Genetic correlations of direct and indirect genetic components of social dominance with fitness and morphology traits in cattle.

BACKGROUND: Within the same species, individuals show marked variation in their social dominance. Studies on a handful of populations have indicated heritable genetic variation for this trait, which is determined by both the genetic background of the individual (direct genetic effect) and of its opponent (indirect genetic effect). However, the evolutionary consequences of selection for this trait are largely speculative, as it is not a usual target of selection in livestock populations. Moreover, studying social dominance presents the challenge of working with a phenotype with a mean value that cannot change in the population, as for every winner of an agonistic interaction there will necessarily be a loser. Thus, to investigate what could be the evolutionary response to selection for social dominance, it is necessary to focus on traits that might be correlated with it. This study investigated the genetic correlations of social dominance, both direct and indirect, with several morphology and fitness traits. We used a dataset of agonistic contests involving cattle (Bos taurus): during these contests, pairs of cows compete in ritualized interactions to assess social dominance. The outcomes of 37,996 dominance interactions performed by 8789 cows over 20 years were combined with individual data for fertility, mammary health, milk yield and morphology and analysed using bivariate animal models including indirect genetic effects. RESULTS: We found that winning agonistic interactions has a positive genetic correlation with more developed frontal muscle mass, lower fertility, and poorer udder health. We also discovered that the trends of changes in the estimated breeding values of social dominance, udder health and more developed muscle mass were consistent with selection for social dominance in the population. CONCLUSIONS: We present evidence that social dominance is genetically correlated with fitness traits, as well as empirical evidence of the possible evolutionary trade-offs between these traits. We show that it is feasible to estimate genetic correlations involving dyadic social traits.

Methodological quality of evidence-based clinical practice guidelines in cariology.

OBJECTIVE: The present study aimed to appraise the methodological quality of evidence-based Clinical Practice Guidelines (CPGs) in the cariology field. MATERIALS AND METHODS: A systematic search on electronic databases (MEDLINE/Pubmed, EMBASE, DARE and Epistemonikos), websites, and guideline organizations were undertaken. Evidence-based CPGs including at least one recommendation for clinical prevention and/or management of dental caries, developed for any clinical setting, were included. The quality of each guideline was evaluated using the AGREE II tool. Descriptive analysis was performed and the average overall score for each domain was calculated. RESULTS: Thirty-two guidelines were included. Most of the CPGs achieved higher scores for the domains of clarity of presentation (66.7%, 95% IC 37.3-52.2) and scope and purpose (59.6%, 95% IC 53.7-65.5) domains; and lower scores for editorial independence (46.1%, 95% IC 37.8-55.7) and applicability domain (44.7%, 95% IC 37-55.3). The reviewers assessed 12 CPGs (37.5%) as recommended for use, 15 (46.9%) recommended with modifications, and 5 (15.6%) as not recommended. CONCLUSION: The overall methodological quality of evidence-based CPGs in the cariology field is moderate, and there is a need for improvements in reporting related to most domains. The poorest reporting was found in the description of the domains' applicability of its recommendations and editorial independence. CLINICAL RELEVANCE: Clinical Practice Guidelines provide guidance to patients, healthcare professionals, and stakeholders. The quality of these documents is essential for establishing trust in their recommendations.

Exploring the Italian equine gene pool via high-throughput genotyping.

Introduction: The Italian peninsula is in the center of the Mediterranean area, and historically it has been a hub for numerous human populations, cultures, and also animal species that enriched the hosted biodiversity. Horses are no exception to this phenomenon, with the peculiarity that the gene pool has been impacted by warfare and subsequent "colonization". In this study, using a comprehensive dataset for almost the entire Italian equine population, in addition to the most influential cosmopolitan breeds, we describe the current status of the modern Italian gene pool. Materials and Methods: The Italian dataset comprised 1,308 individuals and 22 breeds genotyped at a 70 k density that was merged with publicly available data to facilitate comparison with the global equine diversity. After quality control and supervised subsampling to ensure consistency among breeds, the merged dataset with the global equine diversity contained data for 1,333 individuals from 54 populations. Multidimensional scaling, admixture, gene flow, and effective population size were analyzed. Results and Discussion: The results show that some of the native Italian breeds preserve distinct gene pools, potentially because of adaptation to the different geographical contexts of the peninsula. Nevertheless, the comparison with international breeds highlights the presence of strong gene flow from renowned breeds into several Italian breeds, probably due to historical introgression. Coldblood breeds with stronger genetic identity were indeed well differentiated from warmblood breeds, which are highly admixed. Other breeds showed further peculiarities due to their breeding history. Finally, we observed some breeds that exist more on cultural, traditional, and geographical point of view than due to actual genetic distinctiveness.

Evaluation of behavior in veal calves fed milk containing different levels of hempseed cake (Cannabis sativa L.).

The present study aimed to evaluate the effect on behavioral patterns of veal calves fed with increasing levels of hempseed cake (HSC) diluted in the milk replacer. In total, 48 Belgian Blue veal calves (12 females and 36 males), with a body weight (BW) of 62.0 kg and age of 42.6 days, were offered the same type and quantity of solid and liquid feed two times a day but randomly assigned to one of the three different HSC inclusion levels: 0% (CTR), 3% (T3), and 6% (T6). The study lasted for 6 months until slaughter. During this time, their behavior was recorded using video cameras provided with a surveillance system. The results indicated that HSC had negligible effect on calves' behavior and that calves, in general, spend most of their time resting and ruminating as they normally do with conventional diets. Hempseed cake inclusion (T3 and T6) increased (P < 0.05) the appetite for solid food and licking behavior during the late afternoon. T3 female calves increased (P < 0.05) their movement in the late afternoon. Male calves decreased (P < 0.05) their positive interaction, movement, and cross-sucking in the late afternoon as the inclusion of HSC increased. The inclusion of HSC into veal calves' diet did not negatively affect the animal's behavior; therefore, it can be suggested as a novel ingredient.

Eficácia de distrações audiovisuais em crianças no comportamento, controle da dor e da ansiedade durante procedimentos odontológicos: um estudo transversal / Effectiveness of audiovisual distractions in children on behavior, pain and anxiety control during dental procedures: a cross-sectional study

Objetivo: Avaliar se distrações audiovisuais em crianças são eficazes a fim de manejar comportamento, dor e ansiedade em atendimentos odontopediátricos. Materiais e Métodos: Este estudo transversal foi derivado de um ensaio clínico randomizado, realizado entre março e dezembro de 2019 com 48 crianças de 6 a 10 anos que necessitavam de tratamento restaurador, endodôntico ou exodôntico, na Clínica Infantil da Faculdade de Odontologia da Universidade Federal de Pelotas (UFPEL). Foi aprovado pelo Comitê de Ética em Pesquisa da UFPel, sob número 3700062. As crianças foram alocadas em dois grupos: controle e intervenção (óculos de realidade virtual e tablet). O comportamento da criança foi avaliado a partir da Versão Brasileira da Escala de Venham e a ansiedade através da Venham Picture Test Modified (VPTM). A partir das escalas Face, Legs, Activity, Cry and Consolability (FLACC) e Faces Pain Scale-Revised (FPS-R) foi realizada a avaliação da dor. Resultado: Observou-se que o grupo óculos possuiu melhores resultados do que o grupo tablet, porém sem diferença significativa, já que os dois obtiveram melhores resultados se comparados ao controle. Ademais, o comportamento apresentou diferença significativa (p=0,035) em relação às outras variáveis. Discussão: Um ensaio clínico que analisou uso dos óculos em crianças entre 6 e 9 anos, concluiu que não houve diferença estatística importante entre os grupos em relação ao comportamento. Assim, o presente estudo demonstrou resultados mais relevantes se comparados aos achados na literatura. Conclusão: O uso das distrações audiovisuais por crianças durante procedimentos odontológicos foram eficazes no manejo da dor, comportamento e ansiedade.

Aim: To assess whether audiovisual distractions in chil-dren are effective in managing behavior, pain and anxiety in pediatric dental care. Materials and Methods: This cross-sectional study was derived from a randomized clinical trial, carried out between March and December 2019 with 48 children aged 6 to 10 years who required restorative, endodontic or exodontic treatment, at the Children's Clinic of the Faculty of Dentistry of the Federal University of Pelotas (UFPEL). It was approved by the Re-search Ethics Committee at UFPel, under number 3700062. The children were allocated into two groups: control and intervention (virtual reality glasses and tablet). The child's behavior was assessed using the Brazilian Version of the Venham Scale and anxiety using the Venham Picture Test Modified (VPTM). Pain assessment was performed using the Face, Legs, Activity, Cry and Consolability (FLACC) and Faces Pain Scale-Revised (FPS-R) scales. Result: It was observed that the glasses group had better results than the tablet group, but without significant difference, since the two obtained better results compared to the control. Furthermore, the behavior showed a significant difference (p=0.035) in relation to the other variables. Discussion: A clinical trial that analyzed the use of glasses in children between 6 and 9 years old concluded that there was no significant statistical difference between the groups in relation to behavior. Thus, the present study showed more relevant results when compared to findings in the literature. Conclusion: The use of audiovisual distractions by children during den-tal procedures was effective in managing pain, behavior and anxiety.

Improvement of Genomic Predictions in Small Breeds by Construction of Genomic Relationship Matrix Through Variable Selection.

Genomic selection has been increasingly implemented in the animal breeding industry, and it is becoming a routine method in many livestock breeding contexts. However, its use is still limited in several small-population local breeds, which are, nonetheless, an important source of genetic variability of great economic value. A major roadblock for their genomic selection is accuracy when population size is limited: to improve breeding value accuracy, variable selection models that assume heterogenous variance have been proposed over the last few years. However, while these models might outperform traditional and genomic predictions in terms of accuracy, they also carry a proportional increase of breeding value bias and dispersion. These mutual increases are especially striking when genomic selection is performed with a low number of phenotypes and high shrinkage value-which is precisely the situation that happens with small local breeds. In our study, we tested several alternative methods to improve the accuracy of genomic selection in a small population. First, we investigated the impact of using only a subset of informative markers regarding prediction accuracy, bias, and dispersion. We used different algorithms to select them, such as recursive feature eliminations, penalized regression, and XGBoost. We compared our results with the predictions of pedigree-based BLUP, single-step genomic BLUP, and weighted single-step genomic BLUP in different simulated populations obtained by combining various parameters in terms of number of QTLs and effective population size. We also investigated these approaches on a real data set belonging to the small local Rendena breed. Our results show that the accuracy of GBLUP in small-sized populations increased when performed with SNPs selected via variable selection methods both in simulated and real data sets. In addition, the use of variable selection models-especially those using XGBoost-in our real data set did not impact bias and the dispersion of estimated breeding values. We have discussed possible explanations for our results and how our study can help estimate breeding values for future genomic selection in small breeds.

Genotype by Environment Interaction and Selection Response for Milk Yield Traits and Conformation in a Local Cattle Breed Using a Reaction Norm Approach.

Local breeds are often reared in various environmental conditions (EC), suggesting that genotype by environment interaction (GxE) could influence genetic progress. This study aimed at investigating GxE and response to selection (R) in Rendena cattle under diverse EC. Traits included milk, fat, and protein yields, fat and protein percentage, and somatic cell score, three-factor scores and 24 linear type traits. The traits belonged to 11,085 cows (615 sires). Variance components were estimated in a two-step reaction norm model (RNM). A single trait animal model was run to obtain the solutions of herd-EC effect, then included in a random regression sire model. A multivariate response to selection (R) in different EC was computed for traits under selection including beef traits from a performance test. GxE accounted on average for 10% of phenotypic variance, and an average rank correlation of over 0.97 was found between bull estimated breeding values (EBVs) by either including or not including GxE, with changing top ranks. For various traits, significantly greater genetic components and R were observed in plain farms, loose housing rearing system, feeding total mixed ration, and without summer pasture. Conversely, for beef traits, a greater R was found for mountain farms, loose housing, hay-based feeding and summer pasture.

Genomic Prediction in Local Breeds: The Rendena Cattle as a Case Study.

The maintenance of local cattle breeds is key to selecting for efficient food production, landscape protection, and conservation of biodiversity and local cultural heritage. Rendena is an indigenous cattle breed from the alpine North-East of Italy, selected for dual purpose, but with lesser emphasis given to beef traits. In this situation, increasing accuracy for beef traits could prevent detrimental effects due to the antagonism with milk production. Our study assessed the impact of genomic information on estimated breeding values (EBVs) in Rendena performance-tested bulls. Traits considered were average daily gain, in vivo EUROP score, and in vivo estimate of dressing percentage. The final dataset contained 1691 individuals with phenotypes and 8372 animals in pedigree, 1743 of which were genotyped. Using the cross-validation method, three models were compared: (i) Pedigree-BLUP (PBLUP); (ii) single-step GBLUP (ssGBLUP), and (iii) weighted single-step GBLUP (WssGBLUP). Models including genomic information presented higher accuracy, especially WssGBLUP. However, the model with the best overall properties was the ssGBLUP, showing higher accuracy than PBLUP and optimal values of bias and dispersion parameters. Our study demonstrated that integrating phenotypes for beef traits with genomic data can be helpful to estimate EBVs, even in a small local breed.

Selection Response Due to Different Combination of Antagonistic Milk, Beef, and Morphological Traits in the Alpine Grey Cattle Breed.

Selection in local dual-purpose breeds requires great carefulness because of the need to preserve peculiar traits and also guarantee the positive genetic progress for milk and beef production to maintain economic competitiveness. A specific breeding plan accounting for milk, beef, and functional traits is required by breeders of the Alpine Grey cattle (AG), a local dual-purpose breed of the Italian Alps. Hereditability and genetic correlations among all traits have been analyzed for this purpose. After that, different selection indexes were proposed to identify the most suitable for this breed. Firstly, a genetic parameters analysis was carried out with different datasets. The milk dataset contained 406,918 test day records of milk, protein, and fat yields and somatic cells (expressed as SCS). The beef dataset included performance test data conducted on 749 young bulls. Average daily gain, in vivo estimated carcass yields, and carcass conformation (SEUROP) were the phenotypes obtained from the performance tests. The morphological dataset included 21 linear type evaluations of 11,320 first party cows. Linear type traits were aggregated through factor analysis and three factors were retained, while head typicality (HT) and rear muscularity (RM) were analyzed as single traits. Heritability estimates (h2) for milk traits ranged from 0.125 to 0.219. Analysis of beef traits showed h2 greater than milk traits, ranging from 0.282 to 0.501. Type traits showed a medium value of h2 ranging from 0.238 to 0.374. Regarding genetic correlation, SCS and milk traits were strongly positively correlated. Milk traits had a negative genetic correlation with the factor accounting for udder conformations (-0.40) and with all performance test traits and RM. These latter traits showed also a negative genetic correlation with udder volume (-0.28). The HT and the factor accounting for rear legs traits were not correlated with milk traits, but negatively correlated with beef traits (-0.32 with RM). We argue that the consequence of these results is that the use of the current selection index, which is mainly focused on milk attitude, will lead to a deterioration of all other traits. In this study, we propose more appropriate selection indexes that account for genetic relationships among traits, including functional traits.

Genome Wide Association Study of Beef Traits in Local Alpine Breed Reveals the Diversity of the Pathways Involved and the Role of Time Stratification.

Knowledge of the genetic architecture of key growth and beef traits in livestock species has greatly improved worldwide thanks to genome-wide association studies (GWAS), which allow to link target phenotypes to Single Nucleotide Polymorphisms (SNPs) across the genome. Local dual-purpose breeds have rarely been the focus of such studies; recently, however, their value as a possible alternative to intensively farmed breeds has become clear, especially for their greater adaptability to environmental change and potential for survival in less productive areas. We performed single-step GWAS and post-GWAS analysis for body weight (BW), average daily gain (ADG), carcass fleshiness (CF) and dressing percentage (DP) in 1,690 individuals of local alpine cattle breed, Rendena. This breed is typical of alpine pastures, with a marked dual-purpose attitude and good genetic diversity. Moreover, we considered two of the target phenotypes (BW and ADG) at different times in the individuals' life, a potentially important aspect in the study of the traits' genetic architecture. We identified 8 significant and 47 suggestively associated SNPs, located in 14 autosomal chromosomes (BTA). Among the strongest signals, 3 significant and 16 suggestive SNPs were associated with ADG and were located on BTA10 (50-60 Mb), while the hotspot associated with CF and DP was on BTA18 (55-62 MB). Among the significant SNPs some were mapped within genes, such as SLC12A1, CGNL1, PRTG (ADG), LOC513941 (CF), NLRP2 (CF and DP), CDC155 (DP). Pathway analysis showed great diversity in the biological pathways linked to the different traits; several were associated with neurogenesis and synaptic transmission, but actin-related and transmembrane transport pathways were also represented. Time-stratification highlighted how the genetic architectures of the same traits were markedly different between different ages. The results from our GWAS of beef traits in Rendena led to the detection of a variety of genes both well-known and novel. We argue that our results show that expanding genomic research to local breeds can reveal hitherto undetected genetic architectures in livestock worldwide. This could greatly help efforts to map genomic complexity of the traits of interest and to make appropriate breeding decisions.

The Genomic Variation in the Aosta Cattle Breeds Raised in an Extensive Alpine Farming System.

The Aosta Red Pied (Valdostana Pezzata Rossa (VRP)), the Aosta Black Pied (Valdostana Pezzata Nera (VBP)) and the Aosta Chestnut (Valdostana Castana (CAS)) are dual-purpose cattle breeds (meat and milk), very well adapted to the harsh environmental conditions of alpine territories: their farming is in fact characterized by summer pasture at very high altitude. A total of 728 individuals were genotyped with the GeenSeek Genomic Profiler® (GGP) Bovine 150K Illumina SNP chip as a part of the DUALBREEDING-PSRN Italian-funded research project. The genetic diversity among populations showed that the three breeds are distinct populations based on the FST values, ADMIXTURE and Principal Component Analysis (PCA) results. Runs of Homozygosity (ROH) were obtained for the three populations to disclose recent autozygosity. The genomic inbreeding based on the ROH was calculated and coupled with information derived from the F (inbreeding coefficient) and FST parameters. The mean FROH values were low: CAS = 0.06, VBP = 0.05 and VRP = 0.07, while the average F values were -0.003, -0.01 and -0.003, respectively. The annotation and enrichment analysis, performed in the identified most frequent ROH (TOP_ROH), showed genes that can be linked to the resilience capacity of these populations to harsh environmental farming conditions, and to the peculiar characteristics searched for by farmers in each breed.

Genetic Variability in the Italian Heavy Draught Horse from Pedigree Data and Genomic Information.

This study aimed to investigate the genetic diversity in the Italian Heavy Horse Breed from pedigree and genomic data. Pedigree information for 64,917 individuals were used to assess inbreeding level, effective population size (Ne), and effective numbers of founders and ancestors (fa/fe). Genotypic information from SNP markers were available for 267 individuals of both sexes, and it allowed estimating genomic inbreeding in two methods (observed versus expected homozygosity and from ROH) to study the breed genomic structure and possible selection signatures. Pedigree and genomic inbreeding were greatly correlated (0.65 on average). The inbreeding trend increased over time, apart from periods in which the base population enlarged, when Ne increased also. Recent bottlenecks did not occur in the genome, as fa/fe have shown. The observed homozygosity results were on average lower than expected, which was probably due to the use of French Breton stallions to support the breed genetic variability. High homozygous regions suggested that inbreeding increased in different periods. Two subpopulations were distinguished, which was probably due to the different inclusion of French animals by breeders. Few selection signatures were found at the population level, with possible associations to disease resistance. The almost low inbreeding rate suggested that despite the small breed size, conservation actions are not yet required.

Genetic Parameters of Linear Type Traits Scored at 30 Months in Italian Heavy Draught Horse.

The Italian Heavy Draught Horse (IHDH) breed is selected based on linear type traits (LTT) evaluated at young age on six-month-old foals. However, animals retained for reproduction are scored also at adults age (about 30 months), and the evaluation is mandatory for the final official admission to the stud book of candidate mares and stallions. This study aimed to estimate genetic parameters of LTT scored at 30 months to consider if they are feasible for selection instead of using foal data and to reduce costs of selection plan. Data included 19 years of evaluation for 14 LTT and an overall score. Analyses were performed on 5835 females and 856 males via animal model. The heritability ranged from 0.03 (upper line length) to 0.40 (frame size). Traits of selection interest (head size and expression; temperament/movement; fleshiness; fore diameter; rear diameter) reported heritability between 0.21 and 0.31. High genetic correlations were obtained among traits related to muscular development, 0.73 on average. Positive genetic trends were found in traits of selection interest, already selected from foal type trait data. Accounting for genetic parameters estimated in adult animals instead in foals is feasible in IHDH selection.

Genetics of Lifetime Reproductive Performance in Italian Heavy Draught Horse Mares.

Our aims were to find a phenotypic variable to express mares' lifetime reproductive performance after 6 breeding seasons (BS) in Italian Heavy Draught Horse breed (IHDH), and to estimate its heritability. At first, 1487 mares in a training dataset were used to implement and validate a set of predictive coefficients (LFR-C) or equations (LFR-E) to estimate a lifetime foaling rate (LFR) after 6 BS, i.e., the number of foals generated divided by the opportunities to do so. Then, 3033 mares in a dataset with at least 3 registered BS, was used to estimate LFR for mares with 3, 4, or 5 registered RS. This dataset contained actual (n = 1950) and estimated (n = 1443) LFR, obtained by LFR-C, and LFR-E; Arcsine transformation of LFR-C and LFR-E were also analyzed in single trait animal models to estimate heritability. Overall, the LFR showed a moderate but significant genetic variation, and the heritability of the trait was high (0.24) considering it is a fitness trait. The arcsine transformation of LFR did not show any improvement of heritability. The present study indicates the possible use of a linear LFR variable for breeding purposes in IHDH breed considering both complete and incomplete reproductive careers.

Digit ratio and length asymmetry in calves' limbs.

This study considered possible sexual dimorphism in the relative lengths of the second, third and fourth digits (digit ratio), in calves. Furthermore, a different length of the bone structures of the third (3D) and of the fourth (4D) digits has been examined as an evolutionary adaptation to locomotion on soft ground. The length of the digital bones of the right fore-limb of 33 females and 15 male calves was measured in vivo using a portable X-ray machine. The vestigial structure of the second digit (2D), and 3D and 4D, from metacarpus to the third phalanx were considered in a mixed model, as well as some ratios between 2D and different parts of 3D or 4D (2D:3D and 2D:4D). A covariate for the mean finger length was considered for digit ratios to control for possible biases due to shape allometry. Shorter first phalanx and trotter were found in 3D than in 4D, and the reverse for the third phalanx. The 2D was significantly shorter in females, as well as the second phalanges of 3D and 4D. Significant sex differences in 2D:3D and 2D:4D were found for some digit parts of 3D and 4D and for the first phalanges of 3D:4D. These ratios were always shorter in females, in contrast to that found in most mammals. The asymmetry between 3D and 4D could mean a functional adaptation for locomotion. Sex differences in 2D:4D and 3D:4D were found, but with a reverse pattern than in most mammal species (males > females rather than males < females). In this regard digit ratio in calves was similar to that of Old World monkeys. This study is the first investigation of digit ratio in Ungulates, whose limbs differ from the limbs of most mammals, maintaining five digits. The reverse pattern of sex differences (digit ratios: males> females) could be due to the peculiar nature of the vestigial dewclaw of 2D and to the hormone patterns acting on this digit during development, but further research is required around this topic.

Milk microbial composition of Brazilian dairy cows entering the dry period and genomic comparison between Staphylococcus aureus strains susceptible to the bacteriophage vB_SauM-UFV_DC4.

Brazil has the second-largest dairy cattle herd in the world, and bovine mastitis still can cause significant losses for dairy farmers. Despite this fact, little information is available about milk microbial composition of Brazilian dairy cows, as well as the potential use of bacteriophages in the control of S. aureus. Here, we investigated milk bacterial composition of 28 Holstein Fresian cows (109 teats), selected in the dry-off period, using 16S rRNA analysis. Furthermore, a representative S. aureus strain (UFV2030RH1) was obtained at drying-off for isolation of a bacteriophage (vB_SauM-UFV_DC4, UFV_DC4) and bacterial genomic comparison purposes. Our outcomes revealed that Staphylococcus was the third most prevalent genus and positively correlated with subclinical mastitis events. As a major finding, genomic analyses showed the presence of adhesive matrix molecules that recognize microbial surface components (MSCRAMM) in UFV2030RH1 and might indicate great biofilm formation capability. A minimum inhibitory concentration (MIC) assay showed that resistance to ampicillin was the highest among the antibiotic tested in S. aureus 3059 and UFV2030RH1, displaying values four and sixteen times greater than MIC resistance breakpoint, respectively. Together, our results suggest that Staphylococcus is highly prevalent in dairy cows at drying-off and the use of the phage UFV_DC4 as a biocontrol agent must be investigated in future studies.

Genetic parameters of different measures of somatic cell counts in the Rendena breed.

The objective of this study was to consider different and alternative methods of using somatic cell count (SCC) data recorded according to the Italian official milk recording system, estimating its genetic parameters and the correlations with the yield traits (milk, fat, and protein) in the Rendena breed. The SCC traits defined for genetic evaluation were somatic cell score, log of the total daily SCC (LTSCC, i.e., SCC multiplied by daily milk yield) individually recorded in a day of official control, and 3 different thresholds (≥80,000, ≥150,000, and ≥400,000 cells/mL) for somatic cells. A total of 187,052 test-day monthly records of milk, fat, and protein yields and SCC belonging to 11,718 cows were used to estimate heritability and genetic correlations between SCC and yield traits via a bi-trait repeatability test-day model using a Bayesian approach. The heritability values estimated for the threshold traits ranged from 0.036 to 0.065, less than those observed for monthly somatic cell score and LTSCC traits that were equivalent to 0.088 and 0.103, respectively. Higher genetic correlations were estimated between LTSCC trait and all productive traits (0.379 for milk, 0.240 for fat, and 0.370 for protein). The other SCC traits considered have shown low or almost null genetic correlations with the productive traits (from 0.008 between fat yield and SCC ≥150,000 cells/mL to 0.234 between protein yield and SCC ≥400,000 cells/mL) and almost all estimates included zero in the 95% highest posterior density region interval. These results indicated that genetic selection for milk, fat, and protein production negatively affects the LTSCC content and SCC ≥400,000 cells/mL but does not negatively influence the other somatic cell and threshold SCC traits in the Rendena breed. However, the complete framework of genetic relationships of SCC with all traits under selection should be considered when deciding on the possible inclusion of SCC in the breeding program of this small cattle population.

Hydrogen-Fueled Microbial Pathways in Biogas Upgrading Systems Revealed by Genome-Centric Metagenomics.

Biogas upgrading via carbon dioxide hydrogenation is an emerging technology for electrofuel production. The biomethanation efficiency is strongly dependent on a balanced microbial consortium, whose high- resolution characterization along with their functional potential and interactions are pivotal for process optimization. The present work is the first genome-centric metagenomic study on mesophilic and thermophilic biogas upgrading reactors aiming to define the metabolic profile of more than 200 uncultivated microbes involved in hydrogen assisted methanogenesis. The outcomes from predictive functional analyses were correlated with microbial abundance variations to clarify the effect of process parameters on the community. The operational temperature significantly influenced the microbial richness of the reactors, while the H2 addition distinctively alternated the abundance of the taxa. Two different Methanoculleus species (one mesophilic and one thermophilic) were identified as the main responsible ones for methane metabolism. Finally, it was demonstrated that the addition of H2 exerted a selective pressure on the concerted or syntrophic interactions of specific microbes functionally related to carbon fixation, propionate and butanoate metabolisms. Novel bacteria were identified as candidate syntrophic acetate oxidizers (e.g., Tepidanaerobacter sp. DTU063), while the addition of H2 favored the proliferation of potential homoacetogens (e.g., Clostridia sp. DTU183). Population genomes encoding genes of Wood-Ljungdahl pathway were mainly thermophilic, while propionate degraders were mostly identified at mesophilic conditions. Finally, putative syntrophic interactions were identified between microbes that have either versatile metabolic abilities or are obligate/facultative syntrophs.

Microbial population dynamics in urban organic waste anaerobic co-digestion with mixed sludge during a change in feedstock composition and different hydraulic retention times.

Microbial communities play an essential role in the biochemical pathways of anaerobic digestion processes. The correlations between microorganisms' relative abundance and anaerobic digestion process parameters were investigated, by considering the effect of different feedstock compositions and hydraulic retention times (HRTs). Shifts in microbial diversity and changes in microbial community richness were observed by changing feedstock composition from mono-digestion of mixed sludge to co-digestion of food waste, grass clippings and garden waste with mixed sludge at HRT of 30, 20, 15 and 10 days. Syntrophic acetate oxidation along with hydrogenotrophic methanogenesis, mediated by Methanothermobacter, was found to be the most prevalent methane formation pathway, with the only exception of 10 days' HRT, in which Methanosarcina was the most dominant archaea. Significantly, the degradation of complex organic polymers was found to be the most active process, performed by members of S1 (Thermotogales), Thermonema and Lactobacillus in a reactor fed with a high share of food waste. Conversely, Thermacetogenium, Anaerobaculum, Ruminococcaceae, Porphyromonadaceae and the lignocellulosic-degrading Clostridium were the significantly more abundant bacteria in the reactor fed with an increased share of lignocellulosic biomass in the form of grass clippings and garden waste. Finally, microbes belonging to Coprothermobacter, Syntrophomonas and Clostridium were correlated significantly with the specific methane yield obtained in both reactors.

Genetic correlations between type and test-day milk yield in small dual-purpose cattle populations: The Aosta Red Pied breed as a case study.

This study aimed at estimating the relationships between linear type traits and milk production in the dual-purpose Aosta Red Pied (ARP) cattle breed, by expressing type traits as factor scores with the same biological meaning of the individual traits. Factor analysis was applied to individual type traits for muscularity and udder of 32,275 first-parity ARP cows, obtaining 3 factor scores for individual muscularity (F1), udder side (F2), and udder conformation (F3). Data from 169,008 test-day records of milk, fat, and protein yield (kg), belonging to the first 3 lactations of 16,605 cows, were also analyzed. After obtaining genetic parameters for both morphological factors and milk production traits through a series of AIREML single-trait models, bivariate analyses were performed on a data set accounting for 201,283 records of 35,530 cows, to assess the phenotypic and genetic correlations among all factor scores and milk yield traits. The heritability estimates obtained proved to be moderate for both groups of traits, ranging from 0.132 (fat) to 0.314 (F1). Muscularity factor showed moderate and negative genetic correlations (ra) with udder size (-0.376) and udder conformation (0.214) factors. A low and negative ra was found between udder factors. Strong and positive ra were found among all the 3 milk production traits and F 0010 (ra≥0.597). Negative ra with milk traits were obtained for both F 0005 and F3, ranging from -0.417 to -0.221. Phenotypic correlations were lower than the genetic ones, and sometimes close to zero. The antagonism between milk production and meat attitude traits suggests that great attention should be paid in assigning proper weight to the traits, comprising functional traits such as udder conformation, included in selection indices for the dual-purpose breed. The ra obtained for factor scores are consistent with previous estimates for the corresponding individual type traits, and this confirms the possible use of factor analysis to improve type traits relevant to beef attitude.