Fabio Pilla

Genome-wide analysis of Italian sheep diversity reveals a strong geographic pattern and cryptic relationships between breeds.

Italy counts several sheep breeds, arisen over centuries as a consequence of ancient and recent genetic and demographic events. To finely reconstruct genetic structure and relationships between Italian sheep, 496 subjects from 19 breeds were typed at 50K single nucleotide polymorphism loci. A subset of foreign breeds from the Sheep HapMap dataset was also included in the analyses. Genetic distances (as visualized either in a network or in a multidimensional scaling analysis of identical by state distances) closely reflected geographic proximity between breeds, with a clear north-south gradient, likely because of high levels of past gene flow and admixture all along the peninsula. Sardinian breeds diverged more from other breeds, a probable consequence of the combined effect of ancient sporadic introgression of feral mouflon and long-lasting genetic isolation from continental sheep populations. The study allowed the detection of previously undocumented episodes of recent introgression (Delle Langhe into the endangered Altamurana breed) as well as signatures of known, or claimed, historical introgression (Merino into Sopravissana and Gentile di Puglia; Bergamasca into Fabrianese, Appenninica and, to a lesser extent, Leccese). Arguments that would question, from a genomic point of view, the current breed classification of Bergamasca and Biellese into two separate breeds are presented. Finally, a role for traditional transhumance practices in shaping the genetic makeup of Alpine sheep breeds is proposed. The study represents the first exhaustive analysis of Italian sheep diversity in an European context, and it bridges the gap in the previous HapMap panel between Western Mediterranean and Swiss breeds.

Lipid composition of meat and backfat from Casertana purebred and crossbred pigs reared outdoors

The study aimed to evaluate, with regard to the human nutrition, the lipid profile of meat and backfat from gilts and barrows of the Italian autochthonous genotype Casertana and its crossbreed (Casertana×Large White) slaughtered at two different live weights. Meat from the Casertana cross was nutritionally comparable to that from the purebreed and both would be considered healthy, irrespective of sex and weight, due to the relatively low levels of intramuscular lipids and cholesterol. Muscle cholesterol was considerably lower in the heavy pigs than in the light ones and, as weight increased, cholesterol decreased but only in gilts. Females supply meat with higher polyunsaturated fatty acids (PUFA) and slightly lower saturated fatty acids (SFA) respect to barrows and, thus, higher PUFA/SFA ratio. Casertana crossbreds can represent a good alternative to pure Casertana, mainly in the production of Colonnata lard, due to the better fatty acid profile of the subcutaneous adipose tissue. From the nutritional point of view, the optimal slaughtering weight was about 150kg for both genotypes. Heavy pigs, compared to the light ones, produced loin with lower atherogenic and thrombogenic indexes, lower SFA/unsaturated fatty acids ratio, and higher PUFA/SFA ratio.

Analysis of adiponectin gene and comparison of its expression in two different pig breeds.

Adiponectin, an adipokine secreted from adipose tissue (AT), exerts beneficial pleiotropic effects on obesity‐related metabolic diseases. We have analyzed the adiponectin gene (ACDC) and its expression in two genetically different breeds of pigs, lean type, large white (LW) and fat type, Casertana (CE). DNA, RNA, and protein extracts from 10 LW and 10 CE pigs were analyzed by sequence analysis, enzyme‐linked immunosorbent assay (ELISA), fast protein liquid chromatography, and northern and western blotting. Sequence analysis revealed an identity of 100% between the ACDC gene from the two breeds, but the expression of the adiponectin protein was higher in LW than in CE pigs. We identified sexual dimorphism of adiponectin in both breeds, namely a balanced distribution of the low isoforms (∼50 kDa), whereas the middle isoforms (∼75–150 kDa) were increased in sows. In conclusion, in this study, we demonstrate that adiponectin is produced and secreted differently in the two breeds of pig, namely adiponectin is more abundant in LW than in CE. Moreover, the visceral AT of LW expresses more adiponectin than the subcutaneous AT. This relationship is absent in CE. These observations provided the first evidence that adiponectin expression is correlated with the “fat” phenotype in pig.

A novel method for species identification in milk and milk-based products.

This study describes a method for species-specific detection of animal DNA from different species (cattle, sheep, goat, water buffalo) in milk and dairy products. A primer set was designed in conserved region on the basis of the alignment of the sequence codifying the genomic kappa-casein gene in order to amplify all four species with a single primer pair. Polymorphisms were detected via minisequencing with extension primers designed in conserved sequences for haplotype determination that allow unambiguous assignment to each species. The method was successfully applied to the detection of raw and pasteurized milk from the four different species considered as well as to cheese products from the retail trade. Estimation of the limit of detection was carried out using a progression of dilutions of genomic DNA as well as DNA isolated from milk of a known number of somatic cells from different species in order to be able to achieve detection rates as low as 0.1% bovine milk mixed with buffalo milk.

Morphological traits, reproductive and productive performances of Casertana pigs reared outdoors

Abstract Casertana is an Italian autochthonous pig breed. In the past, the breed was common in Campania and the surrounding area in South Italy because it was valued for its productive performance, particularly regarding the fattening tendency, but in recent decades, autochthonous swine have been replaced by cosmopolitan lean-type pigs and the Casertana breed also experienced a dramatic reduction in numbers. Concern over the preservation of genetic resources and the increased demand for regional food suggest a new way of maintaining the breed. Unfortunately, few recent data on the morphological as well as on the productive traits are available. To ascertain the characteristics of the Casertana breed a productive trial was performed by comparing Casertana and Large White pure breed and their cross. Sixteen females and 6 males of pure breed Casertana and 18 females and 2 males of pure breed Italian Large White were mated twice to produce Casertana, Large White and Casertana x Large White piglets. The average number of piglets born was significantly lower in Casertana gilts, but no difference in the number of weaned piglets among genetic types was observed. Sixty-eight animals of the three genetic types were reared outdoors and received two distinct diets differing in energy content. Pigs were weighted individually every month to calculate average daily gain. Morphological traits of Casertana pigs were also recorded. A total of 54 animals (21 Casertana at 151 kg live weight, 15 crossbreed at 157 kg live weight and 18 Large White at 179 kg live weight) were slaughtered and data on carcasses were collected. Average daily weight gain differed markedly (P< 0.05) among genetic types (450; 552; 695 g/d, respectively for Casertana; Casertana x Large White; Large White) and consequently the slaughter weight also differed. Casertana showed higher dressing percentages that the Italian Large White (P< 0.05). Backfat thickness was also clearly affected by genetic type (P< 0.05): Casertana pigs had the highest value (44.91 mm). The diet had no influence on the average daily weight gain and backfat thickness. However, pigs fed with higher energy component had higher (P< 0.05) dressing percentage.

Structural analysis and haplotype diversity in swine LEP and MC4R genes

Knowledge about structural variation of candidate genes could be important to improve breeding selection scheme and preserve genetic variability in livestock species. Leptin (LEP) and melanocortin-4 receptor (MC4R) genes are involved in the energetic pathway and are obvious candidate genes for fatness. By sequencing LEP and MC4R genes in 72 pigs belonging to lean (Large White and Duroc), fat (Meishan and Casertana) breeds and also Wild Boar, 98 polymorphic sites, of which 91 were novel, were found in the Leptin sequence while only the previously described mutation was found in the MC4R gene. A total of 18 LEP haplotypes were observed and their distribution was unequal among the breeds. The phylogenetic analysis showed two haplotype branches distinguishing between lean and fat breeds.

A new polymorphism in goat β-lactoglobulin promoter region

Abstract An individual variability in β-lactoglobulin content has been previously observed in Girgentana goat milk by HPLC analysis. To identify eventual mutations affecting the transcription level of the gene, the promoter region was characterized in goats showing an anomalous phenotype, consisting in a reduced content of β-lactoglobulin respect to a-lactoalbumine. A single nucleotide substitution not previously reported has been detected. A PCR-RFLP procedure was developed for fast detection of the mutation in different goat breeds: Girgentana, Garganica, Sarda, Alpine, Montefalcone and Saanen. The Montefalcone goat showed the highest frequency of the mutation, confirming once more the peculiarity of this breed.

Effects of slaughter weight and sex on carcass traits and meat quality of Casertana pigs reared outdoors

Abstract The effects of different slaughter weights (W) and sex (S) on carcass traits and longissimus dorsi meat quality (pH, WHC, colour, cholesterol and collagen) of Casertana pigs were studied. Thirty-six pure breed Casertana pigs, 24 barrows (B) and 12 gilts (G), were evaluated in a 2x2 factorial design involving different slaughter live weights (L, 125.6 kg; H, 152.5 kg) and S (B and G). H pigs had higher carcass weight (P<0.01), dressing percentage (P<0.05), ham yield (+ 7.9 %; P<0.01), lean meat cuts (P<0.01) and backfat thickness (+13.3%; P<0.05), and lower (P<0.01) loin yield and fatty cuts. W did not affect pH and WHC. L pigs produced lighter (P<0.01) and more yellow meat (P<0.01), while H pigs showed lower (P<0.01) hue value. Cholesterol content resulted higher (P<0.05) in H pig meat. Collagen properties were affected by W. Compared to G, B had higher dressing percentage (P<0.05) and backfat thickness (P<0.01), smaller loin area (P<0.01), slightly lower (P<0.08) loin yield and less (P<0.01) lean cuts. S did not affect any meat quality traits.

Expression profiles of Toll-like receptors 1, 2 and 5 in selected organs of commercial and indigenous chickens

Toll-like receptors (TLRs) are members of the cellular receptors that constitute a major component of the evolutionary conserved pattern recognition system (PRR). TLRs are expressed in a wide variety of tissues and cell types. In this study we compared the expression profiles of the chicken TLR1, TLR2 and TLR5 genes in a range of organs (lung, ovary, liver, thymus, duodenum, spleen and large intestine) in commercial Hy-Line (HL) and indigenous Green-legged Partridgelike (GP) chickens. The level of mRNA was determined with RT-qPCR using the TaqMan probes for target and reference (ACTB) genes. We determined that the tissue profiles differed with respect to each TLR and they were ranked as follows: spleen, lungs, large intestine (TLR1), large intestine, lungs, thymus/ovary (TLR2) and lungs, thymus, liver (TLR5). A differential expression between HL and GP chickens was determined for TLR1 and TLR5 genes in large intestine and thymus of HL (P < 0.05) and GP (P < 0.05) chickens. We conclude that the commercial chickens expressed higher levels of TLR1 mRNA in large intestine and TLR5 mRNA in thymus than indigenous chickens.

Merino and Merino-derived sheep breeds: a genome-wide intercontinental study

BackgroundMerino and Merino-derived sheep breeds have been widely distributed across the world, both as purebred and admixed populations. They represent an economically and historically important genetic resource which over time has been used as the basis for the development of new breeds. In order to examine the genetic influence of Merino in the context of a global collection of domestic sheep breeds, we analyzed genotype data that were obtained with the OvineSNP50 BeadChip (Illumina) for 671 individuals from 37 populations, including a subset of breeds from the Sheep HapMap dataset.ResultsBased on a multi-dimensional scaling analysis, we highlighted four main clusters in this dataset, which corresponded to wild sheep, mouflon, primitive North European breeds and modern sheep (including Merino), respectively. The neighbor-network analysis further differentiated North-European and Mediterranean domestic breeds, with subclusters of Merino and Merino-derived breeds, other Spanish breeds and other Italian breeds. Model-based clustering, migration analysis and haplotype sharing indicated that genetic exchange occurred between archaic populations and also that a more recent Merino-mediated gene flow to several Merino-derived populations around the world took place. The close relationship between Spanish Merino and other Spanish breeds was consistent with an Iberian origin for the Merino breed, with possible earlier contributions from other Mediterranean stocks. The Merino populations from Australia, New Zealand and China were clearly separated from their European ancestors. We observed a genetic substructuring in the Spanish Merino population, which reflects recent herd management practices.ConclusionsOur data suggest that intensive gene flow, founder effects and geographic isolation are the main factors that determined the genetic makeup of current Merino and Merino-derived breeds. To explain how the current Merino and Merino-derived breeds were obtained, we propose a scenario that includes several consecutive migrations of sheep populations that may serve as working hypotheses for subsequent studies.