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The gilthead seabream (Sparus aurata) is a species of relevance for the Mediterranean aquaculture industry. Despite the advancement of genetic tools for the species, breeding programs still do not often include genomics. In this study, we designed a genomic strategy to identify signatures of selection and genomic regions of high differentiation among populations of farmed fish stocks. A comparative DNA pooling sequencing approach was applied to identify signatures of selection in gilthead seabream from the same hatchery and from different nuclei that had not been subjected to genetic selection. Identified genomic regions were further investigated to detect SNPs with predicted high impact. The analyses underlined major genomic differences in the proportion of fixed alleles among the investigated nuclei. Some of these differences highlighted genomic regions, including genes involved in general metabolism and development already detected in QTL for growth, size, skeletal deformity, and adaptation to variation of oxygen levels in other teleosts. The obtained results pointed out the need to control the genetic effect of breeding programs in this species to avoid the reduction of genetic variability within populations and the increase in inbreeding level that, in turn, might lead to an increased frequency of alleles with deleterious effects.

Cluster of differentiation 4 (CD4) is the accessory protein non-covalently bound to the T cell receptor that recognizes an invariant region of MHC class II on antigen presenting cells. Its cytoplasmic tail, physically associated with a protein tyrosine kinase, is important in the activation of helper/inducer T lymphocytes. In Bos taurus, CD4 gene is located on chromosome 5 from which two isoforms are transcribed, with a different number of amino acids due to splicing of exon 7 and variation in the reading frame. The aim of this study was to investigate the sequence of the entire CD4 gene in Simmental sires to evaluate the effects of genomic variants on the indexes of the bulls for milk, fat and protein yields, as well as somatic cell score. The associations among genomic variants and indexes were analysed using the Allele and GLM procedures of SAS 9.4. The analysis indicated that only four of the thirty-one identified SNPs influenced the considered traits. Identified variants insist on coding zones and intronic sequences, where we revealed the presence of sites for transcription factors. To evaluate the existence of haplotypic effects, combinations among the four genomic variants (SNP 3, SNP 8, SNP 11 and SNP 19) were investigated. Six different haplotypic alleles were identified, but only four of them were frequent enough to allow for an evaluation of any haplotypic effect (at least six copies in the examined sample): Hap1, Hap2, Hap3 and Hap6. The analysis of associations between the selected haplotypes in the CD4 gene with milk related indexes showed that bulls with Hap2 (T-A-C-C) had better indexes for milk and protein yields (P < 0.05), whereas the presence of the Hap1 haplotype (A-G-A-T) caused a significant decrease of the index for protein yield (P < 0.05). Frequencies of the two alleles Hap1 and Hap2 (9 and 36% respectively) make them of interest for their possible inclusion in breeding schemes and support the hypothesis of considering this gene as a candidate for the improvement of milk-related traits in the Simmental breed.

CXCL8 (also known as IL-8) is a member of the CXC subfamily of chemokines that binds two of the seven transmembrane G-protein-coupled receptors (GPCRs), CXCR1 and CXCR2, to mediate and regulate leucocyte accumulation and activation at sites of inflammation. They are known to play a critical role in both disease susceptibility and infection outcome. The aim of this study was to investigate the entire sequences of CXCL8 and CXCR2 genes in thirty-one Simmental sires to evaluate the effects of genomic variants on the indexes of the bulls for milk, fat and protein yields, and for somatic cell score (SCS). Five new single nucleotide polymorphisms (SNPs) were found in CXCR2 gene. The analysis of association indicated that one SNP in CXCL8 and two in CXCR2 influenced the considered traits. To evaluate the existence of functional haplotypic effects, combinations among the three genomic variants (SNP 1 in CXCL8, SNP 6 and SNP 7 in CXCR2) were investigated. Four different haplotypic alleles were identified in the experimental population, one of which at a high frequency (61%). Bulls with Hap 4 (G-C-G at SNP 1, SNP 6, and SNP 7 respectively) had more favourable indexes for SCS (P < 0.05). These results suggest that the SNPs in CXCL8 and CXCR2 may be potential genetic markers to improve udder health in the Simmental breed.

European consumers prefer wild over farmed aquatic food and consider it healthier and tastier. Consumers are increasingly paying attention to sustainability and welfare of farmed fish. Such expecta...

Previous studies on the immune system of water buffalo (Bubalus bubalis) using cross-reactive monoclonal antibodies (mAbs) revealed significant similarities and differences to the bovine immune system. Herein, we extend these studies and document the pattern of expression of CD14, CD16, CD163 and CD172a on buffalo leukocytes using a set of cross-reactive mAbs that are known to recognize conserved epitopes within orthologous molecules in cattle, sheep and goats. Buffalo leukocytes were isolated and subjected to mAb labelling for flow cytometry. Single color flow cytometry confirmed mAbs recognition of buffalo orthologues of CD14, CD16, CD163 and CD172a, and revealed consistent patterns of expression similar to that reported in other ruminants. Multicolor flow cytometry revealed that buffalo CD14+ monocytes uniquely co-express CD16, CD163 and CD172a, whereas buffalo granulocytes co-express CD16 and CD172a. This study expands mAbs available to define and study the buffalo monocytes, and also extends information available on the unique features of the buffalo immune system.

This study examined the environmental performance of mussel (Mytilus galloprovincialis) farming in the view of reduction of greenhouse gas emissions, through the Life Cycle Assessment (LCA) methodology. The LCA has been integrated with the evaluation of the carbon sequestration potential of the biocalcification process. Three case studies of mussel farming sited along the coastal area in the north Adriatic Sea, Italy, were analyzed. Two of them concerned mussels that do not require a depuration process (area Class A), and one inspected mussel production in the rearing area of Class B, which imposes a depuration phase after harvesting. This study examined all the relevant flows of materials and energy across the systems and explored the potential role of mussel biocalcification in stocking seawater carbon into the shells. Global Warming (GW) -related emissions amounted to 0.07-0.12 kg CO

In organic poultry production it is important to rear animals with a dynamic attitude to take advantage of outdoor areas. Farmers are reluctant to use such strains due to their lower productivity and older slaughtering age. However, fast growing lines grown in organic system often suffer poor health and welfare conditions. The kinetic metabolism of chickens is correlated with different types of muscle fiber: type I (in red muscles or oxidative) for prolonged and moderate movement and type II (in white muscles or glycogenic) for fast movements. Red muscle metabolism produces energy mainly by β-oxidation of Highly Unsaturated n-3 Fatty Acids (HUFA). Accordingly, kinetic activity causes higher consume of HUFA in red muscles than in white muscles, so the ratio between n-3 HUFA and their precursor C18:3 n-3 (ALA) is likely to be smaller in red than in white muscles. However, these ratios are highly affected by the environment. To reduce the effect of environmental variables, we propose an “Activity index” as the difference between n-3 HUFA/ALA in white and red muscle within the same bird. This index, measured after slaughtering, should represent the activity performed by the chicken during its life. Given that birds in good health had the possibility of moving, the “Activity index” would measure the activity actually performed by the animals. Should birds of a given strain show a higher activity level, this would be an indication of the suitability of that strain to outdoor systems. This work verified the application of this “Activity index” on 90 birds from 6 genetic strains with known kinetic behavior reared in an experimental farm. The “Activity index” was also tested on chicken strains collected form commercial organic farms. The results confirmed that strains recognized for higher kinetic attitude actually walked more and their behavior was clearly detected by the “Activity index” estimated from their muscles.

In the European rabbit (Oryctolagus cuniculus), a polytocous livestock species, the number of teats indirectly impacts the doe reproduction efficiency and, in turn, the sustainable production of rabbit meat. In this study, we carried out a genome-wide association study (GWAS) for the total number of teats in 247 Italian White does included in the Italian White rabbit breed selection program, by applying a selective genotyping approach. Does had either 8 (n=121) or 10 teats (n=126). All rabbits were genotyped with the Affymetrix Axiom OrcunSNP Array. Genomic data from the two extreme groups of rabbits were also analysed with the single-marker fixation index statistic and combined with the GWAS results. The GWAS identified 50 significant SNPs and the fixation index analysis identified a total of 20 SNPs that trespassed the 99.98th percentile threshold, 19 of which confirmed the GWAS results. The most significant SNP (P=4.31×10−11) was located on OCU1, close to the NUDT2 gene, a breast carcinoma cells proliferation promoter. Another significant SNP identified as candidate gene NR6A1, which is well known to play an important role in affecting the correlated number of vertebrae in pigs. Other significant markers were close to candidate genes involved in determining body length in mice. Markers associated with increased number of teats could be included in selection programmes to speed up the improvement for this trait in rabbit lines that need to increase maternal performances.

The gilthead seabream (Sparus aurata, Sparidae family) is commonly used for aquaculture. Despite its great economic value, several problems in its cultivation remain. One of the major concerns is the high frequency of morphological abnormalities occurring during the early developmental stages. Partial and/or total lack of operculum is the most frequent anomaly affecting the fish cranial region. The existence of genetic factors that can at least partially determine this defect has been hypothesized. In this work, two DNA pools of highly related fry, one composed of normal-looking (control) fish and the other lacking an operculum (case), were constructed and whole-genome resequencing data produced from the two were compared. The analysis revealed a 1Mb region on chromosome 2 with higher heterozygosity in the lack of operculum DNA pool than in the control DNA pool, consistent with the enrichment, in the first DNA pool, of one or more haplotypes causing or predisposing to the defect together with other normal haplotypes. A window-based FST analysis between the two DNA pools indicated that the same region had the highest divergence score. This region contained 2921 SNVs, 10 of which, with predicted high impacts (three splice donor and seven stop-gained variants), were detected in novel genes that are homologous to calcium-sensing receptor-like genes, probably involved in bone development. Other studies are needed to clarify the genetic mechanisms involved in predisposing fry to this deformity and then to identify associated markers that could be used in breeding programs to reduce the frequency of this defect in the broodstock.

Flow cytometry is a powerful technology used in many fields of cell biology. It is also used as a routine method to count somatic cells in milk and to characterize bovine milk leukocytes. In this study, we used flow cytometry to simultaneously assess the viability, the percentage of the single subsets of leukocytes and to quantify the expression of CD11b, an immunological marker of cell activation status. Immunological markers were then related with on farm recorded parameters as milk electrical conductivity (MEC) and average milk flow rate (MFR). Composite milk samples were collected from 43 cows, nine of which had naturally infected udders and 34 of which had no infected udders. First, the milk samples were classified according to bacteriological test in positive and negative. The results showed that the negative samples to bacteriological test had: (i) significantly higher percentages of live lymphocytes, (ii) significantly lower percentages of CD11b+ leukocytes, (iii) significantly lower MEC and higher MFR values. Then, samples were classified in three groups according to somatic cell count (SCC): Group A (n = 15), samples with SCC &le, 100,000 cells/mL, all negative to bacteriological analysis, Group B (n = 11), samples with 100,000 &lt, SCC &lt, 300,000 cells/m, with four samples positive to bacteriological analysis, Group C (n = 17), samples with SCC &ge, 300,000 cell/mL with five samples positive to bacteriological analysis. Multivariate discriminant analysis was used to verify which flow cytometry immunological markers and on farm recorded parameters could better discriminate among the different groups of SCCs. Linear discriminant analysis (LDA) indicated that 5 of the 10 parameters could best be used to reveal the differences between positive and negative samples among the considered groups of SCCs. Furthermore, the Canonical discriminant analysis (CDA) indicated that composite milk samples with different SCC and infection status were clearly separated from each other in a two-dimensional space. In conclusion, the study highlighted that: (1) the conventional flow cytometry analysis applied on milk samples is a useful tool to investigate immunological parameters as potential indicators of udder health, (2) the combined evaluation of live milk leukocytes and recorded farm parameters could be useful to assess udder health status in dairy cows. The results obtained from this pilot study on few data require new and larger trials to be confirmed.

Longevity is one of the most important traits determining dairy cow profitability. In the last decades dairy cows suffered a lowering in the age at culling. With the aim to identify the genes involved in longevity, dates of birth, yields, dates of calving during lifespan and culling dates were collected for 946 culled cows which had been genotyped with the Bovine High Density panel. Using the GenABEL package in R, genome-wide association analysis was performed on three potential traits of longevity: (1) 'days in production,' (2) 'days in herd,' (3) number of calvings over lifespan.' Five genome-wide significant single nucleotide polymorphisms (SNPs) associated with all three longevity traits were detected. Several consecutive SNPs identified on chromosomes 16 and 30 indicated the presence of two suggestive quantitative trait loci (QTL). The genes comprised in the QTL regions had biological functions related to fertility, reproductive disorders, heat stress and welfare of cows. These findings might contribute to improving breeding strategies to improve longevity.

Subcutaneous fat thickness and fatty acid composition (FAC) play an important role on seasoning loss and organoleptic characteristics of seasoned hams. Dry-cured ham industry prefers meats with low contents of polyunsaturated fatty acids (PUFA) because these negatively affect fat firmness and ham quality, whereas consumers require higher contents in those fatty acids (FA) for their positive effect on human health. A population of 950 Italian Large White pigs from the Italian National Sib Test Selection Programme was investigated with the aim to estimate heritabilities, genetic and phenotypic correlations of backfat FAC, Semimembranosus muscle intramuscular fat (IMF) content and other carcass traits. The pigs were reared in controlled environmental condition at the same central testing station and were slaughtered at reaching 150 kg live weight. Backfat samples were collected to analyze FAC by gas chromatography. Carcass traits showed heritability levels from 0.087 for estimated carcass lean percentage to 0.361 for hot carcass weight. Heritability values of FA classes were low-to-moderate, all in the range 0.245 for n-3 PUFA to 0.264 for monounsaturated FA (MUFA). Polyunsaturated fatty acids showed a significant genetic correlation with loin thickness (0.128), backfat thickness (-0.124 for backfat measured by Fat-O-Meat'er and -0.175 for backfat measured by calibre) and IMF (-0.102). Obviously, C18:2(n-6) shows similar genetic correlations with the same traits (0.211 with loin thickness, -0.206 with backfat measured by Fat-O-Meat'er, -0.291 with backfat measured by calibre and -0.171 with IMF). Monounsaturated FA, except with the backfat measured by calibre (0.068; P

Protected designation of origin dry-cured hams are obtained from heavy pigs (slaughtered at about 160 kg of live weight). A specific breeding program designed to improve meat quality for this production has included as key traits the level of intermuscular fat between the leg muscles and ham weight loss during the seasoning period together with a balance between fat and lean cuts. In this study we carried out genome-wide association studies for seven traits used in the genetic merit of Italian Duroc heavy pigs, five related to meat and carcass quality traits (visible intermuscular fat, ham weight loss at first salting, backfat thickness, ham weight and lean cuts), and two related to performance and efficiency traits (average daily gain and feed : gain ratio). A total of 573 performance-tested pigs were genotyped with the Illumina PorcineSNP60 BeadChip and genome-wide association analyses were carried out using the Bayes B approach with the 1 Mb window option of GenSel and random residuals for each of the seven traits. Detected windows were supported by independent single nucleotide polymorphism analyses with a linear mixed model (LMM) approach on the same animals for the same traits. A total of 30 windows identifying different quantitative trait loci (QTL) were detected and among those, 27 were confirmed by LMM in one of these traits. Among the confirmed windows, three QTL were reported for visible intermuscular fat, seven for ham weight loss at first salting and five and four for backfat thickness and lean cut, respectively. A total of eight QTL were detected for the other production traits. No overlapping QTL were reported except for one window on porcine chromosome 10 between lean cuts and ham weight that contained the CACNB2 gene that has been already associated with loin marbling score in other Duroc pigs. Several regions contained genes that have been already associated with production traits in other pig breeds, including Duroc lines, related to fat deposition or muscle structure. This work reports, for the first time, genome-wide association study results for several traits in Italian Duroc heavy pigs. These results will be useful to dissect the genetic basis for dry-cured ham production traits that determine the total genetic merit index of Italian Duroc pigs.

The gilthead seabream (Sparus aurata) is an important cultivated species in the Mediterranean area. A major problem for the gilthead seabream aquaculture sector derives from the high frequency of phenotypic abnormalities, including discolorations. In this study, we applied a whole-genome resequencing approach to identify a genomic region affecting a pigmentation defect that occurred in a cultivated S.aurata population. Two equimolar DNA pools were constructed using DNA extracted from 30 normally coloured and 21 non-pigmented fish collected among the offspring of the same broodstock nucleus. Whole-genome resequencing reads from the two DNA pools were aligned to the S.aurata draft genome and variant calling was performed. A whole-genome heterozygosity scan from single pool sequencing data highlighted a peak of reduced heterozygosity of approximately 5Mbp on chromosome 6 in the non-pigmented pool that was not present in the normally coloured pool. The comparison of the non-pigmented with the normally coloured fish using a whole-genome FST analysis detected three main regions within the coordinates previously detected with the heterozygosity analysis. The results support the presence of a major locus affecting this discoloration defect in this fish population. The results of this study have practical applications, including the possibility of eliminating this defect from the breeding stock, with direct economic advantages derived from the reduction of discarded fry. Other studies are needed to identify the candidate gene and the causative mutation, which could add information to understand the complex biology of fish pigmentation.

The widespread use of genome-wide association studies resulted in the discovery of genomic regions associated with fatty acid (FA) composition in different porcine tissues, but little information exists about the genes involved in FA composition of meat obtained from heavy pigs selected for the production of Italian dry-cured hams. To this objective, we genotyped with a single nucleotide polymorphism (SNP) panel 795 Italian Large White heavy pigs to identify the markers and genomic regions associated with Semimembranosus muscle FA profile. Heritability estimates for intramuscular fat FA profile were of low-to-moderate magnitude, suggesting that these traits may be improved with genomic selection. On the whole, 45 SNPs were significantly associated with 14 FAs, and 4 of them (ALGA008109, ALGA0081097, CASI0010164 and SIRI0000267) were associated with more than 1 FA. The palmitoleic:palmitic and oleic:stearic ratios displayed the highest number of significant markers and the most significant associations (Bonferroni adjusted P < 5.00E-07). Of particular interest, the palmitoleic:palmitic ratio was strongly associated with markers located at 111 to 114 Mb on chromosome 14, in the same chromosomal region where Stearoyl-CoA desaturase Δ9 (SCD) gene is located. Several significant chromosomal regions were found; some of them harbour key genes playing pivotal roles in FA desaturation and elongation, such as SCD and some members of the Elongation of Very Long-Chain FA (ELOVL) gene family. The results suggest that the identification of causal mutations in these regions may provide a set of markers useful for selection schemes aimed at improving FA composition in pork products.

Semimembranosus muscle samples from 795 Large White heavy pigs were used to determine their intramuscular fatty acid composition and to estimate the heritability and the genetic correlations of these traits. Muscle fatty acids showed heritability estimates of low-to-moderate magnitude, ranging from 0.157 for total fatty acids to 0.237 for docosahexaenoic acid. Only small differences in heritability appeared among fatty acids based on their chain length, saturation and double bond position. Omega-6 polyunsaturated fatty acids showed positive genetic correlations with carcass lean % (0.563 ± 0.005) and loin thickness (0.438 ± 0.005) while being negatively related to backfat thickness measured both by calibre (−0.225 ± 0.008) and Fat-O-Meat'er (FOM) apparatus (−0.603 ± 0.004). Interestingly, the monounsaturated fatty acid class was not correlated with carcass measures and presented only a weak positive genetic correlation with intramuscular fat (0.145 ± 0.002). This result suggests that in heavy pig breeds monounsaturated fatty acids in muscle could be selected for without interfering with carcass traits.

Italian heavy pig selection programs are based on production (average daily gain, ADG; feed gain ratio, FGR), carcass (weight of lean cuts, LC; ham weight, HW; backfat thickness, BFT) and meat quality traits of the green hams (ham weight loss at first salting, HWLFS; and visible intermuscular fat, VIF). In this study, we evaluated whether a selective genotyping approach previously designed for BFT could identify markers associated with other traits (ADG, FGR, HW, HWLFS, LC and VIF), most of which correlated with BFT. Italian Large White gilts were chosen according to their extreme estimated breeding values for BFT (275 with the most negative and 278 with the most positive EBVs) within a population of about 12,000 sib-tested pigs. A total of 736 single nucleotide polymorphisms (SNPs) in candidate genes for fat deposition and/or related traits were genotyped. After filtering, a total of 279 SNPs in 234 genes remained for association analyses that were carried out using random residuals (RRs) for the six mentioned traits. Four SNPs in three candidate genes were associated with some of the considered traits. A SNP in the exosome component 1 (EXOSC1) gene and a SNP in the glycogen phosphorylase L (PYGL) gene were associated with HWLFS RRs. Two SNPs within the TBC1 (tre-2/USP6, BUB2, cdc16) domain family, member 1 (TBC1D1) gene were associated with LC RRs and suggestively associated with other performance, carcass and meat traits. Association analysis using six TBC1D1 haplotypes, inferred from four genotyped SNPs within this gene, confirmed the results of the single-marker association study. This study contributes to dissect the biological mechanisms underlying the genetic correlations among BFT, HWLFS and LC, which are critical for the sustainable implementation of tailored selection programs in heavy pigs.

Intermuscular fat content in protected designations of origin dry-cured hams is a very important meat quality trait that affects the acceptability of the product by the consumers. An excess in intermuscular fat (defined as the level of fat deposition between leg muscles) is a defect that depreciates the final product. In this study we carried out a genome-wide association study for visible intermuscular fat (VIF) of hams in the Italian Large White pig breed. This trait was evaluated on the exposed muscles of green legs in 1122 performance-tested gilts by trained personnel, according to a classification scale useful for routine and cheap evaluation. All animals were genotyped with the Illumina PorcineSNP60 BeadChip. The genome-wide association study identified three QTL regions on porcine chromosome 1 (SSC1; accounting for ~79% of the SNPs below the 5.0E−04 threshold) and SSC2, two on SSC7 and one each on SSC3, SSC6, SSC9, SSC11, SSC13, SSC15, SSC16 and SSC17. The most significant SNP (ALGA0004143 on SSC1 at 77.3 Mb; PFDRÂ

This study seeks to verify the feasibility of increasing twinning in a herd of the Italian autochtonous Maremmana breed. The data set included 1260 individuals born from 1963 to 2014, 527 males and 733 females, 402 of them calving at least once from 1983 through 2015. Breeding values for twinning were estimated by a single-trait linear animal model. However, since twinning is a dichotomous trait and the frequency of twins is far smaller than the frequency of single births, breeding values were also estimated by a single-trait animal threshold model. Heritability of twinning was 0.014±0.018 and 0.062±0.093 for the linear and the threshold models, respectively. Repeatability was 0.071±0.004 and 0.286± 0.012, respectively, for the two models. Genotyping with the Illumina BovineSNP54 BeadChip was performed for cows living on farm in 2012 (119 cows) and a genome-wide association analysis was performed on the corrected phenotype of all calving during the lifespan of each cow, using the GenABEL package in R and a three step GRAMMAR-GC approach. Genomic heritability, calculated from the genomic kinship matrix estimated through genomic marker data, was 0.29±0.021. The most significant detected single nucleotide polymorphisms (Hapmap22923-BTA-129564) was located in proximity of two genes, ARHGAP8 and TMEM200C, which might be potential functional candidates for twinning rate in cattle.

Summary Calcium, magnesium and phosphorus are essential electrolytes involved in a large number of biological processes. Imbalance of these minerals in blood may indicate clinically relevant conditions and are important in inferring acute or chronic pathologies in humans and animals. In this work, we carried out a genome-wide association study (GWAS) for the level of these three electrolytes in the serum of 843 performance-tested Italian Large White pigs. All pigs were genotyped with the Illumina PorcineSNP60 BeadChip, and GWAS was carried out using genome-wide efficient mixed-model association. For the level of Ca2+, eight single nucleotide polymorphisms (SNPs) were significant, considering a false discovery rate (FDR)

Infectious diseases have large economic impacts on the pig breeding industry worldwide. A few genetic markers associated to disease resistance have been recently identified and used in marker-assisted selection (MAS) in a few pig populations, as part of disease control programs. Neonatal Diarrhea (ND), Post-weaning Diarrhea (PWD), caused by enterotoxigenic E. coli, and Porcine Reproductive and Respiratory Syndrome, caused by PRRS virus (PRRSV), are diseases with high priority for the pig industry. Since interactions or antagonism between growth, innate immunity and disease resistance traits could exist, this work investigated if four disease resistance gene markers [mucin 4 (MUC4), rs338992994 associated with resistance to ND; fucosyltransferase 1 (FUT1), rs335979375 associated with resistance to PWD; and guanylate binding protein 1 (GBP1), rs340943904 and rs80800372 (also known as WUR10000125) associated with resistance to PRRS] could affect seven production traits (average daily gain, back fat thickness, lean meat cuts, feed gain ratio, ham weight, visible intermuscular fat and ham weight loss at first salting) and 15 haematological parameters in about 550 performance tested Italian Large White pigs. We also monitored allele frequencies of the same markers on Italian Large White boars sampled under the national selection breeding program over a 20 years-period. Moreover, we evaluated allele frequencies of these polymorphisms in four Italian local pig breeds (Apulo-Calabrese, Casertana, Cinta Senese and Nero Siciliano). The frequency of the resistance-associated alleles for the four polymorphisms was usually higher in all local pig breeds, indirectly supporting a higher rusticity of autochthonous breeds, compared to commercial populations. The two GBP1 polymorphisms were not in complete linkage disequilibrium in all breeds, except in Apulo-Calabrese. No significant allele frequency change for the investigated markers occurred over 20 years in the Italian Large White boar population in three of these markers. Only FUT1 showed a modest but significant change of allele frequencies over this period. Association analyses carried out in Italian Large White pigs for production traits, meat quality or haematological parameters under investigation showed no significant effect of any genotyped polymorphisms. Our results indicate that implementing MAS programs in Italian Large White pigs with polymorphisms associated with disease resistance have no direct effects on production traits. The selection program running for this heavy pig breed might not negatively impact disease resistance derived by the investigated major genes.

Genomic selection is becoming a common practise in dairy cattle, but only few works have studied its introduction in pig selection programs. Results described for this species are highly dependent on the considered traits and the specific population structure. This paper aims to simulate the impact of genomic selection in a pig population with a training cohort of performance-tested and slaughtered full sibs. This population is selected for performance, carcass and meat quality traits by full-sib testing of boars. Data were simulated using a forward-in-time simulation process that modeled around 60K single nucleotide polymorphisms and several quantitative trait loci distributed across the 18 porcine autosomes. Data were edited to obtain, for each cycle, 200 sires mated with 800 dams to produce 800 litters of 4 piglets each, two males and two females (needed for the sib test), for a total of 3200 newborns. At each cycle, a subset of 200 litters were sib tested, and 60 boars and 160 sows were selected to replace the same number of culled male and female parents. Simulated selection of boars based on performance test data of their full sibs (one castrated brother and two sisters per boar in 200 litters) lasted for 15 cycles. Genotyping and phenotyping of the three tested sibs (training population) and genotyping of the candidate boars (prediction population) were assumed. Breeding values were calculated for traits with two heritability levels (h(2) = 0.40, carcass traits, and h(2) = 0.10, meat quality parameters) on simulated pedigrees, phenotypes and genotypes. Genomic breeding values, estimated by various models (GBLUP from raw phenotype or using breeding values and single-step models), were compared with the classical BLUP Animal Model predictions in terms of predictive ability. Results obtained for traits with moderate heritability (h(2) = 0.40), similar to the heritability of traits commonly measured within a sib-testing program, did not show any benefit from the introduction of genomic selection. None of the considered genomic models provided improvements in prediction ability of pigs with no recorded phenotype. However, a few advantages were found for traits with low heritability (h(2) = 0.10). These heritability levels are characteristic for meat quality traits recorded after slaughtering or for reproduction or health traits, typically recorded on field and not in performance stations. Other scenarios of data recording and genotyping should be evaluated before considering the implementation of genomic selection in a pig-selection scheme based on sib testing of boars.

Poly(ADP-ribosyl)ation (PAR) is a post-translational protein modification catalysed by enzyme member of the poly(ADP-ribose) polymerases (PARPs) family. The activation of several PARPs is triggered by DNA strand breakage and the main PARP enzyme involved in this process is PARP1. Besides its involvement in DNA repair, PARP1 is involved in several cellular processes including transcription, epigenetics, chromatin re-modelling as well as in the maintenance of genomic stability. Moreover, several studies in human and animal models showed PARP1 activation in various inflammatory disorders. The aims of the study were (1) to characterize PARP1 expression in bovine peripheral blood mononuclear cells (PBMC) and (2) to evaluate PAR levels as a potential inflammatory marker in cells isolated from blood and milk samples following different types of infection, including mastitis. Our results show that (i) bovine PBMC express PARP1; (ii) lymphocytes exhibit higher expression of PARP1 than monocytes; (iii) PARP1 and PAR levels were higher in circulating PBMCs of infected cows; (iv) PAR levels were higher in cells isolated from milk with higher Somatic Cell Counts (SCC > 100,000 cells/mL) than in cells from milk with low SCCs. In conclusion, these findings suggest that PARP1 is activated during mastitis, which may prove to be a useful biomarker of mastitis.

The GPR120 gene (also known as FFAR4 or O3FAR1) encodes for a functional omega-3 fatty acid receptor/sensor that mediates potent insulin sensitizing effects by repressing macrophage-induced tissue inflammation. For its functional role, GPR120 could be considered a potential target gene in animal nutrigenetics. In this work we resequenced the porcine GPR120 gene by high throughput Ion Torrent semiconductor sequencing of amplified fragments obtained from 8 DNA pools derived, on the whole, from 153 pigs of different breeds/populations (two Italian Large White pools, Italian Duroc, Italian Landrace, Casertana, Pietrain, Meishan, and wild boars). Three single nucleotide polymorphisms (SNPs), two synonymous substitutions and one in the putative 3'-untranslated region (g.114765469C > T), were identified and their allele frequencies were estimated by sequencing reads count. The g.114765469C > T SNP was also genotyped by PCR-RFLP confirming estimated frequency in Italian Large White pools. Then, this SNP was analyzed in two Italian Large White cohorts using a selective genotyping approach based on extreme and divergent pigs for back fat thickness (BFT) estimated breeding value (EBV) and average daily gain (ADG) EBV. Significant differences of allele and genotype frequencies distribution was observed between the extreme ADG-EBV groups (P < 0.001) whereas this marker was not associated with BFT-EBV.

Melanocortin 4 receptor (MC4R) plays a key role in controlling energy homeostasis. Several studies have already reported effects on production traits of polymorphisms identified in the porcine MC4R gene. In this study we analysed data on 6 MC4R polymorphisms (c.-780C>G; c.-135C>T; c.175C>T; c.707G>A or p.Arg236His; and c.892G>A or p.Asp298Asn; c.*430A>T) genotyped from (1) two groups of Italian Large White pigs (280+280 animals) with extreme estimated breeding values (EBVs) for back fat thickness (BFT), selected among a performance tested population of about 12,000 pigs, and from (2) 19 Italian Duroc pigs. Two haplotypes, differentiated by the c.892G>A, were identified in the Duroc populations. Four haplotypes were identified in the Italian Large White population, one of which (haplotype 4) was identified for the first time in this study. Single marker and haplotype association analyses for BFT were obtained by comparing allele and haplotype frequency differences from the two extreme tails using χ2 and Cochran-Armitage trend tests. Results confirmed the effects of the c.892G>A single nucleotide polymorphism (SNP) on BFT, as also defined by different distributions in the two tails of haplotypes carrying the alternative nucleotides at this polymorphic site (P

In this study we evaluated the effects of candidate single nucleotide polymorphisms (SNPs) on reproduction traits of Italian Large White (ITLW) purebred sows at first parity. We genotyped DNA samples extracted from hair roots of 1,548 sows distributed across six farms located in Northern Italy. A total of 21 SNPs in 20 genes, selected from literature, were genotyped. Seventeen SNPs showed minor allele frequencies >0.05 in the ITLW breed. Association analyses were performed with the following traits: number of piglets born alive (NBA1), number of stillborn piglets (NSB1), total number born (TNB1), NBA1 estimated breeding values (EBVs) and NBA1 random residuals (RRs). SNPs in BMPR1B, FUT1, GPX5, RBP4 and TGFBR1 genes showed significant association (P nominal C and STAT5B) presented suggestive effects (P nominal

Several arthropod-borne diseases are now rising with increasing impact and risks for public health, due to environmental changes and resistance to pesticides currently marketed. In addition to community surveillance programs and a careful management of herds, a next-generation of effective products is urgently needed to control the spread of these diseases, with special reference to arboviral ones. Natural product research can afford alternative solutions. Recently, a re-emerging of bluetongue disease is ongoing in Italy. Bluetongue is a viral disease that affects ruminants and is spread through the bite of bloodsucking insects, especially Culicoides species. In this review, we focused on the importance of vector control programs for prevention or bluetongue outbreaks, outlining the lack of effective tools in the fight against Culicoides vectors. Then, we analyzed a field case study in Sardinia (Italy) concerning the utilization of the neem cake (Azadirachta indica), to control young instar populations of Culicoides biting midges, the vectors of bluetongue virus. Neem cake is a cheap and eco-friendly by-product obtained from the extraction of neem oil. Overall, we propose that the employ of neem extraction by-products as aqueous formulations in muddy sites close to livestock grazing areas may represent an effective tool in the fight against the spread of bluetongue virus in the Mediterranean areas. © 2017 Elsevier Ltd

The aim of this study was to evaluate the effects of single nucleotide polymorphisms (SNPs) and haplotypes in porcine calpastatin (CAST) gene on performance and carcass traits in Italian Large White (ILW) pigs. Seven SNPs located from promoter to exon 17 of CAST gene were genotyped by the Illumina GoldenGate genotyping assay in 280 ILW pigs and seven haplotypes were inferred from four informative SNPs. Association analyses were performed for SNPs and haplotypes with performance and carcass estimated breeding values in the ILW population. Significant association (P

Combining different approaches (resequencing of portions of 54 obesity candidate genes, literature mining for pig markers associated with fat deposition or related traits in 77 genes, and in silico mining of porcine expressed sequence tags and other sequences available in databases), we identified and analyzed 736 SNP within candidate genes to identify markers associated with back fat thickness (BFT) in Italian Large White sows. Animals were chosen using a selective genotyping approach according to their EBV for BFT (276 with most negative and 279 with most positive EBV) within a population of ≈ 12,000 pigs. Association analysis between the SNP and BFT has been carried out using the MAX test proposed for case-control studies. The designed assays were successful for 656 SNP: 370 were excluded (low call rate or minor allele frequency A polymorphism (P(nominal) G polymorphism (P(nominal) = 8.0E-05). The third top SNP (P(nominal) = 6.2E-04) was the intronic TBC1D1 g.219G>A polymorphic site, in agreement with our previous results obtained in an independent study. The list of significant markers also included SNP in additional genes (ABHD16A, ABHD5, ACP2, ALMS1, APOA2, ATP1A2, CALR, COL14A1, CTSF, DARS, DECR1, ENPP1, ESR1, GH1, GHRL, GNMT, IKBKB, JAK3, MTTP, NFKBIA, NT5E, PLAT, PPARG, PPP2R5D, PRLR, RRAGD, RFC2, SDHD, SERPINF1, UBE2H, VCAM1, and WAT). Functional relationships between genes were obtained using the Ingenuity Pathway Analysis (IPA) Knowledge Base. The top scoring pathway included 19 genes with a P(nominal) < 0.1, 2 of which (IKBKB and NFKBIA) are involved in the hypothalamic IKKβ/NFκB program that could represent a key axis to affect fat deposition traits in pigs. These results represent a starting point to plan marker-assisted selection in Italian Large White nuclei for BFT. Because of similarities between humans and pigs, this study might also provide useful clues to investigate genetic factors affecting human obesity.

In pigs, susceptibility to enterotoxigenic Escherichia coli (ETEC) K88 strains (locus F4bcR) is determined by a dominant allele, with the recessive allele determining resistance. The susceptible allele also appeared to be associated with higher growth rate even if with discordant results. A single nucleotide polymorphism (SNP) in exon 7 of the mucin 4 (MUC4) gene (DQ848681:g.8227C>G), shown to be in close linkage disequilibrium with the F4bcR locus, has been used as marker to identify susceptible pigs, substituting invasive villous adhesion tests. We herein analysed this SNP in Italian local breeds and applied a selective genotyping approach in Italian Large White, Italian Landrace and Italian Duroc comparing allele frequency distribution in groups of pigs with extreme estimated breeding values (EBV) for average daily gain (ADG) and backfat thickness (BFT) to evaluate if this marker is associated with these traits. Allele G (associated with susceptibility to ETEC) resulted associated with higher ADG and BFT in Italian Large White (P=6.66E-04 and P=0.012, respectively) and higher ADG in Italian Landrace (7.23E-12). This polymorphism was poorly informative in Italian Duroc. Antagonistic associations of the MUC4 g.8227C>G alleles on susceptibility to ETEC and growth performances evidence the complexity of applying marker assisted selection in pig breeding.

PLIN2 (perilipin 2) is a cytosolic protein that promotes the formation and stabilization of the intracellular lipid droplets, organelles involved in the storage of lipid depots. Porcine PLIN2 gene represents a biological and positional candidate for fat deposition, a polygenic trait that affects carcass and meat quality. The aim of the present study was to screen PLIN2 gene for polymorphisms, to evaluate the association with carcass quality traits, and to investigate the gene expression in skeletal muscle. Six new single nucleotide polymorphisms (SNP) were detected by sequencing 32 samples from five pig breeds (Italian Large White, Italian Duroc, Italian Landrace, Belgian Landrace, Pietrain). Two SNP localized in introns, two in the 3′-untranslated region (UTR), and two missense SNP were found in exons. A 3′-UTR mutation (GU461317:g.98G>A), genotyped in 290 Italian Duroc pigs by High Resolution Melting, resulted significantly associated (P < 0.01) with average daily gain, feed conversion ratio, lean cuts and hams weight estimated breeding values. PLIN2 gene expression analysis in skeletal muscle of Italian Large White and Italian Duroc pigs divergent for backfat thickness and visible intermuscular fat showed a trend of higher expression level in pigs with higher intermuscular fat. These results suggest that PLIN2 can be a marker for carcass quality in pigs. Further investigation at both gene and protein level could elucidate its role on fat deposition.

The objective of this study was to determine the distribution of glycolytic potential (GP) and its relationships with meat pH and the estimated breeding values (EBVs) of some traits in Italian Large White pigs. GP was determined on samples taken from the semimembranosus muscle at 120 min postmortem. Values of GP were normally distributed around a mean value of µmol/g 103.5 ± 23.0. Increasing GP was associated with decreasing pH at 2 and 24 h postmortem. A nonlinear relationship was found between GP and pHu. GP also showed no relationship with the EBVs of daily gain and feed : gain ratio and a weak relationship with EBVs of carcass traits such as backfat thickness and lean cut weight. The positive but weak correlation between GP and EBV of ham weight loss during the first salting period may suggest a potential risk of using meat with high GP in dry-cured ham production. PRACTICAL APPLICATIONS Glycolytic potential is considered to be a determinant parameter for pork quality, especially when the meat is going to be processed. A better knowledge of its variation and its relationship with other valuable traits in vivo and postmortem is important in a breed such as the Italian Large White, largely used in the production of heavy pigs destined to produce meat for seasoned products. Data reported here on the variation of GP could suggest to breeder association the need to control this parameter in selection programs irrespectively to the presence of the RN- negative allele, as the relationship of GP with processing losses could hinder dry-cured ham producers.

The adiponectin (adiponectin, C1Q and collagen domain containing) encoded by ADIPOQ is an adipokine that modulates several biological processes such as lipogenesis, gluconeogenesis, fatty acid oxidation, glucose uptake and insulin sensitivity. An objective of this study was to identify SNPs in the ADIPOQ gene both in cosmopolitan and local pig breeds reared in Italy and in Meishan samples. Resequencing of ADIPOQ gene regions in 16 pigs of 12 breeds revealed only two SNPs ( EU489740 : g.1611G > A synonymous and EU489740 : g.1735G > A missense mutations) already reported. The g.1735G > A polymorphism was genotyped by PCR-RFLP in 510 pigs from 11 breeds reared in Italy (Italian Large White, Italian Duroc, Italian Landrace, Belgian Landrace, Hampshire, Pietrain, Calabrese, Casertana, Cinta Senese, Mora Romagnola and Nero Siciliano) and from Chinese Meishan breed. The Italian local breeds were homozygous for the g.1735G allele while the Meishan samples resulted homozygous for the g.1735A allele. The polymorphism segregates in the cosmopolitan breeds, except for Hampshire, and the rarer g.1735A allele showed the highest frequency in Italian Duroc (0.12). Association analysis of g.1735G > A polymorphism with estimated breeding values (EBVs) for average daily gain (ADG), feed:gain ratio (FGR), weight of neck and loin (lean cuts, LC), weight of ham (H) and backfat thickness (BFT) were performed in Italian Duroc heavy pigs. The GA vs GG pigs showed higher least square means for ADG ( P = 0.003) and LC ( P = 0.036) EBVs and lower value for FGR EBV ( P = 0.033).

In humans, common variants in the fat mass and obesity associated (FTO) gene are associated with body mass index and obesity. Here we sequenced exon 4, parts of introns 3 and 4 and two portions of the 3'-untranslated region of the porcine FTO gene in a panel of nine pigs of different breeds and identified three SNPs. Allele frequencies of the g.276T>G (AM931150) mutation were studied in seven pig breeds. This mutation was used to linkage-map FTO to SSC6. Association analyses between the g.276T>G polymorphism and several traits [pH of semimembranosus muscle and estimated breeding values (EBV) for average daily gain, back fat thickness, lean cuts, ham weight and feed:gain ratio] were carried out in 257 sib-tested Italian Large White pigs. Only feed:gain ratio showed P

To identify DNA markers associated with performance, carcass, and meat production traits including muscle postmortem cathepsin activity, several porcine genes encoding for lysosomal proteinases (cathepsin B, CTSB; cathepsin D, CTSD; cathepsin F, CTSF; cathepsin H, CTSH; cathepsin L, CTSL; and cathepsin Z, CTSZ) and for a cathepsin inhibitor (cystatin B) were investigated. Single nucleotide polymorphisms were identified in CTSD, CTSH, CTSL, and CTSZ genes with a combination of in silico expressed sequence tag database mining and single-strand conformation polymorphism analysis. Sequencing and PCR-RFLP protocols were used to validate the identified polymorphisms. Allele frequencies at these loci were investigated in Italian Large White, Landrace, Duroc, Pietrain, Belgian Landrace, Hampshire, and Meishan breeds. Genotyping CTSD and CTSH markers made it possible to genetically map these genes to SSC 2 and 7, respectively. Markers in CTSD, CTSH, CTSL, and CTSZ genes, together with mutations we previously reported in cystatin B, CTSB, and CTSF genes, were genotyped in an Italian Large White sib-tested population (272 or 482 animals). For these animals, meat quality traits (cathepsin B activity, pH measured at 2 h postmortem, pH measured at 24 h postmortem, glycogen, lactate, and glycolytic potential of semimembranosus muscle) and EBV for ADG, lean cuts (LC), backfat thickness (BFT), ham weight (HW), and feed:gain ratio (FGR) were determined. Analyzed markers did not show any association with muscle cathepsin B activity. Thus, it could be possible that different genes, other than these investigated candidates, affect this trait, which is correlated with the excessive softness defect of dry-cured hams. The results of association analysis confirmed the effects we already reported in another study for CTSF on ADG (P = 0.008), LC (P = 0.001), and BFT (P = 0.02). Moreover, CTSD was associated with ADG, LC (P < 0.0001), BFT, HW, and FGR (P < 0.001); CTSH was associated with FGR (P = 0.026); and CTSZ was associated with ADG (P = 0.006), LC (P = 0.01), HW (P = 0.024), and FGR (P = 0.029). The biochemical and physiological functions of the lysosomal proteinases, together with the results obtained in our investigation, suggest that the cathepsin gene family might play important roles affecting economic traits in pigs.