Genomic prediction of blood biomarkers of metabolic disorders in Holstein cattle using parametric and nonparametric models.

BACKGROUND: Metabolic disturbances adversely impact productive and reproductive performance of dairy cattle due to changes in endocrine status and immune function, which increase the risk of disease. This may occur in the post-partum phase, but also throughout lactation, with sub-clinical symptoms. Recently, increased attention has been directed towards improved health and resilience in dairy cattle, and genomic selection (GS) could be a helpful tool for selecting animals that are more resilient to metabolic disturbances throughout lactation. Hence, we evaluated the genomic prediction of serum biomarkers levels for metabolic distress in 1353 Holsteins genotyped with the 100K single nucleotide polymorphism (SNP) chip assay. The GS was evaluated using parametric models best linear unbiased prediction (GBLUP), Bayesian B (BayesB), elastic net (ENET), and nonparametric models, gradient boosting machine (GBM) and stacking ensemble (Stack), which combines ENET and GBM approaches. RESULTS: The results show that the Stack approach outperformed other methods with a relative difference (RD), calculated as an increment in prediction accuracy, of approximately 18.0% compared to GBLUP, 12.6% compared to BayesB, 8.7% compared to ENET, and 4.4% compared to GBM. The highest RD in prediction accuracy between other models with respect to GBLUP was observed for haptoglobin (hapto) from 17.7% for BayesB to 41.2% for Stack; for Zn from 9.8% (BayesB) to 29.3% (Stack); for ceruloplasmin (CuCp) from 9.3% (BayesB) to 27.9% (Stack); for ferric reducing antioxidant power (FRAP) from 8.0% (BayesB) to 40.0% (Stack); and for total protein (PROTt) from 5.7% (BayesB) to 22.9% (Stack). Using a subset of top SNPs (1.5k) selected from the GBM approach improved the accuracy for GBLUP from 1.8 to 76.5%. However, for the other models reductions in prediction accuracy of 4.8% for ENET (average of 10 traits), 5.9% for GBM (average of 21 traits), and 6.6% for Stack (average of 16 traits) were observed. CONCLUSIONS: Our results indicate that the Stack approach was more accurate in predicting metabolic disturbances than GBLUP, BayesB, ENET, and GBM and seemed to be competitive for predicting complex phenotypes with various degrees of mode of inheritance, i.e. additive and non-additive effects. Selecting markers based on GBM improved accuracy of GBLUP.

Milk metagenomics and cheese-making properties as affected by indoor farming and summer highland grazing.

The study of the complex relationships between milk metagenomics and milk composition and cheese-making efficiency as affected by indoor farming and summer highland grazing was the aim of the present work. The experimental design considered monthly sampling (over 5 mo) of the milk produced by 12 Brown Swiss cows divided into 2 groups: the first remained on a lowland indoor farm from June to October, and the second was moved to highland pastures in July and then returned to the lowland farm in September. The resulting 60 milk samples (2 kg each) were used to analyze milk composition, milk coagulation, curd firming, and syneresis processes, and to make individual model cheeses to measure cheese yields and nutrient recoveries in the cheese. After DNA extraction and Illumina Miseq sequencing, milk microbiota amplicons were also processed by means of an open-source pipeline called Quantitative Insights Into Microbial Ecology (Qiime2, version 2018.2; https://qiime2.org). Out of a total of 44 taxa analyzed, 13 bacterial taxa were considered important for the dairy industry (lactic acid bacteria, LAB, 5 taxa; and spoilage bacteria, 4) and for human (other probiotics, 2) and animal health (pathogenic bacteria, 2). The results revealed the transhumant group of cows transferred to summer highland pastures showed an increase in almost all the LAB taxa, bifidobacteria, and propionibacteria, and a reduction in spoilage taxa. All the metagenomic changes disappeared when the transhumant cows were moved back to the permanent indoor farm. The relationships between 17 microbial traits and 30 compositional and technological milk traits were investigated through analysis of correlation and latent explanatory factor analysis. Eight latent factors were identified, explaining 75.3% of the total variance, 2 of which were mainly based on microbial traits: pro-dairy bacteria (14% of total variance, improving during summer pasturing) and pathogenic bacteria (6.0% of total variance). Some bacterial traits contributed to other compositional-technological latent factors (gelation, udder health, and caseins).

People's attitudes towards the agrifood system influence the value of ecosystem services of mountain agroecosystems.

Studies covering the social valuation of ecosystem services (ES) are increasingly incorporating people's attitudes, which allows social heterogeneity to be identified. This is especially relevant in mountain areas, where diverse complex interactions occur among the environment, the socioeconomic system, and a wide variety of farming practices. In this context, we aimed to: (i) identify the attitudinal dimensions that build people views about the agrifood system; and (ii) analyse how these attitudinal dimensions influence the value given to ES delivered by mountain agroecosystems of two European countries. We conducted a survey with a sample of 1008 individuals evenly distributed in the Italian Alps and Spanish Mediterranean mountain areas to collect information on people's attitudes toward: (i) the economy and the environment; (ii) rural development and agricultural intensification; (iii) food quality, production, and consumption; and (iv) agricultural and environmental policies. The survey included a choice experiment to assess the value that individuals attach to the most relevant ES provided by mountain agroecosystems in these areas (i.e., landscape, biodiversity, quality local products, wildfires prevention and water quality). The results showed four common attitudinal dimensions, namely Economy over environment, Mass-Market distribution reliability, Agricultural productivism, and Environmentalism and rural lifestyle. These attitudinal dimensions resulted in six groups of respondents. Most groups positively valued an increase in the delivery of all the analysed ES, which suggests that agricultural policies which aim to promote ES are likely to receive social support in the study areas. However, the differing attitudinal dimensions underlying people's preferences may result in disagreements about the steps to be taken to achieve the desired increase in ES delivery.

Animal Welfare and Farmers' Satisfaction in Small-Scale Dairy Farms in the Eastern Alps: A "One Welfare" Approach.

The multidimensional concept of animal welfare includes physical health, good emotional state, and appropriate behavior of the animals. The most recent methods for its assessment are inspired by the Welfare Quality, a project compiling animal-, resource-, and management-based measures. Recently, animal welfare assessment has also considered the human factor in a so-called "One Welfare" approach. The One Welfare framework highlights the interconnections between animal welfare, human well-being, and the environment. The concept seems to fit particularly well to mountain areas where the relationship between human, animals, and the environment is stronger. In such disadvantaged areas, farmers' well-being plays a key role in maintaining livestock farming profitably and sustainably. This study aims to investigate the relationship between farmers' satisfaction, animal welfare outcomes, and overall farm performance in 69 small-scale dairy farms in the Eastern Alps. Animal welfare assessment consisted of animal-based measures and was performed using the methodology proposed by the European Food Safety Authority for this type of farm. Moreover, the farmers were interviewed to retrieve data on farm characteristics and on their level of satisfaction toward workload, land organization, relationship with the agricultural/non-agricultural community, and the future of local agriculture. The results show that good animal welfare can be obtained in a mountain farming system. Clinical indicators show a low prevalence of diseases and of very lean cows as opposed to integument alterations. The workload is not perceived as a problem in traditional farms (i.e., tie-stall and with no participation in quality-certification schemes). Animal welfare is higher in those farms where farmers have a positive engagement with both the agricultural and non-agricultural community and where farmers are satisfied with their land organization. A One Welfare approach could be applied on a larger scale to fully understand the links between animal and human well-being in mountain areas.

Behavioural heat-stress compensation in a cold-adapted ungulate: Forage-mediated responses to warming Alpine summers.

Alpine large herbivores have developed physiological and behavioural mechanisms to cope with fluctuations in climate and resource availability that may become maladaptive under climate warming. We tested this hypothesis in female Alpine ibex (Capra ibex) by modelling annual and daily movement and activity patterns in relation to temperature, vegetation productivity and reproductive status based on bio-logging data and climate change projections. In summer, ibex moved upslope, tracking the green wave. Ibex decreased diel activity sharply above a threshold temperature of 13-14°C, indicating thermal stress, but compensated behaviourally by foraging both earlier and later in the day, and by moving further upslope than on cooler days, especially reproductive females. This critical temperature will be exceeded three times as often under climate change projections. Under such scenarios, the altitudinal extent of the area will limit the available habitat providing thermal shelter, potentially impacting performance and population distribution of this emblematic mountain ungulate.

A multi-kingdom metabarcoding study on cattle grazing Alpine pastures discloses intra-seasonal shifts in plant selection and faecal microbiota.

Diet selection by grazing livestock may affect animal performance as well as the biodiversity of grazed areas. Recent DNA barcoding techniques allow to assess dietary plant composition in faecal samples, which may be additionally integrated by the description of gut microbiota. In this high throughput metabarcoding study, we investigated the diversity of plant, fungal and bacterial taxa in faecal samples of lactating cows of two breeds grazing an Alpine semi-natural grassland during summer. The estimated plant composition of the diet comprised 67 genera and 39 species, which varied remarkably during summer, suggesting a decline of the diet forage value with the advancing of the vegetative season. The fungal community included Neocallimastigomycota gut symbionts, but also Ascomycota and Basidiomycota plant parasite and coprophilous taxa, likely ingested during grazing. The proportion of ingested fungi was remarkably higher than in other studies, and varied during summer, although less than that observed for plants. Some variation related to breed was also detected. The gut bacterial taxa remained stable through the summer but displayed a breed-specific composition. The study provided insights in the reciprocal organisms' interactions affecting, and being affected by, the foraging behaviour: plants showed a high temporal variation, fungi a smaller one, while bacteria had practically none; conversely, the same kingdoms showed the opposite gradient of variation as respect to the animal host breed, as bacteria revealed to be the group mostly characterized by host-specificity.

Early-Life Dam-Calf Contact and Grazing Experience Influence Post-Weaning Behavior and Herbage Selection of Dairy Calves in the Short Term.

Rearing dairy calves with their mothers could teach them how to graze, optimizing grass use, and improving their welfare and performance. We tested the short-term effects of dam-calf contact experience on grazing and social behavior of weaned calves, monitored over seven days for their first post-weaning grazing experience. "Dam" (D) calves were reared and grazed with their mothers until weaning. "Mixed" calves (M) were separated from their mothers after 4 ± 0.5 weeks, they experienced dam-calf contact, but not grazing. "Standard" (S) calves had never experienced either dam-calf contact (separated at birth) or grazing. Each group grazed an equivalent pasture plot offering heterogeneous herbage. Scan sampling of calves' activities was performed every 5 min, 6 h per day, on Days 0, 1, 2, 3, and 7. Daily, the time when calves started grazing after introduction to pasture, and the number and duration of their grazing cycles were measured. Daily activities were differentiated into ingestion, rumination, and idling. The proportion of time that calves spent grouped with other individuals or isolated, and standing or lying were recorded. When grazing, their bites were characterized by botanical family group, height of the selected bite and vegetation status. Individual average daily gains from the 2-week periods before and after grazing were calculated, and were equivalent between groups (313 ± 71 g/d). On Day 0, D-calves started grazing immediately (1 ± 4.1 min), unlike M- and S-calves (39 ± 4.1 and 23 ± 4.1 min), and D-calves grazed patches of dry grass 21.7 times less than M-calves and 16.9 times less than S-calves. Dry herbage patch preference and grazing start time differences disappeared on Day 1. Calves spent the same time ingesting and idling, but M-calves spent on average 1.6 times less ruminating than D- or S-calves. The D-calves showed grazing behavior similar to that of adult cows, selecting grasses throughout pasture utilization, although legumes and forbs were present in the grazed layer. On the contrary, M- and S-calves did not express any specific preference. The S-calves spent more time isolated but had more positive reciprocal interactions than the calves in the other groups.

Effect of Feeding Adaptation of Italian Simmental Cows before Summer Grazing on Animal Behavior and Milk Characteristics.

According to the alpine transhumance system, dairy cows are moved from indoor feeding with conserved forage to fresh herbage feeding on pasture. The aim of this study was to assess, as a feeding adaptation technique, the effect of a gradual inclusion of fresh herbage in the diet of Italian Simmental dairy cows before their transfer to alpine pasture on performance, behavior, and milk characteristics. Eighteen cows were assigned to three groups: animals transferred to alpine pasture with a 10-d feeding adaptation period consisting in gradual access to a pasture close to the valley farm (GT), animals transferred to alpine pasture without a feeding adaptation period (AT), and animals kept in the valley farm (IND). During the first two weeks of summer grazing, GT and AT showed higher rumination time and different concentrations of ketones, hydrocarbons, organic acids, toluene, alcohols, phenols, and dimethyl sulfone in milk as compared to IND, whereas no differences were found in milk yield, composition, or coagulation properties. No differences between GT and AT were evident for the studied variables. The feeding adaptation technique used in this study did not influence the performance and milk characteristics of Italian Simmental dairy cows grazing on alpine pasture.

Influence of dietary protein content on the chemico-physical profile of dry-cured hams produced by pigs of two breeds.

The use of low-protein (LP) feeds is a good strategy to reduce the environmental release of N compounds, but their influence on the quality of the products must be considered. This study explored the influence of LP diet and two pig breeds (BR) with different lean growth ability on the quality traits of dry-cured hams. We analysed 40 left dry-cured hams from pigs of two BR [Duroc-Danbred crosses (Danbred) and Duroc × Large White crosses (Anas)] fed either conventional (147 to 132 g/kg, crude protein) or LP diet. The LP had a crude protein content reduced by 20% with respect to the conventional. The differences in ham quality resulting from protein reduction were small, with a decrease of the protein and an increase of the lipid content of the ham slice in Anas, but not in Danbred (BR × Diet interaction; P = 0.043). Therefore, the use of LP would be feasible and sustainable, without detrimental effects on products. It was found the pig genotypes with different potentials for lean growth may affect the initial ham weight, fat cover and seasoning losses of hams, but they appear to affect little other chemical, physical and textural quality traits of the dry-cured hams.

Responses of Pigs of Different Genotypes to a Variation in the Dietary Indispensable Amino Acid Content in Terms of Their Growth and Carcass and Meat Quality Traits.

We studied the response of pigs from two crossbred genetic lines (GL) in the 60 to 145 kg body weight interval to a variation in the indispensable amino acid (AA) content of their feed. Ninety-six barrows of two paternal GLs (Hypor Maxter and PIC 337) were housed in eight pens and fed quasi ad libitum on feeds differing in their standardized ileal digestible (SID) indispensable AA contents. Pigs in four pens received feeds containing 9.4 to 8.0 g/kg of SID Lys (HAA), considered non-limiting, while the others received feeds containing 8.5 to 6.5 g/kg of SID Lys (LAA). The two feeds had identical indispensable lysine, methionine, tryptophan and threonine contents per unit of crude protein (CP). Feed intake, growth, carcass weight, and the weights of the lean and fat cuts were recorded, and samples of longissimus lumborum were analyzed. Data were analyzed using a two-way factorial mixed model. The LAA feed lowered the estimated N excretion (p < 0.001) compared with HAA, without affecting growth, carcass or meat quality traits. Genetic line had trivial effects and the AA level × genotype interaction was never significant. The two pig genotypes did not differ sufficiently in growth potential and leanness to respond differently.

Effects of Summer Transhumance of Dairy Cows to Alpine Pastures on Body Condition, Milk Yield and Composition, and Cheese Making Efficiency.

Summer transhumance to alpine pastures (ALP) is widespread in dairy systems of alpine regions. This study aimed to investigate the effects of transhumance of Brown Swiss cows to ALP on the yield, composition, and coagulation properties of milk (MCP), and on cheese yield (CY). The study involved 12 multiparous cows kept at a mountain lowland permanent farm (PF), which were divided into two equal groups: One remained at the PF, the other was moved to the ALP (1860 m above sea level) from July to September. Every month (June to October), daily milk yield (MY) and body condition score (BCS) were recorded, and individual milk samples (n = 60, 2000 mL each) were collected to assess milk composition, MCP, and CY. Compared with PF, ALP cows had a reduced MY and BCS, which was maintained on return to the PF, greater fat and lower protein contents of milk. Neither MCP nor CY were affected by summer transhumance. In conclusion, summer transhumance did not affect the cheese making efficiency of milk but depressed MY and consequently daily cheese yield, which was nearly 2 kg/d lower for the ALP than the PF cows and was only partially recovered after returning to the PF in autumn.

Variation of milk coagulation properties, cheese yield, and nutrients recovery in curd of cows of different breeds before, during and after transhumance to highland summer pastures.

This paper aimed at evaluating the effect of summer transhumance to mountain pastures of dairy cows of different breeds on cheese-making ability of milk. Data were from 649 dairy cows of specialized (Holstein Friesian and Brown Swiss) dual purpose (Simmental) and local (mostly Rendena and Alpine Grey) breeds. The Fourier-Transform Infra-Red Spectra (FTIRS) of their milk samples were collected before and after transhumance in 109 permanent dairy farms, and during transhumance in 14 summer farms (with multi-breeds herds) of the Trento Province, north-eastern Italy. A variety of 18 traits describing milk coagulation, curd firming, cheese yield and nutrients recovery in curd/loss in whey were predicted on the basis of FTIRS collected at the individual cow level. Moving the cows to summer farms improved curd firming traits but reduced cheese yields because of an increase of water and fat lost in the whey. During summer grazing, most of cheese-making traits improved, often non-linearly. The milk from summer farms supplementing cows with more concentrates showed better curd firming and cheese yield, because of lower fat lost in the whey. The breed of cows affected almost all the traits with a worst cheese-making ability for milk samples of Holsteins through all the trial, and interacted with concentrate supplementation because increasing compound feed tended to improve cheese-making traits for all breed, with the exception of local breeds for coagulation time and of Brown Swiss for curd firming time. In general, summer transhumance caused a favourable effect on cheese-making aptitude of milk, even though with some difference according to parity, initial days in milk, breed and concentrate supplementation of cows.

Lungworms in Alpine ibex (Capra ibex) in the eastern Alps, Italy: An ecological approach.

Host-parasite relationships have been frequently investigated in mountain dwelling ungulates, though mostly focusing on gastrointestinal nematodes. On the contrary, very few studies were conducted on broncopulmonary nematodes, which may result in severe parenchymal lesions and act as predisposing factor for multifactorial pneumonia. The epidemiological and ecological features of lungworms infecting an Alpine ibex population in the Eastern Alps, Italy, were non-invasively investigated by means of a modified Baermann technique with an original quantitative methodology. Out of a total of 269 samples collected monthly from July to November 2013 and from July to October 2014, 212 (78.8%) were positive for Muellerius and 26 (9.7%) for Protostrongylus, whereas Neostrongylus and Cystocaulus were less prevalent (4.1% and 0.7%, respectively). None of the investigated samples tested positive for dictyocaulids. The genus Muellerius showed the highest larval output intensity (134.2 L1/g), followed by Protostrongylus with 33.8 L1/g. A contrasting age-related pattern of Muellerius and Protostrongylus was revealed, with the former significantly more prevalent and abundant in adult animals, while the latter in kids. Due to the limited accessibility of the study area during winter and spring, it was difficult to describe clear seasonal trends in larval output, although Muellerius showed a minimum in the late summer and a rise in the autumn. The newly developed diagnostic method showed a fair repeatability, thus representing an interesting tool to investigate the ecology of lungworms in protected species, such as the A. ibex. Based on results, ibex in the Marmolada massif seem to have an ecologically stable relationship with their lungworm community.