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Abstract Heterozygosity-rich regions (HRR) are genomic regions of high heterozygosity, which may harbor loci related to key functional traits such as immune response, survival rate, fertility, and other fitness traits. This study considered 30 Italian and 19 worldwide goat breeds genotyped with the Illumina GoatSNP50k BeadChip. The aim of the work was to study inter-breed relationships and HRR patterns using Sliding Window (SW) and Consecutive Runs (CR) detection methods. Genetic relationships highlighted a clear separation between non-European and European breeds, as well as the north–south geographic cline within the latter. The Pearson correlation coefficients between the descriptive HRR parameters obtained with the SW and CR methods were higher than 0.9. A total of 166 HRR islands were detected. CHI1, CHI11, CHI12 and CHI18 were the chromosomes harboring the highest number of HRR islands. The genes annotated in the islands were linked to various factors such as productive, reproductive, immune, and environmental adaptation mechanisms. Notably, the Montecristo feral goat showed the highest number of HRR islands despite the high level of inbreeding, underlining potential balancing selection events characterizing its evolutionary history. Identifying a species-specific HRR pattern could provide a clearer view of the mechanisms regulating the genome modelling following anthropogenic selection combined with environmental interaction.

Abstract Robertsonian translocation 1;29 (rob(1;29)), a widespread chromosomal anomaly affecting cattle fertility, appears to have originated from a common ancestor. This study utilizes routine SNP data to investigate the chromosomal region associated with rob(1;29) and confirm the presence of a shared haplotype among carriers in diverse Italian breeds. Three datasets were employed: Dataset 1 included 151 subjects from 5 beef cattle breeds genotyped with the GGP Bovine 33 k SNP chip; Dataset 2 encompassed 800 subjects from 32 Italian breeds genotyped with the Illumina 50 k SNP chip, sourced from the BOVITA dataset; Dataset 3 combined Dataset 2 with 21 karyologically tested subjects from breeds with a high carrier frequency, genotyped using the Affymetrix 65 K SNP chip. FST analysis pinpointed a distinctive genomic region on the first six Mb of BTA29, the centromeric region involved in the translocation. Haplotype comparisons within this non-recombining region revealed a common haplotype shared among all carriers, supporting the theory of a common ancestor. Principal component and haplotype analysis allowed clear differentiation of rob(1;29) homozygous and heterozygous carriers. Expanding to Dataset 2 revealed rob(1;29) carriers in unexpected breeds, all sharing the same ancestral haplotype. Notably, previously untested breeds, including Cinisara, exhibited a high carrier prevalence (nearly 50%), confirmed by karyological analysis. This study validates the presence of a shared haplotype among all identified rob(1;29) carriers, reinforcing the common ancestor theory as the origin of this translocation's spread throughout the cattle population. Furthermore, it underscores the potential of SNP data analysis as a rapid, accurate, and cost-effective tool for broad rob(1;29) screening, given the translocation's consistent nature across all analyzed breeds.

Climate change and heat stress pose significant challenges to livestock. Local breeds, particularly small ruminants, are gaining importance due to their adaptability to harsh climates. However, the extensive system they are commonly reared in leaves them exposed to the effects of climate change. This study aims to describe the distribution and climate-related challenges faced by registered Italian sheep and goat breeds over the past seven decades. Geolocalized data from all registered small ruminant farms were combined with climatic information retrieved from the “ERA-5-Land hourly data from 1950 to present” dataset. These data were used to calculate average daily temperature, temperature humidity index (THI), and total precipitation during summer. Additionally, THI-based heat waves (HWs) were examined, including the yearly number of HW days and mean THI during HW days. These data were analysed through linear regression models including region or breed, year, and their interaction as fixed factors. The climate data indicate a concerning trend of rising summer temperatures, THI, and HW frequency and intensity, particularly over the past three decades. Central-northern Italy, including the Po Valley and the Alpine Arch, is the most affected region, impacting breeds like Rosset and Brogne sheep, and Lariana and Frisa Valtellinese goats. This is of particular concern because these populations have not been selected for hot climates, and their already small population size exacerbates the problem. Conversely, southern Italy, characterized by hotter and drier temperatures, remained relatively stable. Breeds from this region, such as Girgentana and Nicastrese goats and Nera di Arbus sheep, might represent excellent case studies for climatic adaptation and potential resources for selection for resilience in the face of ongoing climate changes. The findings presented here are essential for the development of monitoring and intervention strategies for breeds facing future vulnerabilities, as well as for designing experiments to explore environmental adaptability in small ruminants.

The tumor microenvironment is considered one of the main players in cancer development and progression and may influence the behavior of cancer cells. Periostin (POSTN) is an extracellular matrix protein, and its main functions are induction of fibrillogenesis, fibroblastic cell proliferation and migration, enhancing regeneration in normal tissue, and promoting metastasis in case of neoplasia. POSTN has already been studied in humans in several normal tissues, inflammatory processes, and neoplasms, revealing an important role in tumor progression in various types of cancer, such as colon, lung, head and neck, breast, ovarian, and prostate. In these latter, high levels of POSTN are usually associated with a more aggressive tumor behavior, tumor advanced stages, and poor prognosis, while in human bladder urothelial carcinoma (BUC), unlike in most tumors, POSTN expression seems to be downregulated. The expression of this marker has been poorly investigated in veterinary medicine; thus, this study aimed to immunohistochemically investigate the presence and the intensity of POSTN expression in canine BUCs and to determine a possible relationship between POSTN expression and histopathological features such as mitotic count and muscular and vascular invasions. For the present retrospective study, archived samples from 45 canine BUCs and 6 non-neoplastic canine bladders were considered for histological evaluation and immunohistochemical examination for the expression of POSTN. POSTN expression was semi-quantitatively assessed considering both the percentage of the neoplastic stroma positive for POSTN and the intensity of the immunohistochemical labeling. Histologically, 38 out of 45 tumors were papillary and 7 out of 45 were non-papillary. All tumors were infiltrating, being that 21 were muscle-invasive, and a significant correlation between this feature and vascular invasion emerged (P = 0.0001). In normal bladder tissue, as reported in humans, a thick and strongly positive belt of POSTN was visible, and in canine BUCs, stating that the expression is comparable with human benign as well as malignant bladder tissue, a general decrease in POSTN expression was observed except for a strongly labeled ring of POSTN observed around some neoplastic nodules infiltrating the muscle layer. Moreover, POSTN expression and mitotic count were significatively inversely correlated (P = 0.0015). The fact that POSTN protein is less expressed in urothelial carcinomas than in the normal bladder supports what was reported in human BUCs and, together with the negative correlation between mitotic count and protein expression that emerged in the present retrospective study, encourages further prospective follow-up studies to verify the possible role of POSTN in canine BUCs as a prognostic marker, and also as a possible target for the development of future anticancer therapies.

The Comune di Sicilia, a local goat breed from Sicily (Italy), is currently undergoing recognition as a distinct breed. This study aims to characterize the population both phenotypically and genomically to advance its recognition process. A total of 78 subjects from two locations were enrolled, and their phenotypic data, including qualitative traits and morphometric measurements of adult animals, were recorded and statistically analyzed. The goats were genotyped using the Illumina 50 k Goat SNPchip, comparing them with 473 goats from 15 Italian breeds. Population structure, phylogenetic relationships, admixture, and genomic inbreeding were analyzed. Additionally, subjects with different morphological traits were compared using FST and runs of homozygosity, leading to the identification of potential candidate genes associated with anotia and wattle presence in goats. The Comune di Sicilia breed exhibited distinctive genomic and phenotypic features, setting it apart from other breeds in the same region. However, moderate variability, possibly influenced by selection practices, was also observed. To ensure the breed’s preservation and prevent excessive inbreeding, a comprehensive approach considering both morphology and genomic background is recommended. This study contributes valuable insights into the genetic peculiarities of the Comune di Sicilia goat, supporting its recognition as a unique and valuable breed.

Abstract Background Climate and farming systems, several of which are considered as low-input agricultural systems, vary between goat populations from Northern and Southern Italy and have led to different management practices. These processes have impacted genome shaping in terms of inbreeding and regions under selection and resulted in differences between the northern and southern populations. Both inbreeding and signatures of selection can be pinpointed by the analysis of runs of homozygosity (ROH), which provides useful information to assist the management of this species in different rural areas. Results We analyzed the ROH distribution and inbreeding (F ROH) in 902 goats from the Italian Goat Consortium2 dataset. We evaluated the differences in individual ROH number and length between goat breeds from Northern (NRD) and Central-southern (CSD) Italy. Then, we identified the signatures of selection that differentiate these two groups using three methods: ROH, ΔROH, and averaged F ST. ROH analyses showed that some Italian goat breeds have a lower inbreeding coefficient, which is attributable to their management and history. ROH are longer in breeds that are undergoing non-optimal management or with small population size. In several small breeds, the ROH length classes are balanced, reflecting more accurate mating planning. The differences in climate and management between the NRD and CSD groups have resulted in different ROH lengths and numbers: the NRD populations bred in isolated valleys present more and shorter ROH segments, while the CSD populations have fewer and longer ROH, which is likely due to the fact that they have undergone more admixture events during the horizontal transhumance practice followed by a more recent standardization. We identified four genes within signatures of selection on chromosome 11 related to fertility in the NRD group, and 23 genes on chromosomes 5 and 6 related to growth in the CSD group. Finally, we identified 17 genes on chromosome 12 related to environmental adaptation and body size with high homozygosity in both groups. Conclusions These results show how different management practices have impacted the level of genomic inbreeding in two Italian goat groups and could be useful to assist management in a low-input system while safeguarding the diversity of small populations.

Abstract Background Since their domestication 10,500 years ago, goat populations with distinctive genetic backgrounds have adapted to a broad variety of environments and breeding conditions. The VarGoats project is an international 1000-genome resequencing program designed to understand the consequences of domestication and breeding on the genetic diversity of domestic goats and to elucidate how speciation and hybridization have modeled the genomes of a set of species representative of the genus Capra. Findings A dataset comprising 652 sequenced goats and 507 public goat sequences, including 35 animals representing eight wild species, has been collected worldwide. We identified 74,274,427 single nucleotide polymorphisms (SNPs) and 13,607,850 insertion-deletions (InDels) by aligning these sequences to the latest version of the goat reference genome (ARS1). A Neighbor-joining tree based on Reynolds genetic distances showed that goats from Africa, Asia and Europe tend to group into independent clusters. Because goat breeds from Oceania and Caribbean (Creole) all derive from imported animals, they are distributed along the tree according to their ancestral geographic origin. Conclusions We report on an unprecedented international effort to characterize the genome-wide diversity of domestic goats. This large range of sequenced individuals represents a unique opportunity to ascertain how the demographic and selection processes associated with post-domestication history have shaped the diversity of this species. Data generated for the project will also be extremely useful to identify deleterious mutations and polymorphisms with causal effects on complex traits, and thus will contribute to new knowledge that could be used in genomic prediction and genome-wide association studies.

IntroductionIntegrating by-products into livestock diet represents a great opportunity for implementing the concept of circular economy while reducing feed costs. Olive cake (OC) is considered an agro-industrial waste, but the high content of valuable metabolites makes it a promising feed integration. Therefore, this study investigated the effect of OC integration in beef cattle diet on different blood parameters.MethodsForty-eight young growing fattening Limousines-−24 bulls (body weight 350 ± 15 kg) and 24 heifers (280 ± 10 kg)—, aged 240 ± 20 days, were randomly allocated to 1 of 3 dietary treatments: concentrate at 0% (Control group: CTR), 10% (Low-olive cake group: L-OC), or 15% (High-olive cake group: H-OC) of OC inclusion. Blood samples and body weights were collected before administrating the supplemented diet (0 d), at the end of the stocker growing phase (56 d), and at the end of the fattening (147 d). After being slaughtered, animal carcasses were weighted. A linear regression model was fitted for each blood parameter with the 0 d as covariate and diet, time, sex, diet × time, and diet × sex as fixed effects.ResultsIn males, body weight was highest in CTR, but carcass weight was similar in all the groups. All the blood parameters were within physiological ranges, independently from the animal diet. CTR group showed the highest alanine aminotransferase (ALT, P = 0.0027) and creatine kinase (P = 0.0119), whereas total bilirubin (P = 0.0023) was higher in H-OC than in CTR. Moreover, ALT was highest in CTR at 56 d, becoming similar in all the groups at 147 d (P = 0.0280). Instead, the increase observed in total cholesterol from 56 to 147 d was lower in H-OC compared with CTR and L-OC (P = 0.0451). A significant effect of diet × sex interaction was observed on triglycerides, urea, liver enzymes, and insulin. These data support the OC inclusion of up to 15% of the concentrate with no detrimental effect on beef cattle metabolic status.DiscussionIn conclusion, OC can be considered as a component in beef diet giving an opportunity to improve agriculture sustainability.

Shepherd and hunting dogs have undergone divergent selection for specific tasks, resulting in distinct phenotypic and behavioural differences. Italy is home to numerous recognized and unrecognized breeds of both types, providing an opportunity to compare them genomically. In this study, we analysed SNP data obtained from the CanineHD BeadChip, encompassing 116 hunting dogs (representing 6 breeds) and 158 shepherd dogs (representing 9 breeds). We explored the population structure, genomic background, and phylogenetic relationships among the breeds. To compare the two groups, we employed three complementary methods for selection signature detection: FST, XP-EHH, and ROH. Our results reveal a clear differentiation between shepherd and hunting dogs as well as between gun dogs vs. hounds and guardian vs. herding shepherd dogs. The genomic regions distinguishing these groups harbour several genes associated with domestication and behavioural traits, including gregariousness (WBSRC17) and aggressiveness (CDH12 and HTT). Additionally, genes related to morphology, such as size and coat colour (ASIP and TYRP1) and texture (RSPO2), were identified. This comparative genomic analysis sheds light on the genetic underpinnings of the phenotypic and behavioural variations observed in Italian hunting and shepherd dogs.

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

Agro-industrial by-products incorporated into livestock feed formulations can positively impact feed costs and promote a circular bio-economy. Italy produces significant amounts of olive cake (OC), a by-product of olive oil extraction, with the potential for incorporation into bovine diets. However, information on its effects on endocrine responses in growing beef calves is lacking. Forty-eight Limousines randomly allocated to dietary treatment (control or 10%-OC or 15%-OC inclusion) were segregated according to sex and body weight. Serum concentrations of TSH, thyroid hormones, and cortisol were measured on day 0, day 56, and at the end of the trial on day 147. Circulating TSH, total (T3, T4) and free (fT3, fT4) iodothyronines, and cortisol concentrations were all within the normal physiological ranges, with no significant effect imparted by diet. However, the diet × time interaction was significant for T3. The cortisol, T3, T4, and fT4 registered on day 147 were higher than those of day 56, and cortisol was higher in heifers than bulls. Final body weight was positively correlated with TSH and T3 and negatively with cortisol concentration. These findings suggest that the inclusion of OC at levels up to 15% in growing/finishing beef diets had no adverse effects on the calves’ thyroid and cortical status.

Cirneco dell’Etna is an old Italian breed of scent hunting dogs. Commonly used genomic measures such as heterozygosity, fixation indexes, and runs of homozygosity can help to improve knowledge about its genetic diversity. This study aimed to: (i) investigate Cirneco’s genomic background, (ii) quantify its genomic inbreeding, and (iii) detect genomic regions differentiating the Cirneco’s two allowed coat colours, self-coloured fawn and tan and white. Canine 230 K SNP BeadChips was used to investigate 24 Cirneco (19 self-coloured fawn, and 5 tan and white) and other 106 dogs from eight phylogenetically and historically related breeds. The genetic distance, ancestry, and relationship among breeds were explored by multidimensional scaling, Reynolds distances, phylogenetic tree, and admixture analysis. The genomic inbreeding (FROH) was calculated for each breed. Averaged Wright’s fixation index ST was used to identify the genes that most differentiated the two groups of Cirneco. All analyses highlighted that Segugio Italiano and Kelb tal Fenek are the closest breeds to Cirneco. Within the breed, tan and white subjects showed a more heterogeneous genetic background and a lower inbreeding in comparison with self-coloured fawn ones, even though more than half of the latter presented a superimposable admixture. The gene that most differentiated these two groups is Microphthalmia-Associated Transcription Factor (MITF), previously associated with white spotting in other breeds. Given the small size of the Cirneco population and its open registry, its management should carefully combine morphological and genealogical evaluations with genetic tools to identify the best breeders while maintaining an acceptable genetic pool.Highlights The genomic analysis demonstrated that Segugio Italiano and Kelb tal Fenek are genetically related to the Cirneco. The MITF gene is responsible for white blazing in Cirneco as in many other dog breeds. Genomic tools should be integrated with phenotypic and genealogic evaluations in the management of Italian autochthonous dog breeds to safeguard their welfare and biodiversity.

Mannara dogs have long been bred in Sicily (Italy) to work alongside shepherds as flock guardians. This study provides a morphologic, genealogic, and genomic characterisation of the Mannara dog, useful in light of its recognition process and to improve the breed standard. Morphologic measurements of body, head, and chest were taken on 111 adult Mannara dogs. The whole population pedigree was used to calculate the inbreeding coefficient (F) and five effective population size (Ne) parameters. Twelve Mannara dogs were genotyped using the Canine 230 K SNP BeadChips and compared with Maremma sheepdog, Caucasian shepherd dog, Cane Corso Italiano, and Neapolitan mastiff for population structure, heterozygosity, and runs of homozygosity. The morphometric evaluation showed that Mannara dogs generally accords with the provisional standard and can be classified as a large/giant, meso-dolicomorphic, and mesocephalic breed. The population consists of 375 individuals, one third of which are founders and the remaining belong to 58 litters; presenting low inbreeding (F = 0.7%) and balanced sires and dams. The Ne estimates range widely: two (NeN=159 and NeFi=50) exceed the FCI limit for breed recognition and one (NeCi=25) did not. Genetically, all the included populations are well distinct, with the Maremma sheepdog being the nearest to the Mannara dog. Five Mannara have a single ancestral component, while the others show higher admixed proportions. The genomic inbreeding and heterozygosity confirm the good management of the breed. Our analyses suggest that the Mannara breed should continue the recognition process, pivotal to preserving an invaluable canine resource for the Sicilian agriculture.Highlights The morphometric measurements of Mannara dogs generally accords with the provisional standard. The pedigree analysis reveals that the population is well managed and meets the criteria for FCI recognition. The Mannara dog presents a unique genomic background.

Abstract Background Assessment of genetic diversity and population structure provides important control metrics to avoid genetic erosion, inbreeding depression and crossbreeding between exotic and locally-adapted cattle breeds since these events can have deleterious consequences and eventually lead to extinction. Historically, the Alpine Arc represents an important pocket of cattle biodiversity with a large number of autochthonous breeds that provide a fundamental source of income for the entire regional economy. By using genotype data from medium-density single nucleotide polymorphism (SNP) arrays, we performed a genome-wide comparative study of 23 cattle populations from the Alpine Arc and three cosmopolitan breeds. Results After filtering, we obtained a final genotyping dataset consisting of 30,176 SNPs for 711 individuals. The local breeds showed high or intermediate values of genetic diversity compared to the highly selected cosmopolitan breeds. Patterns of genetic differentiation, multidimensional scaling, admixture analysis and the constructed phylogenetic tree showed convergence, which indicates the presence of gene flow among the breeds according to both geographic origin and historical background. Among the most differentiated breeds, we identified the modern Brown cattle. In spite of admixture events, several local breeds have preserved distinctive characteristics, which is probably due to differences in genetic origin and geographic location. Conclusions This study represents one of the most comprehensive genome-wide analysis of the Alpine cattle breeds to date. Using such a large dataset that includes the majority of the local breeds found in this region, allowed us to expand knowledge on the evaluation and status of Alpine cattle biodiversity. Our results indicate that although many of the analyzed local breeds are listed as endangered, they still harbor a large amount of genetic diversity, even when compared to some cosmopolitan breeds. This finding, together with the reconstruction of the phylogeny and the relationships between these Alpine Arc cattle breeds, provide crucial insights not only into the improvement of genetic stocks but also into the implementation of future conservation strategies.

The Fonni’s dog is an ancient Sardinian breed for livestock and property guarding. In recent years, the number of new registrations to the breeding book has slumped and, thus, this breed risks being lost forever. This work refocuses attention to the Fonni’s dog, analysing its genomic makeup and comparing different phenotypical and genetic evaluation scores. Thirty Fonni’s dogs were ranked by their general accordance to the breed typicality (typicality score) and to the provisional standard by official judges (judges’ score). They were genotyped with a 230K SNP BeadChip and compared with 379 dogs of 24 breeds. Genomically, the Fonni’s dogs placed themselves near shepherd dogs and showed a unique genetic signature, which was used to create the genomic score. This score better correlated with typicality (ρ = 0.69, p < 0.0001) than the judges’ score (ρ = 0.63, p = 0.0004), which showed little variability among the included dogs. Hair texture or colour were significantly associated in the three scores. The Fonni’s dog is confirmed as a well-distinguished breed, despite being selected mainly for its work abilities. The evaluation criteria used during dog expositions can be improved to increase their variability and include elements typical of the breed. The recovery of the Fonni’s dog would be possible only with a shared vision between the Italian kennel club and breeders, and the support of regional programs.

Livestock guardian (LGD) and herding shepherd (HSD) dogs have distinct morphological and behavioural characteristics, long selected by farmers and breeders, to accomplish different tasks. This study aimed to find the genomic regions that best differentiate and characterise Italian LGD and HSD. Genomic data of 158 dogs of four LGD and five HSD breeds, obtained with the 170K canine SNPchip, were collected. The two groups were compared using FST and XP-EHH analyses, identifying regions containing 29 genes. Moreover, 16 islands of runs of homozygosity were found in LGD, and 15 in HSD; 4 of them were partially shared. Among the genes found that better differentiated HSD and LGD, several were associated with dog domestication and behavioural aspects; particularly, MSRB3 and LLPH were linked to herding behaviour in previous studies. Others, DYSK, MAP2K5, and RYR, were related to body size and muscle development. Prick ears prevailed in sampled HSD, and drop ears in LGD; this explains the identification of WIF1 and MSRB3 genes. Unexpectedly, a number of genes were also associated with eye development and functionality. These results shed further light on the differences that human selection introduced in dogs aimed at different duties, even in a limited geographic area such as Italy.

The inbreeding coefficient is an important parameter for livestock management. Small ruminant breeders and associations mainly rely on pedigree information, but genomic tools are gaining relevance, overcoming possible pedigree inconsistencies. This study investigates the relationship between pedigree-based and genomic inbreeding in two goat and four sheep dairy breeds. Pedigree and genomic data (medium-density SNPchip) were obtained for 3107 goats and 2511 sheep. We estimated pedigree depth (number of fully traced generations, FullGen) and inbreeding (FPED), as well as two genomic inbreeding indexes, using runs of the homozygosity (FROH) and genomic relationship matrix (FGRM). The correlation between the inbreeding coefficients was assessed. A linear regression model (LRM) was fitted for estimating FPED from FROH. After quality control on genomic data, we retained 5085 animals. Mean inbreeding values were low, with higher FROH than FPED and FGRM. Breed differences can partially depend on different managements. The correlation between FPED and FROH was the highest and directly related to pedigree depth. The best LRM was chosen for FullGen ≥4 and ≥6 for goats and sheep, respectively; after excluding animals with extreme residuals, a new refined regression equation was calculated. Since massive genotyping is not affordable to small ruminant breeders, it is important to understand the distinction and relationship between differently calculated inbreeding coefficients, also in view of the introduction of genomic enhanced breeding values. Our study highlights the importance of accurate pedigree information and, especially if not obtainable, of calculating genomic-based inbreeding coefficients. A better estimation of animals’ relatedness contributes to improve animal breeding and conservation.

Global population growth and climate change raise a challenge to agriculture, which, combined with the issues concerning the use of chemical fertilizers, have generated increasing attention in the use of plant-associated bacteria as a sustainable strategy in agri-food systems. The objective of this study is to evaluate the ability of five bacterial strains, previously isolated from the rhizosphere or endosphere of plants adapted to harsh environmental conditions, to act as potential plant biofertilizers in different conditions of water availability. The strain biosafety for a deliberate environmental release was investigated through a literature survey and antibiotic resistance testing. The selected strains were first characterized for their plant growth–promoting (PGP) and rhizocompetence-related traits through in vitro assays and then on short-term in vivo experiments on tomato plants. A long-term greenhouse experiment was further conducted to monitor the PGP effect of the bacteria during the entire life cycle of tomato plants subjected to full irrigation or to severe water deficit conditions, aiming to assess their actual effect on plant productivity, which is the ultimate target of the agricultural sector. Some of the strains showed a potential in improving water use efficiency and mitigating plant water stress. Under severe irrigation deficit, four of the tested strains, Micrococcus yunnanensis M1, Bacillus simplex RP-26, Pseudomonas stutzeri SR7-77, and Paenarthrobacter nitroguajacolicus 2–50, significantly increased the number of productive plants in comparison to non-bacterized control ones. Two of them, Bacillus simplex RP-26 and Paenarthrobacter nitroguajacolicus 2–50, demonstrated also, under full irrigation, to significantly improve the water productivity in comparison with non-bacterized plants. Despite all the strains showed promising PGP potential in short-term assays, the positive effect of the bacterial inoculants on plant physiology and fruit yield was observed in some cases but never corroborated by statistical significance. These results highlight the importance of performing long-term in vivo experiments to define the real PGP ability of a bacterial inoculant to positively impact plant production.

The study examined the effects of different stages of pregnancy and lactation on thyroid, insulin, and glucose responses in dairy cows. In the present study, 30 dairy cows (10 Holstein, 10 Simmental, and 10 Brown) at 30 ± 20 d of lactation were randomly selected and blood samples were collected once every 60 d for one year to measure circulating thyroid stimulating hormone (TSH), total and free triiodothyronines (T3, fT3) and thyroxines (T4, fT4), insulin, and glucose. Pregnant cows showed higher T4 (p = 0.010) and insulin (p = 0.046) concentrations at >180 d than at >60–120 d of pregnancy and in nonpregnant cows. Along the lactation phase, circulating T4 concentrations showed a biphasic trend, decreasing from 0–60 d to >60–120 d phase, which showed the lowest values, and then increasing until the end of lactation (>300 d) (p = 0.016). Glucose showed the highest concentrations at the start of lactation (0–120 days) and the lowest values at the end (p = 0.008). The monitoring of thyroid hormones, insulin, and glucose changes represents an important tool to evaluate the anabolic and/or catabolic adaptation in response to functional periods in dairy cows, which can potentially predispose the cows to an excessive negative energy balance and related metabolic issues.

Background A mutation in the canine multidrug resistance MDR1 gene (also referred as ABCB1), encoding for the multidrug resistance (MDR) P-glycoprotein (P-gp) transponder, causes a pathological condition known as ‘ivermectin toxicosis’. The causative mutation, known since 2001, has been described to affects sheep herding breeds related to collie lineage. The present study is a retrospective investigation of the presence of MDR1 mutated allele in Italian dog populations in a 5 years’ time lapse. The aim of the research is to offer a deep knowledge in MDR1 allelic and genotypic frequencies in canine breeds and populations raised in Italy.Methods Genotype data for the 4-bp deletion (c296_299del4) in MDR1 gene from 811 dogs belonging to 32 breeds/populations were collected.Results The mutated allele has been found in 9 out of 31 breeds: Rough Collie, Smooth Collie, Border Collie, Bearded Collie, Shetland Sheepdog, Australian Shepherd, White Swiss Shepherd, Old English Sheepdog, Whippet and also in crossbreed. The breeds with the highest allelic mutation frequency are Smooth and Rough Collies with 75 per cent and 66 per cent of mutant MDR1 allele, respectively.Conclusions The results support the usefulness of this genetic analysis to optimise medical care in dogs at risk of multidrug resistance and to create an objective basis in breeding programme definition and in the risk evaluation in different breeds.

Abstract Background Since goat was domesticated 10,000 years ago, many factors have contributed to the differentiation of goat breeds and these are classified mainly into two types: (i) adaptation to different breeding systems and/or purposes and (ii) adaptation to different environments. As a result, approximately 600 goat breeds have developed worldwide; they differ considerably from one another in terms of phenotypic characteristics and are adapted to a wide range of climatic conditions. In this work, we analyzed the AdaptMap goat dataset, which is composed of data from more than 3000 animals collected worldwide and genotyped with the CaprineSNP50 BeadChip. These animals were partitioned into groups based on geographical area, production uses, available records on solid coat color and environmental variables including the sampling geographical coordinates, to investigate the role of natural and/or artificial selection in shaping the genome of goat breeds. Results Several signatures of selection on different chromosomal regions were detected across the different breeds, sub-geographical clusters, phenotypic and climatic groups. These regions contain genes that are involved in important biological processes, such as milk-, meat- or fiber-related production, coat color, glucose pathway, oxidative stress response, size, and circadian clock differences. Our results confirm previous findings in other species on adaptation to extreme environments and human purposes and provide new genes that could explain some of the differences between goat breeds according to their geographical distribution and adaptation to different environments. Conclusions These analyses of signatures of selection provide a comprehensive first picture of the global domestication process and adaptation of goat breeds and highlight possible genes that may have contributed to the differentiation of this species worldwide.

Abstract Background International standard panels of single nucleotide polymorphisms (SNPs) have replaced microsatellites in several species for parentage assessment and assignment (PA) purposes. However, such a resource is still lacking in goats. The application of a cheap tool for PA would help the management of goat populations by improving the reliability of pedigree registration and, consequently, allow a better implementation of breeding schemes or conservation programs. Results Using data from the current GoatSNP50 chip, starting from a worldwide dataset of more than 4000 animals belonging to more than 140 breeds and populations from the AdaptMap initiative, we selected a panel of 195 SNPs. The assignment rate of this panel was up to 100% on an additional dataset that included 2000 Alpine and Saanen animals and highly related candidate sires. Conclusions In this study, we defined a highly informative SNP panel, which will be publicly available to worldwide breeders and laboratories. Its development on such a large number of breeds and populations, together with validation on a second set of cosmopolitan breeds, makes it a promising and important genomic tool for the goat species.

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

Abstract Background In the last 50 years, the diversity of cattle breeds has experienced a severe contraction. However, in spite of the growing diffusion of cosmopolite specialized breeds, several local cattle breeds are still farmed in Italy. Genetic characterization of breeds represents an essential step to guide decisions in the management of farm animal genetic resources. The aim of this work was to provide a high-resolution representation of the genome-wide diversity and population structure of Italian local cattle breeds using a medium-density single nucleotide polymorphism (SNP) array. Results After quality control filtering, the dataset included 31,013 SNPs for 800 samples from 32 breeds. Our results on the genetic diversity of these breeds agree largely with their recorded history. We observed a low level of genetic diversity, which together with the small size of the effective populations, confirmed that several breeds are threatened with extinction. According to the analysis of runs of homozygosity, evidence of recent inbreeding was strong in some local breeds, such as Garfagnina, Mucca Pisana and Pontremolese. Patterns of genetic differentiation, shared ancestry, admixture events, and the phylogenetic tree, all suggest the presence of gene flow, in particular among breeds that originate from the same geographical area, such as the Sicilian breeds. In spite of the complex admixture events that most Italian cattle breeds have experienced, they have preserved distinctive characteristics and can be clearly discriminated, which is probably due to differences in genetic origin, environment, genetic isolation and inbreeding. Conclusions This study is the first exhaustive genome-wide analysis of the diversity of Italian cattle breeds. The results are of significant importance because they will help design and implement conservation strategies. Indeed, efforts to maintain genetic diversity in these breeds are needed. Improvement of systems to record and monitor inbreeding in these breeds may contribute to their in situ conservation and, in view of this, the availability of genomic data is a fundamental resource.

Abstract Background Molecular regulation of the hypothalamic-pituitary-gonadal (HPG) axis plays an essential role in the fine tuning of seasonal estrus in Capra hircus. Noncoding RNAs (ncRNAs) are emerging as key regulators in sexual development and mammalian reproduction. In order to identify ncRNAs and to assess their expression patterns, along the HPG axis, we sequenced ncRNA libraries from hypothalamus, pituitary and ovary of three goats. Results Among the medium length noncoding RNAs (mncRNAs) identified, small nucleolar RNAs (snoRNAs) and transfer RNAs (tRNAs) were found to be more abundant in ovary and hypothalamus, respectively. The observed GC content was representative for different classes of ncRNAs, allowing the identification of a tRNA-derived RNA fragments (tRFs) subclass, which had a peak distribution around 32–38% GC content in the hypothalamus. Differences observed among organs confirmed the specificity of microRNA (miRNA) profiles for each organ system. Conclusions Data on ncRNAs in organs constituting the HPG axis will contribute to understanding their role in the physiological regulation of reproduction in goats.

The water buffalo is a fundamental resource, especially in developing countries, however, differently from other species, its genetic potential is still poorly investigated. In this work, we performed a candidate gene association study for milk composition in 491 female buffaloes. Animals were from four farms located in Southern Italy, where the Out-of-Breeding-Season-Mating technique is usually performed. We analysed three genes: (1) the signal transducer and activator of transcription 5A (STAT5A), (2) the tumour necrosis factor alpha (TNFα) and (3) the melatonin receptor 1A (MTNR1A). We confirmed the mutation at the MTNR1A gene and we found five novel single nucleotide polymorphisms (SNPs): one in the TNFα and four in the STAT5A. No associations were found for the SNPs in the MTNR1A and TNFα genes, while we identified a marked association with milk protein % for a C > T substitution at the STAT5A gene. At this locus, the TT buffaloes showed significantly higher protein percentage in milk. Conversely, this genotype class was the less frequent in the population. Moreover, an A > G substitution at the STAT5A showed an influence on reproductive seasonality, with the advantageous allele most frequent in the population, suggesting a possible effect of selection for this trait. The C > T substitution on STAT5A detected in present study could be used in marker assisted selection of Mediterranean Italian buffalo, and should be monitored to understand the reasons behind the low frequency of the favourable genotype at this locus and to stop this unfavourable trend in the population.

The presence of cats in urban environments has a long history. In Italy, stray cats are protected by national and regional laws, and programs of neutering and reintroduction to colonies are ongoing. Colony cats have been widely studied from a behavioral perspective, while surveys regarding their causes of death are limited, although they may provide relevant information related to public health and cat welfare. This retrospective study provides pathological descriptions and statistical analyses of the causes of death of 186 cats from 100 colonies in the city of Milan. Inflammatory processes represent the primary cause of death (37.7%) and include common feline infectious diseases such as feline panleukopenia (67.5%), particularly in kittens, and feline infectious peritonitis (32.5%), most common in adult cats. Trauma was found to be a common cause of death of young/adult cats (14%) with a generally good body condition, while severe parasitosis was less represented (2.6%). The death of old cats was statistically associated with organ failure (24.7%), particularly renal failure, and tumors (11.8%). Knowledge of the most common causes of death of colony cats could make an important contribution to the health monitoring of these cats and sanitary control of their habitats and provide information on possible related emerging animal welfare concerns.

The satisfaction of leisure horses’ behavioral needs has begun to be considered a priority, linked to the awareness that horses kept in single boxes may be deprived of social contact and the possibility to perform natural behaviors. Several factors may influence horses’ quality of life also in the paddock, and there are very few data on the effects of those variables on leisure horses’ chronic stress, measurable in terms of activation of the hypothalamic–pituitary–adrenocortical axis. Therefore, managerial choices faced by owners and stables managers are only based on experience, common sense, and anecdotal beliefs. This study assessed and compared the chronic stress levels in leisure horses hosted in structures in the same geographic and climatic area with different daily routines to verify which management strategy could be the one that better contributes to achieving the welfare of horses. Forty-seven horses were divided into three groups homogeneous in terms of sex and age: Mixed management group (n = 12), Paddock group (n = 19), and Natural management group (n = 16). The hair cortisol concentration, a reliable marker of long-term stress, was analyzed in all the horses the same day at four time points of the year. In addition to management strategies, the influences of other variables (sex, age, coat color, and season) were evaluated. Independently from the management strategies, significantly higher hair cortisol values were detected in the autumn and summer, as well as in individuals older than 15 years. No significant differences were highlighted between the sexes or the coat colors. The comparison of the different management strategies showed that, in the summer, autumn, and winter, the hair cortisol levels were significantly lower in the Mixed management group horses than the Paddock group, highlighting that those subjects had better homeostasis. The Natural management group horses’ hair cortisol levels were intermediate between the other two groups of horses in all the seasons. Spending the night in the stables would seem to positively impact the well-being of the horses. These findings, if confirmed by further studies, may be helpful in enhancing horse welfare and assisting in managerial choice decision-making.

Abstract Background DNA methylation is a frequently studied epigenetic modification due to its role in regulating gene expression and hence in biological processes and in determining phenotypic plasticity in organisms. Rudimentary DNA methylation patterns for some livestock species are publically available: among these, goat methylome deserves to be further explored. Results Genome-wide DNA methylation maps of the hypothalamus and ovary from Saanen goats were generated using Methyl-CpG binding domain protein sequencing (MBD-seq). Analysis of DNA methylation patterns indicate that the majority of methylation peaks found within genes are located gene body regions, for both organs. Analysis of the distribution of methylated sites per chromosome showed that chromosome X had the lowest number of methylation peaks. The X chromosome has one of the highest percentages of methylated CpG islands in both organs, and approximately 50% of the CpG islands in the goat epigenome are methylated in hypothalamus and ovary. Organ-specific Differentially Methylated Genes (DMGs) were correlated with the expression levels. Conclusions The comparison between transcriptome and methylome in hypothalamus and ovary showed that a higher level of methylation is not accompanied by a higher gene suppression. The genome-wide DNA methylation map for two goat organs produced here is a valuable starting point for studying the involvement of epigenetic modifications in regulating goat reproduction performance.

Abscesses are a common problem in goat farms worldwide. In most cases, the disease is caused by Corynebacterium pseudotuberculosis that is the aetiological agent of caseous lymphadenitis (CLA). CLA causes considerable economic losses, due to reduced milk production, and to carcase damage. At present, no effective therapy for CLA is available and vaccine use is limited. The current study presents evidence for loci associated to CLA susceptibility identified using the 50K Goat SNP panel in a case-control genome wide association study. The analysis of the genotype data identified four chromosomal regions associated with disease status: on chromosomes 5, 7, 8 and 11. These results provide the first evidence for genetic loci involved in the immunological response to CLA in goat. Knowledge of genetic variations related to susceptibility will facilitate the incorporation of this information for the improvement of health status in the goat species.

Italy is home to several populations of native dogs that reside only in certain demographic regions. Such dog populations have not been under tight selection by humans and, as such, have never been officially recognised as breeds. One such population is the ‘Cane Fonnese’ or Fonni’s Dog, which features uniform morphologic and behavioural traits that reproduce across generations, thus qualifying Fonni’s Dog as a true breed eligible for recognition by national or international breed registries. The Fonni’s Dog population examined in the present work is native to Sardinia, where they are used as property or livestock guardian dogs. As such, they are greatly appreciated by the local populace. We have carried out morphological evaluations on 200 Fonni’s Dogs with the aim of developing a standard breed definition upon which the foundation of the Fonni’s Dog breed can be based. We have also reported genetic data of the Fonni’s Dog compared to four other established breeds sampled from the same geographic area.

At the end of the last glaciation, Apis mellifera was established in northern Europe. In Italy, Apis melliferaligustica adapted to the mild climate and to the rich floristic biodiversity. Today, with the spread of Varroa destructor and with the increasing use of pesticides in agriculture, the Ligustica subspecies is increasingly dependent on human action for its survival. In addition, the effects of globalization of bee keeping favored the spread in Italy of other honeybee stocks of A. mellifera, in particular the Buckfast bee. The purpose of this study was to characterize the Italian honeybee’s population by sequencing the whole genome of 124 honeybees. Whole genome sequencing was performed by Illumina technology, obtaining a total coverage of 3720.89X, with a mean sample coverage of 29.77X. A total of 4,380,004 SNP variants, mapping on Amel_HAv3.1 chromosomes, were detected. Results of the analysis of the patterns of genetic variation allowed us to identify and subgroup bees according to their type. The investigation revealed the genetic originality of the Sicula, and in A.m. ligustica limited genetic introgression from the other breeds. Morphometric analysis of 5800 worker bees was in agreement with genomic data.

The application of genomic technologies has facilitated the assessment of genomic inbreeding based on single nucleotide polymorphisms (SNPs). In this study, we computed several runs of homozygosity (ROH) parameters to investigate the patterns of homozygosity using Illumina Goat SNP50 in five Italian local populations: Argentata dell’Etna (N = 48), Derivata di Siria (N = 32), Girgentana (N = 59), Maltese (N = 16) and Messinese (N = 22). The ROH results showed well-defined differences among the populations. A total of 3687 ROH segments >2 Mb were detected in the whole sample. The Argentata dell’Etna and Messinese were the populations with the lowest mean number of ROH and inbreeding coefficient values, which reflect admixture and gene flow. In the Girgentana, we identified an ROH pattern related with recent inbreeding that can endanger the viability of the breed due to reduced population size. The genomes of Derivata di Siria and Maltese breeds showed the presence of long ROH (>16 Mb) that could seriously impact the overall biological fitness of these breeds. Moreover, the results confirmed that ROH parameters are in agreement with the known demography of these populations and highlighted the different selection histories and breeding schemes of these goat populations. In the analysis of ROH islands, we detected harbored genes involved with important traits, such as for milk yield, reproduction, and immune response, and are consistent with the phenotypic traits of the studied goat populations. Finally, the results of this study can be used for implementing conservation programs for these local populations in order to avoid further loss of genetic diversity and to preserve the production and fitness traits. In view of this, the availability of genomic data is a fundamental resource.

Cavalier King Charles spaniels (CKCSs) show the earliest onset and the highest incidence of myxomatous mitral valve disease (MMVD). Previous studies have suggested a polygenic inheritance of the disease in this breed and revealed an association with regions on canine chromosomes 13 and 14. Following clinical and echocardiographic examinations, 33 not-directly-related CKCSs were selected and classified as cases (n = 16) if MMVD was present before 5 years of age or as controls (n = 17) if no or very mild MMVD was present after 5 years of age. DNA was extracted from whole blood and genotyped with a Canine 230K SNP BeadChip instrument. Cases and controls were compared with three complementary genomic analyses (Wright’s fixation index—FST, cross-population extended haplotype homozygosity—XP-EHH, and runs of homozygosity—ROH) to identify differences in terms of heterozygosity and regions of homozygosity. The top 1% single-nucleotide polymorphisms (SNPs) were selected and mapped, and the genes were thoroughly investigated. Ten consensus genes were found localized on chromosomes 3-11-14-19, partially confirming previous studies. The HEPACAM2, CDK6, and FAH genes, related to the transforming growth factor β (TGF-β) pathway and heart development, also emerged in the ROH analysis. In conclusion, this work expands the knowledge of the genetic basis of MMVD by identifying genes involved in the early onset of MMVD in CKCSs.

This prospective cross-sectional study aimed to: (1) characterize echocardiographic features of mitral valve in MMVD affected Cavalier King Charles Spaniels (CKCS), focusing on dogs classified as American College of Veterinary Internal Medicine (ACVIM) class B1; (2) compare echocardiographic data in ACVIM B1 dogs divided on the basis of age at time of MMVD diagnosis, in order to understand if different aged subjects had different echocardiographic patterns. Length (AMVL), width (AMVW) and area (AMVA) of the anterior mitral valve leaflet, mitral valve prolapse, diameters of the mitral valve annulus in diastole (MVAd) and systole (MVAs) of 90 CKCS in different ACVIM classes, 64 of which in class B1, were measured. Valvular measurements were indexed to body weight using Wesselowski’s scaling exponents. The presence of heart murmur did not discriminate between A and B1 classes (p = 0.128). Heart enlargement was more frequent in males (r2 = 0.07, p = 0.013). Within class B1, older subjects showed significantly higher values of AMVA, AMVW, MVAd, MVAs and lower sphericity index (SI). Since many CKCS with MMVD have no murmur and their mitral valve has peculiarities, a specifically designed echocardiographic screening should be realized. In addition, different aged B1 dogs have different echocardiographic patterns that may imply different genetic and prognostic profiles.

The SLC24A5 (Solute Carrier family 24, member 5) gene is implicated in skin pigmentation in zebrafish and humans as it regulates the morphogenesis of melanosomes, specialized lysosomes involved in melanin deposit. In humans, the ancestral allele predominates in African and East Asian populations, while the allelic variant is nearly fixed in European populations and correlates with lighter pigmentation. Considering the role of melanin in the protecting of DNA from ultraviolet radiation, the lack of information in cattle and the importance of polymorphisms associated with pigmentation phenotypes, we investigated the SLC24A5 gene in cattle with light and dark skin pigmentation. To identify SNPs (Single Nucleotide Polymorphisms) in this gene and their association to dark skin pigmentation in cattle, each of the nine SLC24A5 exons, three introns (1, 3 and 8) and a portion of intron 5, were sequenced in a set of sixteen animals belonging to four Italian cattle breeds, two African zebu breeds and two African sanga breeds. The region spanning exons 3 and 4 was sequenced in fifteen animals belonging to seven additional breeds. A total of sixteen SNPs were identified: eleven positioned in introns (six in intron 1, one in intron 5 and four in intron 8) and five in exons (one in exon 1, two in exon 6 and two in exon 7). Three SNPs (located in exons 1, 6 and 7) were non synonymous, determining Pro19Leu, Ala238Val, and Met341Ile amino acid changes, respectively. All the SNPs identified were polymorphic between Bos taurus, Bos indicus and Sanga, while none of them resulted associated with the studied phenotype and discriminated the three breeds (Chianina, Mucubal and Goudali) characterized by dark pigmented skin from the others.

Studies on different species, including rats, monkeys and humans, have shown the presence of leukocyte differentiationantigens in the spermatozoa. In some case the expression of these molecules is related to a specific functional state ofthe sperm cell, as was found for the CD 46 antigen, that in humans can be used as a marker of the acrosome reaction.The aim of the present study was to assess wether promoted lipid peroxidation of the spermatozoa induces any variationsin their immunoreactivity with ILA 147 antibody that, in bull spermatozoa, recognizes bovine leukocyte antigens.Freshly ejaculated bovine spermatozoa and cryopreserved semen were tested for ILA 147 reactivity by standardimmunoperoxidase staining, before and after promoted lipid peroxidation. Staining intensity was assessed in the individualcells using the microdensitometric method to measure integrated optical density (IOD), overcoming the disadvantageof an operator’s subjective interpretation of the results. After the lipid peroxidation there was significantlydecreased staining intensity in the fresh spermatozoa, but not in the cryopreserved cells. Furthermore, in the preincubationconditions, the cryopreserved spermatozoa had a lower mean I.O.D. value than the fresh sperm, showing that thefreezing and thawing processes induced an alteration in the antigen exposure. However the mean immunoreactivity ofthe cryopreserved cells was not significantly influenced by lipid peroxidation. The absorbance value maps, made followingimmunoperoxidase staining by the examined antibody, showed that the reaction sites in the fresh and cryopreservedspermatozoa fell mainly within the periacrosomal region. Moreover, after induced lipid peroxidation there were fewerreaction sites in this domain. The present research has confirmed the presence of the examined leukocyte antigenicdeterminant in the bull spermatozoa, and suggests that promoted lipid peroxidation and the freezing and thawing of spermatozoacan produce membrane damage, leading to reduced ILA 147 antigenic site exposure.

BackgroundDuring the past decades, neutral DNA markers have been extensively employed to study demography, population genetics and structure in livestock, but less interest has been devoted to the evaluation of livestock adaptive potential through the identification of genomic regions likely to be under natural selection.Methodology/principal findingsLandscape genomics can greatly benefit the entire livestock system through the identification of genotypes better adapted to specific or extreme environmental conditions. Therefore we analyzed 101 AFLP markers in 43 European and Western Asian goat breeds both with Matsam software, based on a correlative approach (SAM), and with Mcheza and Bayescan, two FST based software able to detect markers carrying signatures of natural selection. Matsam identified four loci possibly under natural selection--also confirmed by FST-outlier methods--and significantly associated with environmental variables such as diurnal temperature range, frequency of precipitation, relative humidity and solar radiation.Conclusions/significanceThese results show that landscape genomics can provide useful information on the environmental factors affecting the adaptive potential of livestock living in specific climatic conditions. Besides adding conservation value to livestock genetic resources, this knowledge may lead to the development of novel molecular tools useful to preserve the adaptive potential of local breeds during genetic improvement programs, and to increase the adaptability of industrial breeds to changing environments.

Aim of this research was to identify a panel of SNPs in coat colour genes useful for breed traceability in Rendena, an autochthonous cattle breed raised in the province of Trento, and other 4 Italian cattle breeds. First, we sequenced some regions of several coat colour genes in 10 animals belonging to 5 breeds characterised by different coat colour phenotypes (Rendena, Italian Brown, Grey Alpine, Italian Friesian, and Italian Red Pied), and we detected 21 SNPs in 13 genes. These markers and 6 additional SNPs were used to genotype 180 animals of the same 5 breeds obtaining useful genotyping data for a total of 22 SNPs in 13 genes. Five out of the 22 SNP markers in the MC1R, KIT, MLPH, and SILV genes had the highest discriminating power. The panel of 22 SNPs is useful to trace Rendena particularly from Red Italian Pied and Italian Friesian.

We presented the preliminary results of the analysis of semen phenotypic and quality data provided by ANARB along with the result of SNPs discovery on seven candidate genes for male fertility and the ongoing study on mtDNA. The phenotypic data recorded by Computer Assisted Sperm Analyzer of fresh semen for 1,014 bulls were evaluated. The least squared means of volumes were lower than data in literature generally referred to mature bulls, whereas the spermatozoa concentrations, total and progressive motility were satisfactory. As expected in young bulls, the percentage of spermatozoa morphological abnormalities was high. The SNPs discovery in seven candidate genes revealed 30 new SNPs and confirmed the polymorphism in STAT5A gene. The complete sequencing of mtDNA of 48 extreme bulls for semen phenotypic traits revealed 274 mutations. Association between SNPs and semen phenotypes is on going. Our results represent a preliminary step towards the sounding of genetic mechanisms of bull fertility and highlight the paramount importance of reliable phenotypes for association studies.