence. Other relevant factors are the costs associated with drenching and the cost associated with treating false positives and not treating false negatives. In addition, this study highlights the benefits of simulation to pinpoint where additional information is needed to further quantify the economic value and required accuracy of an indication-based intervention system.

AdaptMap consortium., [Background]: Since goat was domesticated 10,000 years ago, many factors have contributed to the differentiation of goat breeds and these are classified mainly into two types: (i) adaptation to different breeding systems and/or purposes and (ii) adaptation to different environments. As a result, approximately 600 goat breeds have developed worldwide; they differ considerably from one another in terms of phenotypic characteristics and are adapted to a wide range of climatic conditions. In this work, we analyzed the AdaptMap goat dataset, which is composed of data from more than 3000 animals collected worldwide and genotyped with the CaprineSNP50 BeadChip. These animals were partitioned into groups based on geographical area, production uses, available records on solid coat color and environmental variables including the sampling geographical coordinates, to investigate the role of natural and/or artificial selection in shaping the genome of goat breeds., [Results]: Several signatures of selection on different chromosomal regions were detected across the different breeds, sub-geographical clusters, phenotypic and climatic groups. These regions contain genes that are involved in important biological processes, such as milk-, meat- or fiber-related production, coat color, glucose pathway, oxidative stress response, size, and circadian clock differences. Our results confirm previous findings in other species on adaptation to extreme environments and human purposes and provide new genes that could explain some of the differences between goat breeds according to their geographical distribution and adaptation to different environments., [Conclusions]: These analyses of signatures of selection provide a comprehensive first picture of the global domestication process and adaptation of goat breeds and highlight possible genes that may have contributed to the differentiation of this species worldwide., Authors are grateful to all breeders and AdaptMap members who provided data to the initiative (http://www.goatadaptmap.org/) that are described in Stella et al.. The authors from the University of Milan are grateful to Stefano Frattini who was supported by the GenHome project, for supporting coordinating meetings. Support for Francesca Bertolini was provided by State of Iowa, hatch and Ensminger funds. Financial support provided in part by the Illumina Greater Good grant is appreciated.

Experimental evidences support a direct role for leptin in immunity. Besides controlling food intake and energy expenditure, leptin was reported to be involved in the regulation of the immune system in ruminants. The aim of this work was to highlight the expression of leptin receptor (LEPR) on Bubalus bubalis immune cells using a multi-approach assessment: flow cytometry, confocal microscopy and gene expression analysis. Flow cytometric analysis of LEPR expression showed that peripheral blood monocytes were the predominant cells expressing LEPR. This result was corroborated by confocal microscopy and RT-PCR analysis. Moreover, among lymphocytes, LEPR was mainly expressed by B lymphocytes and Natural Killer cells. Evidence of LEPR expression on buffalo blood leukocytes showed to be a good indicator of the responsivity of these cells to leptin, so confirming the involvement of leptin in buffalo immune response.

The aim of this study was to describe metabolism of early-lactation dairy cows by clustering cows based on glucose, insulin-like growth factor I (IGF-I), free fatty acid, and beta-hydroxybutyrate (BHB) using the k-means method. Predictive models for metabolic clusters were created and validated using 3 sets of milk biomarkers (milk metabolites and enzymes, glycans on the immuno-gamma globulin fraction of milk, and Fourier-transform mid-infrared spectra of milk). Metabolic clusters are used to identify dairy cows with a balanced or imbalanced metabolic profile. Around 14 and 35 d in milk, serum or plasma concentrations of BHB, free fatty acids, glucose, and IGF-I were determined. Cows with a favorable metabolic profile were grouped together in what was referred to as the "balanced" group (n = 43) and were compared with cows in what was referred to as the "other balanced" group (n = 64). Cows with an unfavorable metabolic profile were grouped in what was referred to as the "imbalanced" group (n = 19) and compared with cows in what was referred to as the "other imbalanced" group (n = 88). Glucose and IGF-I were higher in balanced compared with other balanced cows. Free fatty acids and BHB were lower in balanced compared with other balanced cows. Glucose and IGF-I were lower in imbalanced compared with other imbalanced cows. Free fatty acids arid BHB were higher in imbalanced cows. Metabolic clusters were related to production parameters. There was a trend for a higher daily increase in fat- and protein-corrected milk yield in balanced cows, whereas that of imbalanced cows was higher. Dry matter intake and the daily increase in dry matter intake were higher in balanced cows and lower in imbalanced cows. Energy balance was continuously higher in balanced cows and lower in imbalanced cows. Weekly or twice-weekly milk samples were taken and milk metabolites and enzymes (milk glucose, glucose-6-phosphate, BHB, lactate dehydrogenase, N-acetyl-beta-D-glucosaminidase, isocitrate), immunogamma globulin glycans (19 peaks), and Fourier-transform mid-infrared spectra (1,060 wavelengths reduced to 15 principal components) were determined. Milk biomarkers with or without additional cow information (days in milk, parity, milk yield featurs) were used to create predictive models for the metabolic clusters. Accuracy for prediction of balanced (80%) and imbalanced (88%) cows was highest using milk metabolites and enzymes combined with days in milk and parity. The results and models of the present study are part of the GplusE project and identify novel milk-based phenotypes that may be used as predictors for metabolic and performance traits in early-lactation dairy cows.

Unbalanced metabolic status in the weeks after calving predisposes dairy cows to metabolic and infectious diseases. Blood glucose, IGF-I, non-esterified fatty acids (NEFA) and β-hydroxybutyrate (BHB) are used as indicators of the metabolic status of cows. This work aims to (1) evaluate the potential of milk mid-IR spectra to predict these blood components individually and (2) to evaluate the possibility of predicting the metabolic status of cows based on the clustering of these blood components. Blood samples were collected from 241 Holstein cows on six experimental farms, at days 14 and 35 after calving. Blood samples were analyzed by reference analysis and metabolic status was defined by k-means clustering (k=3) based on the four blood components. Milk mid-IR analyses were undertaken on different instruments and the spectra were harmonized into a common standardized format. Quantitative models predicting blood components were developed using partial least squares regression and discriminant models aiming to differentiate the metabolic status were developed with partial least squares discriminant analysis. Cross-validations were performed for both quantitative and discriminant models using four subsets randomly constituted. Blood glucose, IGF-I, NEFA and BHB were predicted with respective R2 of calibration of 0.55, 0.69, 0.49 and 0.77, and R2 of cross-validation of 0.44, 0.61, 0.39 and 0.70. Although these models were not able to provide precise quantitative values, they allow for screening of individual milk samples for high or low values. The clustering methodology led to the sharing out of the data set into three groups of cows representing healthy, moderately impacted and imbalanced metabolic status. The discriminant models allow to fairly classify the three groups, with a global percentage of correct classification up to 74%. When discriminating the cows with imbalanced metabolic status from cows with healthy and moderately impacted metabolic status, the models were able to distinguish imbalanced group with a global percentage of correct classification up to 92%. The performances were satisfactory considering the variables are not present in milk, and consequently predicted indirectly. This work showed the potential of milk mid-IR analysis to provide new metabolic status indicators based on individual blood components or a combination of these variables into a global status. Models have been developed within a standardized spectral format, and although robustness should preferably be improved with additional data integrating different geographic regions, diets and breeds, they constitute rapid, cost-effective and large-scale tools for management and breeding of dairy cows.

Biogas production from agricultural and industrial wastes delivers two benefits: on one side, the treatment of organic residues prevents the environmental and economic impact of their disposal; on the other side, methane and/or hydrogen are generated. The aims of this study were both to produce bio-hydrogen from buffalo wastes and to investigate the relationship between biogas production and bacterial and archaeal community composition. Anaerobic codigestion of livestock by-products (buffalo sludge and low protein cheese whey-scotta), with buffalo rumen and buffalo sludge as inoculum, was performed. The microbial community was analyzed using next-generation sequencing of 16S rRNA gene amplicons. Codigestion showed to be positive because of both sludge buffering capability and highly degradable carbohydrates content in scotta. Rumen inoculum proved more efficient compared to sludge during fermentation. In fact, cumulated production was higher (120.8 Vs 65.4 ml H2 g VS-1 respectively) and the average percentage of hydrogen in biogas was 48.1 (v/v) with maximum peak at 64.6. Moreover, rumen bacterial profile showed higher genera richness. Taxonomic classification showed that among the bacteria, Firmicutes, 23.3% of whom Clostridia; Bacteroidetes, and in particular Bacteroidia; Proteobacteria and Tenericutes, accounted for 88.2% of total sequences. Concerning the Clostridia Family XIII, the C. Incertae Sedis was the most represented (6.6%), and its quantity was twice as much in rumen inoculated hydrogen-producing samples than those non-producing. In the archaeal, community predominated the phylum Euryarcheota, with Methanobrevibacter the most represented, which was higher when hydrogen was produced with rumen inoculum. Studies on buffalo rumen as inoculum for hydrogen production are limited and this paper gives a first overview of microbial community composition by NGS in producing and non-producing samples.

Milk oligosaccharides are typically composed of 3–10 monosaccharide units, including glucose, galactose, and N-acetylglucosamine as well as fucose and sialic acids. Different healthy properties have been attributed to oligosaccharides; they participate in several protective and physiological roles, including prebiotic activity, immunoregulation, and inhibition of pathogen adhesion in the gastrointestinal tract of infants. Recent studies have demonstrated beneficial functions of milk oligosaccharides in vitro indicating them as potential new source of microbiotic modulators. The beneficial effects of oligosaccharides have attracted the interest of food scientists and food companies to isolate the oligosaccharides from dairy by-products. To this aim, membrane filtration technology has been described as green methodology used to obtain oligosaccharides extracts from dairy by-products. At the same time, different analytical methodologies have been used to determine their composition, and recent advancements were made in analytical techniques, including nuclear magnetic resonance spectroscopy, liquid chromatography, anion exchange chromatography, capillary electrophoresis, and mass spectrometry. In this chapter, a comprehensive overview of oligosaccharides present in dairy by-products, including analytical methods for their determination, purification technologies, and healthy effects, has been reported.

Background: Goat populations that are characterized within the AdaptMap project cover a large part of the worldwide distribution of this species and provide the opportunity to assess their diversity at a global scale. We analysed genome-wide 50K single nucleotide polymorphism (SNP) data from 144 populations to describe the global patterns of molecular variation, compare them to those observed in other livestock species, and identify the drivers that led to the current distribution of goats., Results: A high degree of genetic variability exists among the goat populations studied. Our results highlight a strong partitioning of molecular diversity between and within continents. Three major gene pools correspond to goats from Europe, Africa and West Asia. Dissection of sub-structures disclosed regional gene pools, which reflect the main post-domestication migration routes. We also identified several exchanges, mainly in African populations, and which often involve admixed and cosmopolitan breeds. Extensive gene flow has taken place within specific areas (e.g., south Europe, Morocco and Mali-Burkina Faso-Nigeria), whereas elsewhere isolation due to geographical barriers (e.g., seas or mountains) or human management has decreased local gene flows., Conclusions: After domestication in the Fertile Crescent in the early Neolithic era (ca. 12,000 YBP), domestic goats that already carried differentiated gene pools spread to Europe, Africa and Asia. The spread of these populations determined the major genomic background of the continental populations, which currently have a more marked subdivision than that observed in other ruminant livestock species. Subsequently, further diversification occurred at the regional level due to geographical and reproductive isolation, which was accompanied by additional migrations and/or importations, the traces of which are still detectable today. The effects of breed formation were clearly detected, particularly in Central and North Europe. Overall, our results highlight a remarkable diversity that occurs at the global scale and is locally partitioned and often affected by introgression from cosmopolitan breeds. These findings support the importance of long-term preservation of goat diversity, and provide a useful framework for investigating adaptive introgression, directing genetic improvement and choosing breeding targets.

The decrease in sequencing cost and increased sophistication of assembly algorithms for short-read platforms has resulted in a sharp increase in the number of species with genome assemblies. However, these assemblies are highly fragmented, with many gaps, ambiguities, and errors, impeding downstream applications. We demonstrate current state of the art for de novo assembly using the domestic goat (Capra hircus) based on long reads for contig formation, short reads for consensus validation, and scaffolding by optical and chromatin interaction mapping. These combined technologies produced what is, to our knowledge, the most continuous de novo mammalian assembly to date, with chromosome-length scaffolds and only 649 gaps. Our assembly represents a ∼400-fold improvement in continuity due to properly assembled gaps, compared to the previously published C. hircus assembly, and better resolves repetitive structures longer than 1 kb, representing the largest repeat family and immune gene complex yet produced for an individual of a ruminant species.

In this report, we describe the identification of the complete ovine gelsolin (GSN) isoform b cDNA. We sequenced exons 12 and 13 and parts of introns 11, 12 and 13 in 263 sheep of three breeds. We found 11 novel SNPs, of which 2 were missense mutations. GSN is a Ca2+-dependent actin-regulatory protein that modulates actin assembly and disassembly. Because actin is involved in the regulation of intracellular lipid metabolism, particularly in the formation of cytoplasmic fat droplets and in the transport of lipid constituents, we tested the hypothesis that different GSN genotypes might influence actin activity and, consequently, milk yield and quality. An association analysis was performed between each SNP and the following traits, which were evaluated in 464 recorded lactations of the same sheep: milk yield, fat and protein content, as well as somatic cell score. Significant associations (P = 0.02) were found between three SNPs in intron 12 and fat content in the Altamurana breed. For two of the SNPs, the effect was also noted in the Gentile breed (P = 0.09). Suggestive associations were also found between the SNPs and other traits, albeit not in all of the breeds. The three SNPs that affected fat content were located in the consensus sequences of binding sites for the following transcription factors: Tal-1 alpha, Evi-1 and Egr-3. Therefore, we hypothesised that the incorrect modulation of actin assembly occurs in one of the GSN genotypes, with a particularly evident effect on fat content.

SLC11A1 (solute carrier family 11 member 1 protein) gene influences the initial phase of bacterial cellular infections through macrophage activation. Recent literature on buffalo has attempted to associate the genotype of the polymorphic microsatellite located in the 3'untranslated region (3'UTR) of the gene, with either susceptibility to brucellosis or with improved macrophage function. Carriers of the (GT)16 allele have been reported to be resistant to brucellosis. In this study we analyzed the steady-state level of SLC11A1 expression in a serologically negative herd of 26 animals differing by the number of (GT)n microsatellite repeats by using a reverse transcriptase quantitative real-time polymerase chain reaction approach. We evaluated five different reference genes, which had not been reported previously, for use in gene expression experiments in buffalo blood. However, we did not find any significant difference between buffalo carriers of the different microsatellite alleles, with respect to SLC11A1 expression in whole blood or in blood fractions [peripheral blood mononuclear cells (PBMC) and polymorphonuclear leukocytes/granulocytes (PMN/G)]. Conversely, there was a difference between the blood fractions in their SLC11A1 expression levels, with the PMN/G fraction having a higher expression level than the PBMC fraction (P0.015).

The decrease in sequencing cost and increased sophistication of assembly algorithms for short-read platforms has resulted in a sharp increase in the number of species with genome assemblies. However, these assemblies are highly fragmented, with many gaps, ambiguities, and errors, impeding downstream applications. We demonstrate current state of the art for de novo assembly using the domestic goat (Capra hircus), based on long reads for contig formation, short reads for consensus validation, and scaffolding by optical and chromatin interaction mapping. These combined technologies produced the most contiguous de novo mammalian assembly to date, with chromosome-length scaffolds and only 663 gaps. Our assembly represents a >250-fold improvement in contiguity compared to the previously published C. hircus assembly, and better resolves repetitive structures longer than 1 kb, supporting the most complete repeat family and immune gene complex representation ever produced for a ruminant species.

The aim of the present study was to evaluate the genetic variation of milk fat CLA, together with the variation of CLA precursors, including the individual PUFA that are potentially involved in the metabolic pathway of CLA. The allelic substitution effect, upon these FA, was estimated for a number of polymorphisms, that are located within 9 candidate genes known to influence milk FA partitioning. Sheep milk was chosen because it contains higher total fat percentage, and higher CLA levels per gram fat, than milk of other ruminants. Milk FAME analyses were performed on individual milk samples of sheep from three different breeds. Our results reflect the association of three genes (alpha-1-antichymotrypsin; diacylglycerol O-acyltransferase homolog-2; and zona pellucida glycoprotein-2) with the values of both linolenic FA and CLA; of three more genes (insulin-like growth factor I; lecithin-cholesterol acyltransferase and propionyl coenzyme A carboxylase, beta polypeptide) with the variability of linolenic FA; and of one gene, the fatty acid synthetase with the variability of CLA and stearic FA. The current study might contribute to the understanding of the metabolic pathway of PUFA in sheep milk, providing suggestions to modify milk fat composition through selection.

In this study, the effect of polymorphisms in the leptin gene on the hematological variables in periparturient dairy cows was investigated. The hematological profile of 67 Holstein cows was assessed for 6 wk around calving. The DNA of the cows was genotyped at 6 polymorphic loci within the leptin gene, and 7 haplotypes were reconstructed. Significant haplotype substitution effects were found, for haplotype 1, on total white blood cell count for 2 wk around calving (+0.70 10(3)/μL, P = 0.05; +1.38 10(3)/μL, P = 0.0001); on neutrophil cell count in the first week after calving (+0.94 10(3)/μL, P = 0.001); on lymphocyte count during the 3 wk before and the first week after calving (+0.32 10(3)/μL, P = 0.05; +0.27 10(3)/μL, P = 0.03; +0.26 10(3)/μL, P = 0.04; +0.34 10(3)/μL, P = 0.01); on red blood cell count during the last week before calving and wk 1 and 2 after calving (+0.21 10(6)/μL, P = 0.02; +0.23 10(6)/μL, P = 0.01; +0.20 10(6)/μL, P = 0.03); on mean corpuscular volume (-1.35 fL, P = 0.01; -1.29 fL, P = 0.002; -1.18 fL, P = 0.004; -1.09 fL, P = 0.008; -1.23 fL, P = 0.003; -1.31 fL, P = 0.003); and on mean corpuscular hemoglobin (-0.37 pg, P = 0.05; -0.38 pg, P = 0.02; -0.39 pg, P = 0.01; -0.34 pg, P = 0.03; -0.40 pg, P = 0.01; -0.40 pg, P = 0.01) during all 6 wk analyzed. Significant haplotype substitution effects, but opposite those of haplotype-1, were found for haplotype-2 on white blood cell count (-1.10 10(3)/μL, P = 0.01; -1.30 10(3)/μL, P = 0.002; -1.09 10(3)/μL, P = 0.01) and neutrophil count (-0.82 10(3)/μL, P = 0.02; -0.95 10(3)/μL, P = 0.005; -0.92 10(3)/μL, P = 0.01). Haplotype-3 influenced red blood cell count (-0.23 10(6)/μL, P = 0.03; -0.28 10(6)/μL, P = 0.01; -0.34 10(6)/μL, P = 0.002) during the last 2 wk before and the first week after calving, and also, with effects evident only in wk 3 and 2 before calving, mean corpuscular volume (+1.38 fL, P = 0.03; +0.97 fL, P = 0.05; +1.08 fL, P = 0.05), mean corpuscular hemoglobin (+0.58 pg, P = 0.02; +0.38 pg, P = 0.04; 0.51 pg, P = 0.01), and red blood cell distribution width (-0.56% P = 0.02; -0.47%, P = 0.05). The current study provided evidence that several polymorphisms in the leptin gene play a role in the variability of hematological variables during the peripartum period, and might be used as genetic markers for improving the immunological conditions of dairy cows in critical productive periods.

Consumer complaints against the blandness of modern lean meat and the frequent reference to the more strongly flavored meat that was available years ago have prompted reconsideration of high fatdepositing typical pig breeds. Casertana and Large White pig breeds are characterized by a different tendency toward fat accumulation as they exhibit opposite genetic and physiological traits with respect to the energy metabolism. These physiological differences were investigated in longissimus lumborum muscles through proteomics (2-DE, MS/MS) and microarray approaches. Data were analyzed for pathway and network analyses, as well as GO term enrichment of biological functions. As a result, Casertana showed a greater amount of proteins involved in glycolitic metabolism and mainly rely on fast-mobilizable energy sources. Large White overexpressed cell cycle and skeletal muscle growth related genes. Metabolic behavior and other implications are discussed. L'articolo è disponibile sul sito dell'editore http://pubs.acs.org/

Myostatin (GDF8) acts as a negative regulator of muscle growth. Mutations in the gene are responsible for the double muscling phenotype in several European cattle breeds. Here we describe the sequence of the upstream 5′ region of the myostatin gene. The sequence analysis was carried out on three animals of nine European cattle breeds, with the aim to search for polymorphisms. A T/A polymorphism at –371 and a G/C polymorphism at –805 (relative to ATG) were found. PCR- RFLP was used to further screen 353 animals of the nine breeds studied and to assess the frequencies of the SNPs. The promoter region of the gene contains several binding sites for transcription factors found also in other myogenic genes. This may play an important role in the regulation of the protein and consequently on muscular development.

NRAMP1 (natural-resistance-associated macrophage protein) gene influences the initial phase of bacterial cellular infections, regulating macrophage activation. Recent literature on buffalo has attempted to associate the genotypes at the polymorphic microsatellite, that is located in the 3'-UTR of the gene, with either susceptibility to brucellosis or improved macrophage function. However, contradictory results were reported. In the present work, we have sequenced the whole coding region, as well as part of the introns and UTRs, of the NRAMP1 gene in 49 Mediterranean buffaloes, including both serologically positive and negative animals to Brucella abortus test. We have detected 12 mutations. Nineteen haplotypes were built from the detected variant alleles, so demonstrating the high variability of this gene in buffalo, but no significant differences in haplotype frequencies were found between serologically positive/negative animals.

SummaryApricots of two harvests (9–10° Brix and 13–14° Brix) were treated for 6 d at 15°C with 1%, 2% and 4% O2 (low oxygen = LO) and then kept for 7 d and 5 d (respectively for the first and the second harvest) in air at 15°C (shelf life = s.l.). Control fruit were held continuously in air at 15°C or for 6 d at 5°C then moved to 15°C. In early harvest fruit, low O2 (1% and 2%) for 6 d controlled ethylene production even after the transfer and consequently the fruit had lower SCC and were firmer. In fruit from the second harvest, only 1% O2 atmosphere or control fruits at 5°C were able to control the rise of ethylene in s.l. and to reduce the increase of soluble solids content (SSC). A 1% O2 atmosphere maintained acceptable firmness even during s.l. in fruit of both harvests. Respiration rate was better restricted by low temperature during the treatment but at the end of experiment no difference was observed among the samples. Colour of apricots was maintained only by 1% O2 atmosphere or 5°C temperature b...

With the aim to assess if some molecular markers can help to select animals for meat characteristics, we studied 84 individuals equally representing the Marchigiana, Maremmana, and Holstein Friesian cattle breeds genotyped at 288 SNPs located within candidate genes. Several SNPs were found associated with meat quality parameters but with P which was higher than the Bonferroni threshold. However, several SNPs had a low P at different times during meat maturation, suggesting their involvement in the meat quality variation. Of particular interest for the biological role and potential for selection were: cathepsin G affecting MFI, IGF1R affecting pH and collagen XVIII affecting colour.

In this work, the genetic variation of milk FA was investigated in three different bovine breeds, the Jersey, the Piedmontese and the Valdostana, and at different lactation stages. All animals were genotyped for 21 Single Nucleotide Polymorphisms located within nine candidate genes involved in lipid synthesis: diacylglycerol acyltransferase 1 and 2 (DGAT1, 2); stearoyl-CoA desaturase (SCD); growth hormone receptor (GHR); fatty acid synthase (FASN); acyl-CoA dehydrogenase (ACAD); fatty acid binding protein (FABP4); lipoprotein lipase (LPL); and leptin gene (LEP). The highest milk-fat Jersey breed also showed the highest content of saturated FA. Throughout lactation, the breeds showed a similar variation in the FA, with a decrease in the short-chain, this was accompanied by a general increase in the long chain FA at the end of lactation. The increase in long chain saturated FA was particularly evident in the case of the Jersey. The effect ofSCDgene on the C14 desaturation index was confirmed; theDGAT1gene was polymorphic only in the Jersey breed, but its effect was confirmed only on milk fat content; three further potential candidate genes were identified: first, theFABP4gene, which was found to influence medium and long chain FA in all the breeds, but not the desaturation indices; second, theFASNgene, which was found to influence the amount of PUFA in the Piedmontese and the Valdostana, and third, theLPLgene, which was found to affect fat content in the Piedmontese.

Leptin is an adipocyte-derived hormone acting as a major regulator for food intake and energy homeostatis. Previous studies have focused on association between polymorphisms in the coding region of the leptin pig gene and economically important traits. This work was aimed to study the leptin (LEP) gene at the promoter region to search for polymorphisms that could led to a different gene expression regulation. In a 1213 bp 5’ UTR region we identified 15 new single nucleotide polymorphisms (SNP) and 2 deletion (del) in two pig breeds characterized by different fat content namely Casertana (CT) and Large White (LW). In order to investigate whether the polymorphism affects the transcriptional activity of the leptin promoter we evaluated the in vitro reporter-gene activity driven by two constructs harbouring different haplotype and we found a two fold difference in transcription efficiency (Pin vitro results and backfat thikness (BF) and average daily weight gain (ADG) phenotypes, in the considered breeds and we found a weak association of the different allele with backfat thickness. The polymorphisms identified in the 5’-flanking region of the LEP gene may serve as a basis for future studies even in different breeds and might provide molecular data that can be used in the selection schemes.