Luigi Liotta

The Multifaceted Origin of Taurine Cattle Reflected by the Mitochondrial Genome

A Neolithic domestication of taurine cattle in the Fertile Crescent from local aurochsen (Bos primigenius) is generally accepted, but a genetic contribution from European aurochsen has been proposed. Here we performed a survey of a large number of taurine cattle mitochondrial DNA (mtDNA) control regions from numerous European breeds confirming the overall clustering within haplogroups (T1, T2 and T3) of Near Eastern ancestry, but also identifying eight mtDNAs (1.3%) that did not fit in haplogroup T. Sequencing of the entire mitochondrial genome showed that four mtDNAs formed a novel branch (haplogroup R) which, after the deep bifurcation that gave rise to the taurine and zebuine lineages, constitutes the earliest known split in the mtDNA phylogeny of B. primigenius. The remaining four mtDNAs were members of the recently discovered haplogroup Q. Phylogeographic data indicate that R mtDNAs were derived from female European aurochsen, possibly in the Italian Peninsula, and sporadically included in domestic herds. In contrast, the available data suggest that Q mtDNAs and T subclades were involved in the same Neolithic event of domestication in the Near East. Thus, the existence of novel (and rare) taurine haplogroups highlights a multifaceted genetic legacy from distinct B. primigenius populations. Taking into account that the maternally transmitted mtDNA tends to underestimate the extent of gene flow from European aurochsen, the detection of the R mtDNAs in autochthonous breeds, some of which are endangered, identifies an unexpected reservoir of genetic variation that should be carefully preserved.

The Enigmatic Origin of Bovine mtDNA Haplogroup R: Sporadic Interbreeding or an Independent Event of Bos primigenius Domestication in Italy?

Background When domestic taurine cattle diffused from the Fertile Crescent, local wild aurochsen (Bos primigenius) were still numerous. Moreover, aurochsen and introduced cattle often coexisted for millennia, thus providing potential conditions not only for spontaneous interbreeding, but also for pastoralists to create secondary domestication centers involving local aurochs populations. Recent mitochondrial genomes analyses revealed that not all modern taurine mtDNAs belong to the shallow macro-haplogroup T of Near Eastern origin, as demonstrated by the detection of three branches (P, Q and R) radiating prior to the T node in the bovine phylogeny. These uncommon haplogroups represent excellent tools to evaluate if sporadic interbreeding or even additional events of cattle domestication occurred. Methodology The survey of the mitochondrial DNA (mtDNA) control-region variation of 1,747 bovine samples (1,128 new and 619 from previous studies) belonging to 37 European breeds allowed the identification of 16 novel non-T mtDNAs, which after complete genome sequencing were confirmed as members of haplogroups Q and R. These mtDNAs were then integrated in a phylogenetic tree encompassing all available P, Q and R complete mtDNA sequences. Conclusions Phylogenetic analyses of 28 mitochondrial genomes belonging to haplogroups P (N = 2), Q (N = 16) and R (N = 10) together with an extensive survey of all previously published mtDNA datasets revealed major similarities between haplogroups Q and T. Therefore, Q most likely represents an additional minor lineage domesticated in the Near East together with the founders of the T subhaplogroups. Whereas, haplogroup R is found, at least for the moment, only in Italy and nowhere else, either in modern or ancient samples, thus supporting an origin from European aurochsen. Haplogroup R could have been acquired through sporadic interbreeding of wild and domestic animals, but our data do not rule out the possibility of a local and secondary event of B. primigenius domestication in Italy.

Genetic heterogeneity and selection signature at the KIT gene in pigs showing different coat colours and patterns

Mutations in the porcine KIT gene (Dominant white locus) have been shown to affect coat colours and colour distribution in pigs. We analysed this gene in several pig breeds and populations (Sicilian black, completely black or with white patches; Cinta Senese; grey local population; Large White; Duroc; Hampshire; Pietrain; wild boar; Meishan) with different coat colours and patterns, genotyping a few polymorphisms. The 21 exons and parts of the intronic regions were sequenced in these pigs and 69 polymorphisms were identified. The grey-roan coat colour observed in a local grey population was completely associated with a 4-bp deletion of intron 18 in a single copy KIT gene, providing evidence that this mutation characterizes the I(d) allele described in the early genetic literature. The white patches observed in black Sicilian pigs were not completely associated with the presence of a duplicated KIT allele (I(p) ), suggesting that genetic heterogeneity is a possible cause of different coat colours in this breed. Selection signature was evident at the KIT gene in two different belted pig breeds, Hampshire and Cinta Senese. The same mutation(s) may cause the belted phenotype in these breeds that originated in the 18th-19th centuries from English pigs (Hampshire) and in Tuscany (Italy) in the 14th century (Cinta Senese). Phylogenetic relationships of 28 inferred KIT haplotypes indicated two clades: one of Asian origin that included Meishan and a few Sicilian black haplotypes and another of European origin.

Analysis of the MC1R gene in the nero siciliano pig breed and usefulness of this locus for breed traceability

D’Alessandro, E., Fontanesi, L., Liotta, L., Davoli, R., Chiofalo, V., and Russo, V., 2007. Analysis of the MC1R Gene in the Nero Siciliano Pig Breed and Usefulness of this Locus for Breed Traceability. Veterinary Research Communications, 31(Suppl. 1), 389–392

Effect of lairage duration on some blood constituents and beef quality in bulls after long journey

Abstract With the aim to contribute to the determination of an adequate resting time for cattle after long transportation, the effects of different lairage times on some haematic parameters and meat quality of bulls subjected to long commercial journeys were investigated. Thirty-nine Limousine bulls supplied by one farm located near to Saragoza (Spain) were examined after 5 consignments at the final destination, following a journey of 2,550 km to the “San Giorgio” abattoir (Palermo, Italy). Transport time was of 53.6±10.9h; lairage duration for bulls of the 1st, 3rd and 5th consignments was of 31h on average (“Short Lairage” group), whereas, for those of the 2nd and 4th consignments, was of 59 and 57h, respectively (“Long Lairage” group). As regards the blood cell counts, data showed a significant effect (P>0.001) of the lairage duration on leukocyte and platelet counts. No significant effect was observed for erythrocyte count, haemoglobin and hematocrit in relation to the lairage duration, although the repeated measure analysis of variance showed that, irrespective of lairage duration, the hematocrit increased significantly between unloading and slaughter. Haematological parameters showed a significant (P>0.05) effect of the lairage time only on CK and Cortisol. CK enzyme showed an increase in the “Short Lairage” group (33.2% vs. 14.3%) whereas, Cortisol showed a decrease in the “Long Lairage” group (36.3% vs. 3.8%). The different lairage duration did not significantly (P>0.05) affect the incidence of slight and severe carcass bruises. As regards meat quality, lairage duration significantly influenced the pHu which was higher (P>0.01) in the muscle of the “Long Lairage” group, the luminosity at 24h post mortem which was significantly higher (P<0.05) in animals of the “Short Lairage” group, and the red and yellow indices which were higher in the “Long Lairage” group. The “Short Lairage” group showed a lower (P>0.01) value of cooking loss and higher (P<0.01) value of tenderness. Data show that pre-slaughter lairage duration after a long transport may influence the blood parameters as well as meat quality. On the whole, the increase in lairage duration over 36h does not determine any benefit for the animal’s well-being whereas it can cause a reduction in beef quality. For very long transports, it would be better to have an adequate organisation of the facilities in order to diminish the pre-slaughter lairage duration.

Detecting population structure and recent demographic history in endangered livestock breeds: the case of the Italian autochthonous donkeys

Since its domestication, about 5000 years ago, the donkey (Equus asinus) has been extensively used as a work or draft animal in agricultural activities and for the transportation of people and goods. In the last century, technology improvement and growing mechanization strongly affected agriculture and the management and use of this livestock species in the industrialized countries. Nowadays, the use of donkeys for work or transport has almost disappeared, together with the need for mules or hinny breeding. During the last five decades, Italian autochthonous donkey populations suffered from a severe reduction in population size, which led to the extinction of several breeds. At present, eight breeds remain, all classified by FAO as critically endangered or endangered: Asinara, Pantesco, Grigio Siciliano, Romagnolo, Amiatino, Sardo Grigio, Martina Franca, and Ragusano. To evaluate the extant genetic variability of Italian donkeys, we typed 16 microsatellite loci in 258 individuals from these breeds. The results highlighted moderate levels of inbreeding ( F (IS) = 0.127) and a significant partition of genetic variation into breeds, as suggested by fixation index ( F (ST) = 0.109) and analysis of molecular variance (10.86% of total variation assigned to the between-breeds level) analyses. This was confirmed by a Bayesian clustering procedure that also highlighted a further partitioning at lower hierarchical levels corresponding to the farms of origin. This evidence suggests that an effective management strategy for Italian donkey populations should focus on breeds as conservation units. However, this requires a synergic management strategy at the farm level to maintain diversity and avoid inbreeding.

Analysis of single nucleotide polymorphisms in major and candidate genes for production traits in Nero Siciliano pig breed

Abstract Nero Siciliano (NS; Sicilian Black) is a local pig breed reared on the island of Sicily mainly under extensive management. The breed is well adapted to marginal conditions and is appreciated for its reproductive performance, disease resistance and production of tasty meat. For a genetic characterization of this breed we analyzed the allele frequencies of single nucleotide polymorphisms (SNPs) in eight major or candidate genes (ryanodine receptor 1, RYR1; Na+, K+ ATPase subunit α 2, ATP1A2; myosin heavy chain 2B, MYH4; sarcolipin, SLN; cathepsin B, CTSB; cystatin B, CSTB; estrogen receptor, ESR; melanocortin receptor 1, MC1R) for performance and phenotypic traits. The animals that were sampled and analyzed represent about 6-8% of the total NS pig population. PCR-RFLP or PCR-SSCP techniques were used to type the DNA markers in the selected loci. Exact test of Hardy-Weinberg equilibrium was computed for each locus, Fis statistics and heterozygosity were calculated for each locus and over all loci. Allele frequencies obtained in NS breed were compared to the frequencies already available in literature for the Large White, Landrace, Duroc, Belgian Landrace, Piétrain, Hampshire and Meishan breeds. For the ESR locus, as no information on the distribution of the two alleles were available, we typed a sample of unrelated pigs from the considered breeds. Even if only eight loci were studied in NS breed, important elements were obtained from the data. The 1843T (n) allele at the RYR1 locus is present in NS breed, thus the molecular test to identify the carriers of this allele should be adopted to avoid its spreading in the population. Moreover, other studies are needed to clarify the allelic structure of the MC1R gene, which affects coat color, in order to evaluate if this gene could be used in genetic tests for the traceability of the meat products of this breed. Finally, the present work represents an attempt to evaluate data on mutations within major and candidate genes with the final aim to provide information that could be useful for the conservation and valorization of local farm animal genetic resources.

Effects of size and location of regions of interest examined by use of contrast-enhanced ultrasonography on renal perfusion variables of dogs

OBJECTIVE To determine effects of the size and location of regions of interest (ROIs) in the renal cortex of unsedated dogs on renal perfusion variables determined by use of contrast-enhanced ultrasonography (CEUS). ANIMALS 12 client-owned adult (1.5 to 2 years old) Labrador Retrievers (8 males and 4 females; mean ± SD body weight, 27 ± 1.6 kg). PROCEDURES Each dog received 2 bolus injections of sulfur hexafluoride during CEUS. Three small oval ROIs (area of each ROI, 0.11 cm(2)) located in a row with a distance of 1 mm between adjacent ROIs and 1 large oval ROI (area, 1 cm(2)) that encompassed the 3 smaller ROIs were manually drawn in the renal cortex. The ROIs were located at a depth of 1.5 to 2.0 cm in the near field of the renal cortex. Software analysis of time-intensity curves within each ROI was used to identify peak enhancement, time to peak enhancement, regional blood flow, and mean transit time. RESULTS The location and size of the ROIs of unsedated dogs did not cause significant differences in the mean values of the renal perfusion variables. CONCLUSIONS AND CLINICAL RELEVANCE The development of CEUS has provided a unique means for visually examining and quantifying tissue perfusion. Results of this study indicated that it was possible to use small or large ROIs during renal CEUS to evaluate renal perfusion in dogs.

Effects of different nutritional levels on Nero Siciliano pig performance

Riassunto Influenza del livello nutritivo della dieta sulle performance del suino Nero Siciliano. In due recinti collettivi da 1400 m2 ciascuno sono stati allevati in plein air 20 suini Neri Siciliani, suddivisi in due gruppi di 10 soggetti ciascuno, omogenei per sesso (6 maschi castrati e 4 femmine), età (8 mesi) e peso vivo (42±2 kg). Un gruppo riceveva mangime ad libitum (Libitum), l’altro razionato in base al 3% del peso vivo (Restricted). Dopo 95 giorni di allevamento gli animali sono stati macellati. Il peso vivo alla macellazione (93,26 vs. 82,97 kg; P<0,01) come gli IPMG (539,6 vs. 430,6 g/d; P<0,05) sono risultati più elevati nel gruppo “Libitum”, ma ciò ha comportato un peggioramento degli ICA (5,4 vs. 3,9; P<0,001). Il gruppo “Restricted” ha fornito una percentuale maggiore di carne magra (42,25 vs. 39,66%; P<0,05), di tagli carnosi (52,21 vs. 46,55%; P<0,001) e minore di quelli adiposi (37,42 vs. 42,38%; P<0,001).

Milk composition of “Nero Siciliano” sow. Preliminary results

Abstract Quantitative and qualitative milk production is the basis for determining the nutritional requirements of lactating sow; indeed, the gross nutrient composition of sow’s milk is frequently used as a suitable starting point when formulating milk-replacer diets for piglets. Data about the sow’s milk can be found from the literature but, in authors knowledge, no data on milk composition of Nero Siciliano sow exist. This study reports the preliminary results concerning some physical and chemical characteristics of the milk of this autochthonous Sicilian pig race during the lactation. The research was carried out on 10 “Nero Siciliano” sows, 4 primiparous (age: 9-12 months) and 6 pluriparous (age: 2-5 years), stabled in single boxes and fed with a concentrate. From the 10th day after farrowing to the weaning (day 58th), every week, in the morning, the sows were injected with 5 IU oxytocin (i.m.) and hand-milked; all functional mammary glands were milked. Piglets were removed and isolated from the dams for at least 30 min before each milking. Individual milk samples were analysed to determine: pH value, protein (Kjeldhal methods, N x 6.38), fat (Gerber method) and lactose (HPLC method) content; the energy content, expressed in kJ?kg-1 of milk, was calculated using the coefficients reported by Perrin (1958). Data were collected in relation to the stage of lactation in three periods called: “First” (day 7 to 22), “Medium” (day 23 to 38) and “Final” (day 39 to 58) and subjected to ANCO-VA considering as main variable the stage of lactation and as covariate the age (proc. GLM; SAS, 2001). As regards the pH of the milk, no significant differences were observed during the lactation (“First”: 7.14; “Medium”: 7.07; “Final”: 7.27); the mean values were slightly higher than those observed by Others in hybrid pigs. Fat percentages showed significant differences between the “First” and the “Medium” (P<0.001) and the “First” and the “Final” (P=0.012) periods of the lactation, with the highest value at the “First” period (8.68%) followed by a decrease as lactation progressed (“Medium”: 6.34%; “Final”: 7.09%). As regards protein percentages was similar to that of fat, but no significant differences were observed among the three periods of lactation (“First”: 5.48%; “Medium”: 4.72%; “Final”: 5.94%). The mean values of fat and protein percentages as well as their trends are in accordance to those observed by other Authors on white pig races. Lactose, the major carbohydrate in sow’s milk, has shown a linear increase during the whole lactation with the lowest value in the milk of the “First” (4.40%) period and reaching significant differences (P=0.008) at the “Final” period with the highest percentage (6.22%). These results are not in accordance to those reported in literature. The energy content (kJ?kg-1) showed a trend (“First”: 5161; “Medium”: 4525; “Final”: 4864) similar to that observed for fat percentage with significant differences between the “First” and the “Medium” (P=0.005) and the “Medium” and the “Final” (P=0.029) periods. The knowledge of the milk composition of Nero Siciliano sow, characterised by low prolificacy (7±3 piglets), represents a critical point for a better estimation of the requirements of lactating sows as well as of piglets.