Discriminant Analysis as a Tool to Classify Grasslands Based on Near-Infrared Spectra.

This study aims to classify plant communities by applying discriminant analysis based on principal components (DAPC) on near-infrared spectra (FT-NIRS) starting from fresh herbage samples. Grassland samples (n~156) belonged to (i) recent alfalfa pure crops (CAA), (ii) recent grass-legume mixtures (GLM), (iii) permanent meadows derived from old alfalfa stands that were re-colonized (PMA), and iv) permanent meadows originated from old grass-legume mixtures (PLM). Samples were scanned using FT-NIRS, and a multivariate exploration of the original spectra was performed using DAPC. The following two scenarios were proposed: (i) cross-validation, where all data were used for model training, and (ii) semi-external validation, where the group assignment was performed without samples of the training set. The first two components explained 98% of the total variability. The DAPC model resulted in an overall assignment success rate of 77%, and, from cross-validation, it emerged that it was possible to assign the CAA and PMA to their group with more than of 80% of success, which were different in botanical and chemical composition. In comparison, GLM and PLM obtained lower success of assignment (~52%). External validation suggested similarity between PLM and GLM groups (93%) and between GLM and PLM (77%). However, a dataset increase could improve group differentiation.

Persistence of autozygosity in crossbreds between autochthonous and cosmopolitan breeds of swine: a simulation study.

Crossbreeding might be a valid strategy to valorize local pig breeds. Crossbreeding should reduce homozygosity and, as a consequence, yield hybrid vigor for fitness and production traits. This study aimed to quantify the persistence of autozygosity in terminal crossbred pigs compared with purebreds and, in turn, identify genomic regions where autozygosity's persistence would not be found. The study was based on genotyping data from 20 European local pig breeds and three cosmopolitan pig breeds used to simulate crossbred offspring. This study consisted of two steps. First, one hundred matings were simulated for each pairwise combination of the 23 considered breeds (for a total of 276 combinations), ignoring the sex of the parent individuals in order to generate purebred and crossbred matings leveraging all the germplasm available. Second, a few preselected terminal-maternal breed pairs were used to mimic a realistic terminal crossbreeding system: (i) Mora Romagnola (boars) or Cinta Senese (boars) crossed with Large White (sows) or Landrace (sows); (ii) Duroc (boars) crossed with Mora Romagnola (sows) or Cinta Senese (sows). Runs of homozygosity was used to estimate genome-wide autozygosity (FROH). Observed FROH was higher in purebreds than in crossbreds, although some crossbred combinations showed higher FROH than other purebred combinations. Among the purebreds, the highest FROH values were observed in Mora Romagnola and Turopolje (0.50 and 0.46, respectively). FROH ranged from 0.04 to 0.16 in the crossbreds Alentejana × Large White and Alentejana × Iberian, respectively. Persistence of autozygosity was found in several genomic segments harboring regions where quantitative trait loci (QTLs) were found in the literature. The regions were enriched in QTLs involved in fatty acid metabolism and associated with performance traits. This simulation shows that autozygosity persists in most breed combinations of terminal crosses. Results suggest that a strategy for crossbreeding is implemented when leveraging autochthonous and cosmopolitan breeds to obtain most of the hybrid vigor.

Identification of population-informative markers from high-density genotyping data through combined feature selection and machine learning algorithms: Application to European autochthonous and cosmopolitan pig breeds.

Large genotyping datasets, obtained from high-density single nucleotide polymorphism (SNP) arrays, developed for different livestock species, can be used to describe and differentiate breeds or populations. To identify the most discriminating genetic markers among thousands of genotyped SNPs, a few statistical approaches have been proposed. In this study, we applied the Boruta algorithm, a wrapper of the machine learning random forest algorithm, on a database of 23 European pig breeds (20 autochthonous and three cosmopolitan breeds) genotyped with a 70k SNP chip, to pre-select informative SNPs. To identify different sets of SNPs, these pre-selected markers were then ranked with random forest based on their mean decrease accuracy and mean decrease gene indexes. We evaluated the efficiency of these subsets for breed classification and the usefulness of this approach to detect candidate genes affecting breed-specific phenotypes and relevant production traits that might differ among breeds. The lowest overall classification error (2.3%) was reached with a subpanel including only 398 SNPs (ranked based on their mean decrease accuracy), with no classification error in seven breeds using up to 49 SNPs. Several SNPs of these selected subpanels were in genomic regions in which previous studies had identified signatures of selection or genes associated with morphological or production traits that distinguish the analysed breeds. Therefore, even if these approaches have not been originally designed to identify signatures of selection, the obtained results showed that they could potentially be useful for this purpose.

Discriminant analysis as a tool to classify farm hay in dairy farms.

Hay is one of the primary constituents of ruminant feed, and rapid classification systems of nutritional value are essential. A reliable approach to evaluating hay quality is a combination of visual combined inspection by NIRS analysis. The analysis was carried out on 1,639 samples of hay collected from 2016 to 2021 in northern Italy. Discriminant analysis (DAPC) on five hay types (FOM, forage mixtures; APG, first alfalfa cutting with prevalence of graminaceous >50%; PRA, prevailing alfalfa >50%; PUA, purity alfalfa >95%; and PEM, permanent meadows) was performed by ex-ante visual inspection categorization and NIRS analysis. This study aimed to provide a complementary method to differentiate hay types and classify unknown samples. Two scenarios were used: i) all data were used for model training, and the discriminant functions were extracted based on all samples; ii) the assignment of each group was assessed without samples belonging to the training set group. DAPC model resulted in an overall assignment success rate of 66%; precisely, the success was 84, 79, 69, 37, and 27% for PUA, FOM, PRA, APG, and PEM, respectively. In the second scenario, three groups showed percentages of posterior assignment probability higher than 70% to only one group: PUA with PRA (~ 99%), PRA with PUA (~71%), and PEM with FOM (~75%). Discriminant analysis can be successfully used to differentiate hay types and could also be used to assess factors related to hay quality in addition to NIRS analysis.

Temperature-humidity index monitoring during two summer seasons in dairy cow sheds in Mugello (Tuscany).

Many studies have reported that the impact of high temperatures affects physiology, welfare, health, and productivity of farm animals, and among these, the dairy cattle farming is one of the livestock sectors that suffers the greatest effects. The temperature-humidity index (THI) represents the state of the art in the evaluation of heat stress conditions in dairy cattle but often its measurement is not carried out in sheds. For this reason, the aim of this study was the monitoring of the THI in three dairy cattle farms in Mugello (Tuscany) to understand its influence on dairy cows. THI values were calculated using meteorological data from direct observation in sheds and outdoor environments. Data relating to the animal's behavior were collected using radio collars. The Pearson test and Mann-Kendall test were used for statistical analysis. The results highlighted a significant (P < 0.001) upward trend in THImax during the last 30 years both in Low Mugello (+ 1.1 every 10 years) and in High Mugello (+ 0.9 every 10 years). In Low Mugello sheds, during the period 2020-2022, more than 70% of daytime hours during the summer period were characterized by heat risk conditions (THI > 72) for livestock. On average the animals showed a significant (P < 0.001) decrease in time spent to feeding and rumination, both during the day and the night, with a significant (P < 0.001) increase in inactivity. This study fits into the growing demand for knowledge of the micro-climatic conditions within farms in order to support resilience actions for protecting both animal welfare and farm productivity from the effects of climate change. This could also be carried out thanks to estimation models which, based on the meteorological conditions forecast, could implement the thermal stress indicator (THI) directly from the high-resolution meteorological model, allowing to get a prediction of the farm's potential productivity loss based on the expected THI.

Prediction of fatty acid composition in intact and minced fat of European autochthonous pigs breeds by near infrared spectroscopy.

The fatty acids profile has been playing a decisive role in recent years, thanks to technological, sensory and health demands from producers and consumers. The application of NIRS technique on fat tissues, could lead to more efficient, practical, and economical in the quality control. The study aim was to assess the accuracy of Fourier Transformed Near Infrared Spectroscopy technique to determine fatty acids composition in fat of 12 European local pig breeds. A total of 439 spectra of backfat were collected both in intact and minced tissue and then were analyzed using gas chromatographic analysis. Predictive equations were developed using the 80% of samples for the calibration, followed by full cross validation, and the remaining 20% for the external validation test. NIRS analysis of minced samples allowed a better response for fatty acid families, n6 PUFA, it is promising both for n3 PUFA quantification and for the screening (high, low value) of the major fatty acids. Intact fat prediction, although with a lower predictive ability, seems suitable for PUFA and n6 PUFA while for other families allows only a discrimination between high and low values.

Reference patterns for thermoregulation in Italian Massese ewes.

The Massese is an autochthonous Italian sheep breed, used for meat and mainly milk production and thermoregulatory variations can directly affect the performance of these animals. We evaluated the thermoregulatory patterns of Massese ewes and identified the changes due to environmental variations. Data was collected from 159 healthy ewes from herds of four farms/institutions. For thermal environmental characterization, air temperature (AT), relative humidity (RH) and wind speed were measured, and Black Globe Temperature, Humidity Index (BGHI) and Radiant Heat Load (RHL) were calculated. The thermoregulatory responses evaluated were: respiratory (RR), heart rate (HR), rectal temperature (RT) and coat surface temperature (ST). All variables were subjected to analysis of variance with repeated measures over time. A factor analysis was conducted to determine the relationship between environmental and thermoregulatory variables. Multiple regression analyses were also examined using General Linear Models, and Variance Inflation Factors were calculated. Logistic and Broken line non-linear regressions for RR, HR and RT were analyzed. The RR and HR values were outside reference values and associated with normal values of RT. In the factor analysis, most environmental variables were seen to affect the thermoregulation pattern of the ewes, except for RH. In the logistic regression analysis, RT was not affected by any of the variables studied, maybe because BGHI and RHL were not sufficiently high enough. Nevertheless, BGHI and RHL affected RR and HR. The study shows a divergence for Massese ewes from reference thermoregulatory values for sheep.

Soybean Replacement by Alternative Protein Sources in Pig Nutrition and Its Effect on Meat Quality.

Soybean is one of the most expensive and limiting feed ingredients in diet formulations; however, in pig farming, it represents the main source of protein. The production and supply of soybean are critical steps due to their environmental impact and feed/food competition for land use. Therefore, research is focusing on finding alternatives to replace soybean partially or totally. However, alternative ingredients should ensure similar growth performance, carcass traits, and meat quality characteristics compared to conventional soybean-based diets. The objective of this review was to evaluate the impact of different alternative protein sources to soybean in pig nutrition and their effects on growth performance, carcass, and meat quality traits. The review process was performed on Scopus®, and it considered research findings published from 2012 to the present on the Sus scrofa species. Articles without a control group fed with soybean were discarded. The main alternative protein sources identified were other legumes and distillers' dried grain with solubles (fish and animal proteins, oilseed by- and co-products). Interesting innovative protein sources included by-products from other industries (residues), microalgae and insects. Nevertheless, in dietary formulations, close attention must be paid to address the nutritional requirements, balance the supply of amino acids, avoid anti-nutritional or toxic compounds occasionally present in alternative protein sources, as well as determine the availability of protein feed in specific geographical areas.

Admixture and breed traceability in European indigenous pig breeds and wild boar using genome-wide SNP data.

Preserving diversity of indigenous pig (Sus scrofa) breeds is a key factor to (i) sustain the pork chain (both at local and global scales) including the production of high-quality branded products, (ii) enrich the animal biobanking and (iii) progress conservation policies. Single nucleotide polymorphism (SNP) chips offer the opportunity for whole-genome comparisons among individuals and breeds. Animals from twenty European local pigs breeds, reared in nine countries (Croatia: Black Slavonian, Turopolje; France: Basque, Gascon; Germany: Schwabisch-Hällisches Schwein; Italy: Apulo Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano, Sarda; Lithuania: Indigenous Wattle, White Old Type; Portugal: Alentejana, Bísara; Serbia: Moravka, Swallow-Bellied Mangalitsa; Slovenia: Krskopolje pig; Spain: Iberian, Majorcan Black), and three commercial breeds (Duroc, Landrace and Large White) were sampled and genotyped with the GeneSeek Genomic Profiler (GGP) 70 K HD porcine genotyping chip. A dataset of 51 Wild Boars from nine countries was also added, summing up to 1186 pigs (~ 49 pigs/breed). The aim was to: (i) investigate individual admixture ancestries and (ii) assess breed traceability via discriminant analysis on principal components (DAPC). Albeit the mosaic of shared ancestries found for Nero Siciliano, Sarda and Moravka, admixture analysis indicated independent evolvement for the rest of the breeds. High prediction accuracy of DAPC mark SNP data as a reliable solution for the traceability of breed-specific pig products.

Effects of a Ceiling Fan Ventilation System and THI on Young Limousin Bulls' Social Behaviour.

The study investigated the relationship between the temperature humidity index (THI) and the behaviour of 24 young fattening Limousin bulls reared in two farms in Tuscany, Italy. In each farm, six animals were undergone to ceiling fans (switched on at THI values up to 72), and six animals represented the control group. The trial lasted three days for two consecutive weeks in August 2020. Behavioural observations were conducted using scan sampling technique and eating, ruminating, drinking, resting and other social activities were registered every 5 min, from 9.30 am to 4.00 pm. Two different microclimatic conditions were evaluated to assess the effect of the ventilation system: normal (THI < 78) and alert (THI ≥ 78) conditions. Results showed that the ventilation system had significant effects increasing inactivity and lying down compared to control groups and decreasing eating and drinking activities. THI alert condition caused a significant decrease in eating and an increase in lying down behaviours. Ventilation system did not influence the animals' cleanliness. The ceiling fans' efficiency in changing the behaviour of young fattening bulls was demonstrated but further studies are needed to assess the ventilation system effects, especially during longer heat stress periods.

Influence of Wet Ageing on Beef Quality Traits.

Fresh samples of Longissimus thoracis of Charolais (n = 12), Romagnola (n = 15), Limousine (n = 77), and crossbreed (n = 62) animals were evaluated with different storage periods (0, 4, 9, and 14 days). Proximate analysis (i.e., pH, humidity, color, free water content, and physical parameters) was performed for each sample. The data obtained were evaluated with a mixed model, setting 5 fixed effects (breed, storage time, animals age, EUROP conformation, number of animal transports) and the animal as random. The results demonstrated that meat quality was affected mainly by the wet ageing period and that the visual and tactile parameters were also found to be susceptible to the storage time. The conservation entailed a decrease in meat humidity and an increase in L* and b* traits; it also led to a decrease in the hardness of the sample, in turn affecting the other texture profile analysis parameters considered. Fixed effects affected in different ways the traits analyzed i.e., pH and humidity changed with breed, as well as with EUROP classification, animals' age for some TPA parameters, and the number of animal transports for both visual and tactile parameters. Wet ageing influenced the meat quality, often improving it, confirming how important further research would be to identify precise storage times in relation to the parameters studied.

Cardoon Meal as Alternative Protein Source to Soybean Meal for Limousine Bulls Fattening Period: Effects on Growth Performances and Meat Quality Traits.

Soybean meal is the most important protein source in beef cattle feeding. The research of alternative protein sources to replace soy use, avoiding negative effects on in vivo performance and on the product's quality, is an important issue. In this context, cardoon represents a non-OGM resilient crop that can be cultivated in marginal lands for extracting its seed oil (utilized for biodiesel and biodegradable bioplastic production) and whose and the residual meal from its seed oil (utilized for biodiesel and biodegradable bioplastic production) could be a suitable by-product for animal feeding, due to its fairly high protein content. The aim of this study was to evaluate the feasibility of using cardoon meal as an innovative protein source during the Limousine bulls' fattening period. Thirty-two bulls were divided into two groups and fed with a diet containing soybean meal (SG) or partially replacing soybean meal with cardoon meal as a protein source (CG), respectively. The feeding trial lasted about 11 months. Growth performances and meat physical-chemical traits were evaluated. No statistical differences in feed efficiency, average daily gain, or in the main meat quality indicators, as well as in fatty acid profiles were found among the groups. Therefore, cardoon meal could be considered as an alternative to soybean meal in fattening Limousine bulls in order to enhance the sustainability of the farming system.

Distribution of Deer Keds (Diptera: Hippoboscidae) in Free-Living Cervids of the Tuscan-Emilian Apennines, Central Italy, and Establishment of the Allochthonous Ectoparasite Lipoptena fortisetosa.

Lipoptena fortisetosa and L. cervi are hematophagous ectoparasites belonging to the Hippoboscidae family and preferentially living on cervids. In recent years, they have received specific attention due to the great increase in the abundance of their host species, and to their medical and veterinary importance as possible vectors of pathogens harmful to humans and animals. The aim of this study was to investigate the parasitism level of both of these flies on their main hosts in Italy, which are red deer, fallow deer, and roe deer, and to highlight a possible preference for a species, sex, or age class among the hosts. Deer keds were collected by examining 326 cervids hunted in the Tuscan-Emilian Apennines. Outcomes showed that L. fortisetosa has greatly spread throughout the study area, where it competes with the autochthonous L. cervi. Moreover, red deer was the favored host species of both ectoparasites, while different preferences for host sex and age classes were observed in the two hippoboscids. The regular monitoring of deer ked populations, especially the allochthonous L. fortisetosa, which is continuously spreading in Europe, is recommended to expand the knowledge on these parasitic species that are potentially dangerous to public health.

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

In the present study, GeneSeek GGP-LDv4 33k single nucleotide polymorphism chip was used to detect runs of homozygosity (ROH) in eight Italian beef cattle breeds, six breeds with distribution limited to Tuscany (Calvana, Mucca Pisana, Pontremolese) or Sardinia (Sarda, Sardo Bruna and Sardo Modicana) and two cosmopolitan breeds (Charolais and Limousine). ROH detection analyses were used to estimate autozygosity and inbreeding and to identify genomic regions with high frequency of ROH, which might reflect selection signatures. Comparative analysis among breeds revealed differences in length and distribution of ROH and inbreeding levels. The Charolais, Limousine, Sarda, and Sardo Bruna breeds were found to have a high frequency of short ROH (~ 15.000); Calvana and Mucca Pisana presented also runs longer than 16 Mbp. The highest level of average genomic inbreeding was observed in Tuscan breeds, around 0.3, while Sardinian and cosmopolitan breeds showed values around 0.2. The population structure and genetic distances were analyzed through principal component and multidimensional scaling analyses, and resulted in a clear separation among the breeds, with clusters related to productive purposes. The frequency of ROH occurrence revealed eight breed-specific genomic regions where genes of potential selective and conservative interest are located (e.g. MYOG, CHI3L1, CHIT1 (BTA16), TIMELESS, APOF, OR10P1, OR6C4, OR2AP1, OR6C2, OR6C68, CACNG2 (BTA5), COL5A2 and COL3A1 (BTA2)). In all breeds, we found the largest proportion of homozygous by descent segments to be those that represent inbreeding events that occurred around 32 generations ago, with Tuscan breeds also having a significant proportion of segments relating to more recent inbreeding.

Genotype by environment interactions for body weight in Mediterranean buffaloes using reaction norm models / Interacción genotipo × ambiente para peso corporal de búfalos Mediterráneos utilizando modelos de norma de reacción / Interação genótipo × ambiente para peso corporal de búfalos Mediterrâneos utilizando modelos de norma de reação

Abstract Background: Buffalo breeding has significantly increased in Brazil over recent years. However, few genetic evaluations have been conducted. Objective: To assess Genotype x Environment Interactions in the Mediterranean Water Buffalo in Brazil, for weight at 205 days of age, using reaction norm models via random regression. Methods: Data for buffaloes born between 1990 and 2014 were collected from five farms ascribed to the Brazilian Buffaloe Improvement Program, located in the North (1), Northeast (1), South (2) and Southeast (1) regions of Brazil. The initial database consisted of 5,280 observations at 205 days of age (W205). We assessed fit using two hierarchical reaction norm models: a two-step (HRNM2s) and a one-step (HRNM1s). Model fit was estimated using the Deviance Information Criterion, Deviance Based on Bayes Factors and Deviance based on Conditional Predictive Ordinate. The environmental descriptors were created to group individuals into common production environments based on year, season, herd and sex. Results: The best fit was obtained for the hierarchical reaction norm model with one-step (HRNM1s). Direct heritability estimates for this model ranged from 0.17 to 0.67 and the maternal heritability from 0.02 to 0.11 with increasing environmental gradient. Lower correlations among the sire classifications were obtained in comparison with HRNM1s in environments with low and high management, confirming the presence of genotype x environment interactions. Conclusion: We recommend a wider application of genetic evaluation in buffalo aimed at identifying optimal genotypes within specific environments.

Resumen Antecedentes: La cría de búfalos ha aumentado significativamente en Brasil en los últimos años. Sin embargo, se han realizado escasas evaluaciones genéticas. Objetivo: Evaluar las interacciones genotipo x ambiente en búfalos de agua Mediterráneos criados en Brasil, para peso a los 205 días de edad, utilizando modelos de reacción mediante regresión aleatoria. Métodos: Los datos de búfalos nacidos entre 1990 y 2014 se obtuvieron de cinco granjas situadas en el Norte (1), Nordeste (1), Sur (2) y del Sureste (1) de Brasil. Todas estas haciendas participan en el Programa Brasileño de Mejoramiento de Búfalos. Nuestra base de datos inicial consistió de 5.280 observaciones a los 205 días de edad (P205). Evaluamos el ajuste utilizando dos modelos de norma de reacción jerárquica: de dos pasos (HRNM2s) y un paso (HRNM1s). El ajuste del modelo se estimó usando el Criterio de información de la desviación, desviación basado en los factores de bayes y desviación basado en la ordenación predictiva condicional. Los descriptores ambientales fueron creados para agrupar individuos en ambientes de producción comunes basados en año, estación, rebaño y sexo. Resultados: El mejor ajuste se obtuvo para el modelo de norma de reacción jerárquica con un paso (HRNM1s). Las estimaciones de heredabilidad directa para este modelo variaron de 0,17 a 0,67 y la heredabilidad materna de 0,02 a 0,11 con gradiente ambiental creciente. Las correlaciones más bajas entre las clasificaciones de los reproductores se obtuvieron en comparación con las HRNM1s, en ambientes con bajo y alto manejo, confirmando la presencia de interacciones genotipo x ambiente. Conclusiones: Recomendamos la aplicación amplia de la evaluación genética en búfalos para identificar genotipos óptimos en ambientes específicos.

Resumo Antecedentes: A criação de búfalos aumentou significativamente no Brasil nos últimos anos. No entanto, eles raramente foram objeto de avaliações genéticas. Objetivo: Avaliar as interações genótipo x ambiente em búfalo Mediterrâneo criados no Brasil, para peso aos 205 dias de idade, utilizando modelos de reação por meio de regressão aleatória. Métodos: Os dados para búfalos de água do Mediterrâneo nascidos entre 1990 e 2014 foram coletados de cinco fazendas localizadas nas regiões Norte (1), Nordeste (1), Sul (2) e Sudeste (1) do Brasil. Todas essas fazendas participam do Programa Brasileiro de Melhoramento dos Búfalos. Nosso banco de dados inicial consistiu de 5.280 observações aos 205 dias de idade (P205). Nós avaliamos o ajuste usando dois modelos de norma de reação hierárquica: um de dois passos (HRNM2s) e um passo (HRNM1s). O ajuste do modelo foi estimado usando o Critério de informações do desvio, desvio baseado nos fatores de bayes e desvio baseado na ordenação preditiva condicional. Os descritores ambientais foram criados para agrupar indivíduos em ambientes de produção comuns baseados em ano, estação, rebanho e sexo. Resultados: O melhor ajuste foi obtido para o modelo de norma de reação hierárquica com um passo (HRNM1s). As estimativas de herdabilidade direta para este modelo variaram de 0,17 a 0,67 e a herdabilidade materna de 0,02 a 0,11 com gradiente ambiental crescente. As correlações mais baixas entre as classificações dos reprodutores foram obtidas em comparação com as HRNM1s, em ambientes com baixo e alto manejo, confirmando a presença de interações genótipo x ambiente. Conclusões: Recomendamos a aplicação mais ampla da avaliação genética em búfalos visando identificar genótipos ótimos em ambientes específicos.

Describing variability in pig genes involved in coronavirus infections for a One Health perspective in conservation of animal genetic resources.

Coronaviruses silently circulate in human and animal populations, causing mild to severe diseases. Therefore, livestock are important components of a "One Health" perspective aimed to control these viral infections. However, at present there is no example that considers pig genetic resources in this context. In this study, we investigated the variability of four genes (ACE2, ANPEP and DPP4 encoding for host receptors of the viral spike proteins and TMPRSS2 encoding for a host proteinase) in 23 European (19 autochthonous and three commercial breeds and one wild boar population) and two Asian Sus scrofa populations. A total of 2229 variants were identified in the four candidate genes: 26% of them were not previously described; 29 variants affected the protein sequence and might potentially interact with the infection mechanisms. The results coming from this work are a first step towards a "One Health" perspective that should consider conservation programs of pig genetic resources with twofold objectives: (i) genetic resources could be reservoirs of host gene variability useful to design selection programs to increase resistance to coronaviruses; (ii) the described variability in genes involved in coronavirus infections across many different pig populations might be part of a risk assessment including pig genetic resources.

Keep Garfagnina alive. An integrated study on patterns of homozygosity, genomic inbreeding, admixture and breed traceability of the Italian Garfagnina goat breed.

The objective of this study was to investigate the genetic diversity of the Garfagnina (GRF) goat, a breed that currently risks extinction. For this purpose, 48 goats were genotyped with the Illumina CaprineSNP50 BeadChip and analyzed together with 214 goats belonging to 9 other Italian breeds (~25 goats/breed), whose genotypes were available from the AdaptMap project [Argentata (ARG), Bionda dell'Adamello (BIO), Ciociara Grigia (CCG), Di Teramo (DIT), Garganica (GAR), Girgentana (GGT), Orobica (ORO), Valdostana (VAL) and Valpassiria (VSS)]. Comparative analyses were conducted on i) runs of homozygosity (ROH), ii) admixture ancestries and iii) the accuracy of breed traceability via discriminant analysis on principal components (DAPC) based on cross-validation. ROH analyses was used to assess the genetic diversity of GRF, while admixture and DAPC to evaluate its relationship to the other breeds. For GRF, common ROH (more than 45% in GRF samples) was detected on CHR 12 at, roughly 50.25-50.94Mbp (ARS1 assembly), which spans the CENPJ (centromere protein) and IL17D (interleukin 17D) genes. The same area of common ROH was also present in DIT, while a broader region (~49.25-51.94Mbp) was shared among the ARG, CCG, and GGT. Admixture analysis revealed a small region of common ancestry from GRF shared by BIO, VSS, ARG and CCG breeds. The DAPC model yielded 100% assignment success for GRF. Overall, our results support the identification of GRF as a distinct native Italian goat breed. This work can contribute to planning conservation programmes to save GRF from extinction and will improve the understanding of the socio-agro-economic factors related with the farming of GRF.

Can Grassland Chemical Quality Be Quantified Using Transform Near-Infrared Spectroscopy?

Near-infrared spectroscopy (NIRS) and closed spectroscopy methods have been applied to analyse the quality of forage and animal feed. However, grasslands are linked to variability factors (e.g., site, year, occurring species, etc.) which restrict the prediction capacity of the NIRS. The aim of this study is to test the Fourier transform NIRS application in order to determine the chemical characteristics of fresh, undried and unground samples of grassland located in north-central Apennine. The results indicated the success of FT-NIRS models for dry matter (DM), crude protein (CP), acid detergent fibre (ADF), neutral detergent fibre (NDF) and acid detergent lignin (ADL) on fresh grassland samples (R2 > 0.90, in validation). The model can be used to quantitatively determine CP and ADF (residual prediction deviation-RPD > 3 and range error ratio- RER > 10), followed by DM and NDF that maintain a RER > 10, and are sufficient for screening for the lignin fraction (RPD = 2.4 and RER = 8.8). On the contrary, models for both lipid and ash seem not to be usable at a practical level. The success of FT-NIRS quantification for the main chemical parameters is promising from the practical point of view considering both the absence of samples preparation and the importance of these parameters for diet formulation.

Characterization of Subcutaneous Fat of Toscano Dry-Cured Ham and Identification of Processing Stage By Multivariate Analysis Approach Based on Volatile Profile.

During ham processing the action of endogenous proteolytic and lipolytic enzymes leads to the development of volatile compounds (VOCs) responsible of typical aromas. Protected Designation of Origin (PDO) of Toscano ham requires at least 12 months of ripening but extended seasoning might improve flavor and economic value. This study aimed at assessing the evolution of color, fatty acids, and VOCs profile in subcutaneous fat, and, among VOCs, at identifying possible markers characterizing different seasoning length. For this purpose, a reduced pool of VOCs was selected by 3 multivariate statistical techniques (stepwise discriminant analysis, canonical discriminant analysis and discriminant analysis) to classify hams according to ripening (<12 months) or seasoning (≥12 months) periods and also to seasoning length (S12, S14, S16, or S18 months). The main VOCs chemical families steadily increased along ripening. Aldehydes and hydrocarbons reached their peaks at S16, acids and ketones remained constant from R6 to S16, whereas esters started decreasing after 12 months of seasoning. Stepwise analysis selected 5 compounds able to discriminate between ripening and seasoning periods, with 1,1-diethoxyhexane and dodecanoic acid being the most powerful descriptors for ripening and seasoning period, respectively. Instead, 12 compounds were needed to correctly classify hams within seasoning. Among them, undecanoic acid methyl ester, formic acid ethyl ester, 2,4,4-trimethylhexane, and 6-methoxy-2-hexanone had a central role in differentiating the seasoning length.

Whole-genome sequencing of European autochthonous and commercial pig breeds allows the detection of signatures of selection for adaptation of genetic resources to different breeding and production systems.

BACKGROUND: Natural and artificial directional selection in cosmopolitan and autochthonous pig breeds and wild boars have shaped their genomes and resulted in a reservoir of animal genetic diversity. Signatures of selection are the result of these selection events that have contributed to the adaptation of breeds to different environments and production systems. In this study, we analysed the genome variability of 19 European autochthonous pig breeds (Alentejana, Bísara, Majorcan Black, Basque, Gascon, Apulo-Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano, Sarda, Krskopolje pig, Black Slavonian, Turopolje, Moravka, Swallow-Bellied Mangalitsa, Schwäbisch-Hällisches Schwein, Lithuanian indigenous wattle and Lithuanian White old type) from nine countries, three European commercial breeds (Italian Large White, Italian Landrace and Italian Duroc), and European wild boars, by mining whole-genome sequencing data obtained by using a DNA-pool sequencing approach. Signatures of selection were identified by using a single-breed approach with two statistics [within-breed pooled heterozygosity (HP) and fixation index (FST)] and group-based FST approaches, which compare groups of breeds defined according to external traits and use/specialization/type. RESULTS: We detected more than 22 million single nucleotide polymorphisms (SNPs) across the 23 compared populations and identified 359 chromosome regions showing signatures of selection. These regions harbour genes that are already known or new genes that are under selection and relevant for the domestication process in this species, and that affect several morphological and physiological traits (e.g. coat colours and patterns, body size, number of vertebrae and teats, ear size and conformation, reproductive traits, growth and fat deposition traits). Wild boar related signatures of selection were detected across all the genome of several autochthonous breeds, which suggests that crossbreeding (accidental or deliberate) occurred with wild boars. CONCLUSIONS: Our findings provide a catalogue of genetic variants of many European pig populations and identify genome regions that can explain, at least in part, the phenotypic diversity of these genetic resources.