Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip.

Genetic characterization of local breeds is essential to preserve their genomic variability, to advance conservation policies and to contribute to their promotion and sustainability. Genomic diversity of twenty European local pig breeds and a small sample of Spanish wild pigs was assessed using high density SNP chips. A total of 992 DNA samples were analyzed with the GeneSeek Genomic Profiler (GGP) 70 K HD porcine genotyping chip. Genotype data was employed to compute genetic diversity, population differentiation and structure, genetic distances, linkage disequilibrium and effective population size. Our results point out several breeds, such as Turopolje, Apulo Calabrese, Casertana, Mora Romagnola and Lithuanian indigenous wattle, having the lowest genetic diversity, supported by low heterozygosity and very small effective population size, demonstrating the need of enhanced conservation strategies. Principal components analysis showed the clustering of the individuals of the same breed, with few breeds being clearly isolated from the rest. Several breeds were partially overlapped, suggesting genetic closeness, which was particularly marked in the case of Iberian and Alentejana breeds. Spanish wild boar was also narrowly related to other western populations, in agreement with recurrent admixture between wild and domestic animals. We also searched across the genome for loci under diversifying selection based on FST outlier tests. Candidate genes that may underlie differences in adaptation to specific environments and productive systems and phenotypic traits were detected in potentially selected genomic regions.

Effect of dietary protein level on carcass traits and meat properties of Cinta Senese pigs.

The aim of this study was to test the effect of various dietary protein contents (CP) on the carcass traits and the meat quality of Cinta Senese pigs. A total of 60 Cinta Senese pigs were equally distributed in four dietary groups that were balanced for sex (barrows and gilts) and live weight. The animals in the groups were fed one of four diets (80CP, 100CP, 130CP and 160CP) containing different CP contents (80, 100, 130 and 160 g/kg, respectively). The diets were administered to the pigs during the entire growing-fattening period in a controlled dose of 90 g/kg W0.75, to a maximum of 2.5 kg/day per animal. The duration of the trial was ~250 days, ending when the animals reached the target slaughter weight of 145 kg. The 80CP diet produced fatter carcasses than did the other diets; no differences in carcass composition were found among the animals fed the other three diets (total lean cuts: 57.4%, 61.4%, 60.8% and 61.3% for 80CP, 100CP, 130CP and 160CP diet, respectively). The sample joint composition confirmed the highest fatness and the lowest meatiness of pigs fed 80CP. This same pattern was evident for the composition of the muscle (Longissimus lumborum) containing the largest amount of i.m. fat, and the lowest protein content in the 80CP group. Moreover, the 80CP diet resulted in the lightest and yellowest meat with the highest cooking loss. A principal component analysis of the physical and chemical traits of the meat revealed three first factors that explained 56% of the total variance. Among them, only the intersection of Factor1, which combined mainly lower pH at 24 h postmortem and higher drip loss, cooking loss, lightness and yellowness, with Factor2, which associated higher toughness, higher protein and lower fat content, graphically appeared to discriminate the 80CP diet from the other ones. In conclusion, a diet with 80 g/kg of CP content was inadequate for this local breed, while, in consideration of the cost of protein feed and the need to reduce N pollution, the 100CP diet would be an optimal compromise for the growth-fattening of Cinta Senese pigs.

Quality of fresh and seasoned fat of Cinta Senese pigs as affected by fattening with chestnut.

This trial was aimed to verify the effect of fattening with chestnut on carcass characteristics and on quality traits of products of Cinta Senese breed. Thirty-three Cinta Senese pigs were allotted into three groups. One group was fed a commercial feedstuff (0-CH), the other two groups were fed chestnut for one (1-CH) or three (3-CH) months. Pigs were slaughtered at 130 kg of live weight. The 1-CH group showed significantly lower pH value at 24h (P<0.05). For sample joint dissection a significant effect (P<0.05) of feeding system was found only on intermuscular fat, highest in 1-CH. A significant effect of feeding system (P<0.05) was found on physical and chemical parameters of Longissimus lumborum: the 3-CH group showed the highest values (P<0.05) of L, a, b, drip loss, cooking loss, shear force and intramuscular fat on raw meat. The 3-CH showed significantly higher level (P<0.05) of unsaturation for the highest percentage of MUFA and PUFA.

The evolution of volatile compounds profile of "Toscano" dry-cured ham during ripening as revealed by SPME-GC-MS approach.

The volatile compounds profile is an important feature for the characterization of dry-cured hams. Some minor typical Italian products, such as 'Toscano' ham, have been poorly studied in regards to their composition of volatile compounds. In this article, we studied the evolution of the aromatic profile of 'Toscano' dry-cured ham by solid-phase microextraction-gas chromatographic-mass spectrometry (SPME-GC-MS) with ripening. Ten right thighs were cured according to the 'Toscano' PDO protocol, sampled at 0, 1, 3, 6 and 12 months and submitted to volatile compounds analysis by SPME with a Divinylbenzene (DVB)/Carboxen/Polydimethylsiloxane (PDMS) 75-µ Stable Flex fibre. An Agilent 5975C mass selective detector (MSD) spectrometer with electron ionization (EI) source operating in scan mode within the m/z 29-350 range was used for data collection. Seven internal standards, either deuterium labeled or absent in the specimens and chosen to represent low or high boiling esters, alcohols, acids or phenols, were added to the homogenized samples and used to normalize the SPME fibre response to account for response changes upon wearing. Linear calibrations were obtained in this way for selected representative compounds. Over 60 compounds belonging to esters, aldehydes, organic acids, ketones and alcohols were identified by comparison with spectral libraries and Kovats indices. Aldehydes were the most represented chemical family, followed by organic acids, alcohols, ketones and esters. The aldehydes and ketones increased during the first 3 months, when the larger formation of volatiles occurred. For other families, the evolution over time was less evident. The principal component and discriminant analyses of the aromatic profile were effective in classifying the hams at 0, 6 or 12 months of ripening while for 1 and 3 months' samples a partial overlapping was shown. These results represent the first characterization of 'Toscano' ham and may constitute the basis to identify the best ripening time and define an analytical quality standard for this typical ham.

Short communication: effects of nonesterified fatty acids on lymphocyte function in dairy heifers.

This in vitro study was performed to assess the effects of various concentrations of nonesterified fatty acids (NEFA) on lymphocyte function of heifers. Nine Holstein heifers were studied. Peripheral blood mononuclear cells were incubated with various concentrations of NEFA (0, 0.0625, 0.125, 0.25, 0.5, 1, and 2 mmol/L). The mixture of NEFA was represented by C16:0 (30%), C16:1 (5%), C18:0 (15%), C18:1 (45%), and C18:2 (5%). The DNA synthesis was diminished at concentrations of NEFA of 2, 1, and 0.5 mmol/L. The IgM secretion was inhibited at concentrations of NEFA of 2, 1, 0.5, and 0.25 mmol/L. Secretion of IFN-gamma was depressed at concentrations of NEFA of 2, 1, 0.5, 0.25, and 0.125 mmol/L. Increases of plasma NEFA might contribute to explain the higher incidence of infections observed in cows suffering from energy deficit.

Comparison of the performances of Nero Siciliano pigs reared indoors and outdoors: 2. Joints composition, meat and fat traits.

A study on the effect of rearing system on tissue composition of principal joints and chemical-physical traits of meat and subcutaneous fat, was carried out on a local pig breed. A total of 78 Nero Siciliano pigs was used; 41 pigs were reared in woods, 37 pigs were reared in pens and fed a commercial diet. Weight at slaughter was 101.9 and 88.2 kg for indoor and outdoor pigs, respectively. Means were estimated at 77 kg of live weight. At ham dissection outdoor-pigs showed higher percentages of lean (58% vs. 55%) and lower subcutaneous fat (31% vs. 34%). In Longissimus lumborum outdoor-pigs showed a higher intramuscular fat percentage (4.3% vs. 3.3%), a lower protein content (22.2% vs. 23.4%), and higher free water (9.6 vs. 7.9 cm(2)). Outdoor pigs produced more light (L(*)=50 vs. 46.7) and more yellow (b(*)=5.84 vs. 4.88) meat. Subcutaneous fat of outdoor pigs showed higher percentages of MUFA (53.3% vs. 47.2%) and lower percentages of PUFA (10.85% vs. 14.45%), no differences were found for n-3 PUFA. Outdoor-pigs had lower atherogenicity (0.48 vs. 0.53) and thrombogenicity (1.03 vs. 1.21) indices.

The use of multivariate analysis for evaluating relationships among fat depots in heavy pigs of different genotypes.

The aim of the present work was to study distribution and reciprocal relationships of fat depots in heavy pigs of several genetic types. On 161 barrows and gilts belonging to four genetic types (Large White and relative crosses with Italian Landrace, Belgian Landrace and Duroc), slaughtered from 125 to 180 kg l.w., thickness, colour (C.I.E, L*, a*, b*) and weight of backfat and of kidney fat were determined. Subcutaneous and intermuscular fat of ham were weighed. On biceps femoris, semimembranosus and semitendinosus muscles ether extract content was determined. Allometric analysis showed that body growth did not particularly increase the intramuscular fat content of the ham. Principal component analysis indicated that PC1 (0.43% of variation) represented the overall fatness, associated all the depots in a similar manner, and was linked to body weight and sex. PC2 (0.22% of variation), linked to genotypes and body weight, expressed the opposition between intramuscular fat deposition and subcutaneous and internal fat accumulation. Using measurements easily recorded on the side (backfat thickness and colour, percent kidney fat), only the estimate of subcutaneous fat, among ham depots, showed good accuracy (R(2)=0.65).

Influence of thermal and dietary stress on immune response of rabbits.

With the aim of analyzing the effects of prolonged thermal stress or food intake reduction on lymphoid cell proliferation and antibody synthesis, New Zealand White (NZW) male rabbits, both immunized and nonimmunized with Mycobacterium tuberculosis, were kept in individual cages for 24 d at controlled climatic conditions. Both immunized and nonimmunized rabbits were divided into two experimental groups and one control group. The thermal-stressed rabbits (TS) were exposed to a room temperature of 33.5 degrees C, and dietary restricted rabbits (DR) were pair-fed on the basis of the average feed intake of the TS groups and maintained at a room temperature of 18.0 degrees C. The control group (Ctr) was maintained at 18.0 degrees C and was given ad libitum access to feed. All rabbits were maintained at relative humidity 62 +/- 5%. Sera and peripheral blood mononuclear cells (PBMC) were isolated from blood samples collected on d 0, 6, 12, and 24. Sera were used for determining total proteins and immunoglobulins (Ig) specific or not to mycobacterial antigens. Antibodies to heat-shock protein (HSP) were also determined. The PBMC were used to measure cell proliferation and in vitro Ig synthesis. Both experiments in vivo and in vitro suggest that thermal stress and dietary restriction severely affect the immune cell functions. In fact, both stress treatments decreased the capacity of PBMC to proliferate and inhibited the differentiation of B lymphocytes in antibody-secreting cells. However, a recovery of immune cell functions was only observed in vivo after 12 d of treatment, suggesting that other defensive mechanisms may come into play in vivo. Sera collected from both TS and DR rabbits after 24 d presented antibodies to HSP70, suggesting that the analysis of anti-HSP antibodies could represent a useful indicator to reveal the effects of different stress effectors regardless of the nature of the stress.

Differential effect of alpha-tocopherol and ascorbate on oxidative injury induced in immune cells by thermal stress.

As immune cells are often subjected to hyperthermia that can easily occur either after intense and/or prolonged exercise or during defense against pathogens, in this paper we analysed whether superoxide anion production occurred in lymphocytes exposed to high temperature and, consequently, if antioxidants could exert any protective function. The results demonstrated that an increase of superoxide anion was induced in rabbit lymphocytes exposed to 42 degrees C for 1h, although cell viability was no affected. However, suppression of either Pokeweed mitogen (PWM)-driven cell proliferation, or immunoglobulin production or IL-2 synthesis was observed. To evaluate the capacity of antioxidants to restore the immune suppressed responses, two vitamins, alpha-tocopherol and ascorbic acid, were added to PWM-stimulated cultures following heat treatment. The data demonstrated that alpha-tocopherol was able to totally abrogate the inhibitory effects mediated by thermal stress, while ascorbic acid did not give any protective results.

Relationships between adipose tissue characteristics of newborn pigs and subsequent performance: I. Characteristics at 8 days of age and growth rate until slaughter.

The genetic influence on body and adipose tissue characteristics of newborn pigs and their correlations to growth rate, BW, body length, backfat thickness and adipocyte size in the outer and inner layers of backfat in 8-d-old Large White piglets were determined. Samples of adipose tissue were obtained by biopsy. Pigs were born to 32 sows mated with the same boar. Heritability and genetic correlations were estimated with dam component of variance; therefore, bias due to common environmental effects cannot be excluded. The heritability estimate for adipocyte volume (.89 +/- .28) was higher than that for backfat thickness at the first and last thoracic vertebrae (.50 +/- .22; .63 +/- .24) and for body weight (.59 +/- .23) at 8 d. Backfat thickness was more closely related genetically and phenotypically to body weight and length than to adipose tissue cellularity. Heritability estimates were .75 +/- .28 for gain from 8 d to weaning and from weaning to 95 d (probably because of common environmental effects) but were .31 +/- .20 for ADG from 95 d to slaughter. Characteristics at 8 d were closely correlated phenotypically with growth rate until weaning. These correlations became lower in the two subsequent periods (to 95 d and to slaughter). Corresponding genetic correlations were nonsignificant.

Relationships between adipose tissue characteristics of newborn pigs and subsequent performance: II. Carcass traits at 95 and 145 kilograms live weight.

Backfat thickness, carcass length, area of M. longissimus and carcass composition were determined for 253 Large White barrows and gilts to examine the genetic influence on the main characteristics of the carcass and the correlation of these traits with body measurements and fat characteristics at 8 d of age. Pigs were born to 32 sows mated to the same boar. At the age of 8 d, weight, body length and backfat thickness and cellularity were measured. Pigs were slaughtered at 95 and 145 kg live weight. Heritability and genetic correlations were estimated with dam component of variance. Higher adiposity of carcasses was noted for barrows than for gilts and for those animals slaughtered at the heavier vs at the lighter weight. High h2 values were observed for carcass length (.89 +/- .29), area of the M. longissimus (.67 +/- .26) and backfat thickness at the gluteus medius (.77 +/- .28). Percentage of commercial cuts also had high heritabilities. Phenotypic and genetic correlations between the characteristics at 8 d and backfat thickness, carcass length and M. longissimus area at slaughter were not statistically significant. However, significant phenotypic correlations were found between cellularity of the outer and inner layers at 8 d and percentage of major cuts (e.g., rp = .27 with total fat cuts); cellularity of the outer layer at 8 d also was correlated genetically with carcass composition (e.g., rg = .50 +/- .19 with total fat cuts). Genetic predisposition toward intensive fat deposition was more clearly predicted by cellularity than by thickness of adipose tissue in newborn pigs.

Relationships between adipose tissue characteristics of newborn pigs and subsequent performance: III. Histological and chemical characteristics of backfat.

Genetic and phenotypic relationships between adipose tissue characteristics of 253 piglets aged 8 d and qualitative characteristics of their backfat at 95 and 145 kg live weight were studied. Heritability of these qualitative aspects was estimated as well. Backfat samples were tested for cellularity, moisture, lipid content and fatty acid composition of the outer and inner layers. Adipose cellularity at birth proved to be correlated with cell volume, moisture and total unsaturated fatty acid, C18:0 and C18:2 contents present in backfat at slaughter. Estimates of heritability calculated for the outer layer of backfat indicated that progress can be made by selecting for water content and fatty acid composition. Neonatal cellularity furnishes a useful indicator not only of the backfat cell size at slaughter but also of the chemical factors important in determining the physical and organoleptic characteristics of porcine fat.