Polymorphisms at Candidate Genes for Fat Content and Fatty Acids Composition: Effects on Sheep Milk Production and Fatty Acid Profile Using Two Dietary Supplementations.

The nutritional value of sheep's milk and its derivatives is influenced by the lipid fraction, which is affected by diet and genetics. This study aimed to explore the genetic variations in the DGAT1 and SCD genes and assessed the impact of the DGAT1 genotype on milk quality in Valle del Belìce sheep, considering diet supplementation with carob pulp and barley grain. Among the potentially polymorphic sites, only DGAT1 g.127 C > A and SCD g.87 C > A showed variability. The DGAT1 genotype did not significantly impact milk yield and composition, except for higher urea content in the CA genotypes than in the CC ones. Carob pulp increased the milk fat content compared to barley grain. Genetic variation in DGAT1 was associated with changes in the milk fatty acid profile; specifically, the CA genotype exhibited higher levels of short-chain fatty acids and lower levels of polyunsaturated fatty acids compared to the CC genotype. Carob pulp supplementation increased saturated fatty acids and reduced unsaturated fractions, leading to milk with higher atherogenic and thrombogenic indices. No significant interaction was found between genotype and diet. This study provides insights into the genetic and dietary factors influencing sheep's milk composition. Further research is needed to understand the impact of these genetic variations on milk production and composition, as well as to determine optimal levels of carob pulp for improving fat percentage and promoting sustainable sheep breeding practices.

Polymorphism at the CSN1S1 Locus and Energy Intake Level Affect Milk Traits and Casein Profiles in Rossa Mediterranea Goats.

A total of twenty-seven Rossa Mediterranea lactating goats, consisting of nine homozygous for strong alleles (AA), twelve heterozygous (AF) and six homozygous for weak alleles (FF) at the CSN1S1 locus, were used to evaluate the effect of genotype, diet and genotype × diet interaction on goat milk traits and casein profile. The goats were used in a 3 × 3 factorial arrangement of treatments, with three genotypes (AA, AF and FF) and three different energy intake levels: high (H), medium (M) and low (L). The diets supplied a complete pelleted feed containing 65% of alfalfa hay, respectively, at 150%, 100% and 70% of the total energy requirements. Milk yield was significantly affected by the genotype and diet: Lower levels were found in FF goats than in AA and AF genotypes (673.7 vs. 934.5 and 879.8 d/g, respectively; p = 0.002) as well as in goats fed with the L diet (651.5 vs. 1041 and 852.9 g/d for H and M diet, respectively, p < 0.001). The genotype influenced the casein profile. Specifically, AA goat milk exhibited higher concentrations of total casein and αs1-casein compared to AF and FF genotypes (for total casein and αs1-casein, respectively: 24.9 vs. 20.4 and 19.8 g/kg, p = 0.001; 7.2 vs. 3.7 and 0.7 g/kg, p < 0.001), while the FF genotype showed higher values for αs2-casein concentrations compared to homozygous AA and heterozygous AF goats (3.1 vs. 2.4 and 2.5 g/kg, respectively, p < 0.001). A significant genotype x diet interaction occurred for αs2-casein levels (g/kg) (p = 0.034) and αs1-casein yields (p = 0.027): The αs2-casein level was not affected by the diet in AA goats, whereas it increased with energy intake in AF and FF genotypes. Conversely, the αs1-casein yield gradually increased with energy intake in AA and AF groups, whereas the diet in FF goats did not modify it. The results demonstrated that high energy input, as well as the strong allele at the CSN1S1 locus, enhanced milk production and casein concentrations. Furthermore, they confirmed the existence of an interaction between αs1-casein polymorphism and diets, influencing the milk casein composition and yield.

Genome-wide population structure, homozygosity, and heterozygosity patterns of Nero Siciliano pig in the framework of Italian and cosmopolitan breeds.

Analysis of genomic data is becoming more and more common for the effective management of livestock breeding programmes, even in the case of local populations. In this work, the genome-wide data of Nero Siciliano pig breed were compared to that of wild boar, Italian local and cosmopolitan breeds to investigate its genetic structure, and runs of homozygosity (ROH) and heterozygosity patterns. The Nero Siciliano has been reported to have the highest rate of genetic diversity among the Italian breeds, and a genetic variability comparable to that of the cosmopolitan breeds. Analyses of genomic structure and relationships underlined its proximity to wild boar, and an internal substructure probably linked to different family lines. The breed showed a low value of inbreeding estimated from ROH, and the highest diversity index among the Italian breeds, even if lower than that of the cosmopolitans. Four ROH islands in three chromosomes (SSC8, SSC11, and SSC14) and one heterozygosity-rich region (SSC1) were identified in Nero Siciliano, highlighting genomic regions related to productive QTL. Across breeds, SSC8 and SSC14 were the chromosomes with most ROH islands, with Mora Romagnola and wild boar showing the highest level of autozygosity. Chromosomes SSC2, SSC6, SSC8 and SSC13 showed the majority of runs of heterozygosity regions, mainly found in the cosmopolitan pig breeds, which reported several genes associated with health-related QTL. The outlined results can help to better identify the genomic profile of this local breed in order to plan matings, maintain adequate internal diversity and exploit the production system.

High-density SNP markers elucidate the genetic divergence and population structure of Noticiana sheep breed in the Mediterranean context.

Among livestock species, sheep have played an early major role in the Mediterranean area. Italy has a long history of sheep breeding and, despite a dramatic contraction in numbers, still raise several local populations that may represent a unique source of genetic diversity. The Noticiana is a breed of the south-eastern part of Sicily appreciated both for its dairy products and for its resistance to harsh environment. In this study, the high-density Illumina Ovine SNP600K BeadChip array was used for the first genome-wide characterization of 48 individuals of Noticiana sheep to investigate its diversity, the genome structure and the relationship within the context of worldwide and Italian breeds. Moreover, the runs of homozygosity (ROH) pattern and the pairwise FST-outliers were examined. Noticiana reported moderate levels of genetic diversity. The high percentage of short and medium length ROH segments (93% under 4 Mb) is indicative of a within breed relatedness dating back to ancient times, despite the absence of management for the mating plans and the reduced population size. In the worldwide context, the Southern Italian, Spanish and Albanian breeds overlapped in a macro cluster which also included the Noticiana sheep. The results highlighted ancestral genetic components of Noticiana shared with Comisana breed, and showed the clear separation from the other Italian sheep. This is likely the consequence of the combined effects of genetic drift, small population size and reproductive isolation. ROH islands and FST-outliers approaches in Noticiana identified genes and QTLs involved in milk and meat production, as well as related to the local adaptation, and therefore are consistent with the phenotypic traits of the studied breed. Although a wider sampling could be useful to deepen the genomic survey on Noticiana, these results represent a crucial starting point for the characterization of an important local genetic resource, with a view of supporting the local economy and preserving the biodiversity of the sheep species.

Alternative Molecular Tools for the Fight against Infectious Diseases of Small Ruminants: Native Sicilian Sheep Breeds and Maedi-Visna Genetic Susceptibility.

Maedi-visna (MV) is a disease caused by small ruminant lentiviruses. It is included in the list of notifiable terrestrial animal diseases due to economic losses and animal welfare harm in the sheep sector. To date, control programs remain the onliest approach to avoiding infection. The allelic variant p.Glu35Lys (E35K) of the TMEM154 gene has been strongly associated with host vulnerability to MV illness. The present study aimed to investigate the association of TMEM154 E35K allele frequencies with MV susceptibility in native Sicilian sheep breeds. More than 400 animals from 14 local sheep were serologically tested and genotyped for the TMEM154 E35K polymorphism. The local breeds displayed different values of MV seroprevalence, with the lowest antibody prevalence in Barbaresca and Pinzirita breeds. TMEM154 protective allele (K35) was less frequent than the risk allele (E35) in Valle del Belìce breed, whereas the other three breeds showed a more balanced alleles distribution. A positive association between seroprevalence and genotype was found in the entire sample set. The risk of infection resulted in more than 3-fold times as high in sheep with EK and EE genotype compared to the KK genotype. Our data could be helpful in establishing selection breeding programs aimed at reducing MV infection in Sicilian sheep farming and encouraging the breeding of native breeds.

A 20-SNP Panel as a Tool for Genetic Authentication and Traceability of Pig Breeds.

Food authentication in local breeds has important implications from both an economic and a qualitative point of view. Meat products from autochthonous breeds are of premium value, but can easily incur fraudulent or accidental substitution or mislabeling. The aim of this study was to identify a small number of SNPs using the Illumina PorcineSNP60 BeadChip for breed traceability, in particular of the Italian Nero Siciliano pig and its derived products. A panel of 12 SNPs was sufficient to discriminate Nero Siciliano pig from cosmopolitan breeds and wild boars. After adding 8 SNPs, the final panel of 20 SNPs allowed us to discriminate all the breeds involved in the study, to correctly assign each individual to its breed, and, moreover, to discriminate Nero Siciliano from first-generation hybrids. Almost all livestock breeds are being genotyped with medium- or high-density SNP panels, providing a large amount of information for many applications. Here, we proposed a method to select a reduced SNP panel to be used for the traceability of pig breeds.

Genome-wide survey on three local horse populations with a focus on runs of homozygosity pattern.

Purosangue Orientale Siciliano, Sanfratellano and Siciliano represent the Sicilian equine genetic resource. This study aimed to investigate the genetic diversity, population structure and the pattern of autozygosity of Sicilian horse populations using genome-wide single-nucleotide polymorphism (SNP) data generated with the Illumina Equine SNP70 array. The genotyping data of 17 European and Middle East populations were also included in the study. The patterns of genetic differentiation, model-based clustering and Neighbour-Net showed the expected positioning of Sicilian populations within the wide analysed framework and the close connections between the Purosangue Orientale Siciliano and the Arab as well as between Sanfratellano, Siciliano and Maremmano. The highest expected heterozygosity (He ) and contemporary effective population size (cNe) were reported in Siciliano (He  = 0.323, cNe = 397), and the lowest were reported in Purosangue Orientale Siciliano (He  = 0.277, cNe = 10). The analysis of the runs of homozygosity and the relative derived inbreeding revealed high internal homogeneity in Purosangue Orientale Siciliano and Arab horses, intermediate values in Maremmano and Sanfratellano and high heterogeneity in the Siciliano population. The genome-wide SNP analysis showed the selective pressure on Purosangue Orientale Siciliano towards traits related to endurance performance. Our results underline the importance of planning adequate conservation and exploitation programmes to reduce the level of inbreeding and, therefore, the loss of genetic diversity.

Feeding System Resizes the Effects of DGAT1 Polymorphism on Milk Traits and Fatty Acids Composition in Modicana Cows.

The interaction between genetic polymorphism and feeding system on milk traits and fatty acid composition was investigated in Modicana cows. Two DGAT1 K232A genotypes (AK and AA) and two feeding regimes, extensive system (EX) with 8 h of grazing without concentrate (EX) and semi-intensive systems (SI) with 2 h of grazing with concentrate, were investigated. DGAT1 genotype did not influence milk yield and composition. The feeding system affected milk composition: protein was significantly higher in SI and lactose in the EX system. A significant genotype × feeding system interaction was observed: the protein and casein levels of AK cows were higher in the SI compared to the EX system. Milk fatty acids profile, total saturated to total unsaturated fatty acids, n-6 to n-3 ratios, and atherogenic index were affected by the feeding system, improving the healthy properties of milk from animals reared in the extensive system. DGAT1 genotype influenced the fatty acid composition: milk from AA cows had a more favorable fatty acid composition due to lower total saturated fatty acids, saturated to unsaturated ratio, atherogenic index, and higher levels of oleic acid and total unsaturated fatty acids. Furthermore, an interaction genotype x feeding system was observed: the AK milk was richer in short-chain FAs (C4:0-C8:0) and C10:0 only in the EX but not in the SI system. Our data suggest that a high amount of green forage in the diet of Modicana cows can resize the effect of the DGAT1 genotype on milk traits and fatty acids composition.

Effect of GH p.L127V Polymorphism and Feeding Systems on Milk Production Traits and Fatty Acid Composition in Modicana Cows.

Growth hormone participates in the regulation of lactation and lipid metabolism. A trial study was conducted to evaluate the effects of genetic polymorphism at GH p.L127V and its interaction with feeding system (extensive, EX; semi-intensive, SI) on milk traits and fatty acids composition in Modicana cows. In the semi-intensive farm (SI) diet consisted of hay, concentrate and 2 h of grazing. In the extensive farm (EX) feeding consisted in 8 h of grazing and hay. The frequencies of LL, LV and VV genotypes were, respectively: 0.64, 0.34, 0.02. GH polymorphism and its interaction with feeding system did not influence milk yield and composition. Cows carrying LL genotype produced milk with lower 6:0 and 8:0 and higher 16:1 c9 and 18:1 c9, total UFA and total MUFA. Feeding significantly affected fatty acids: in EX cows lower SFA and higher PUFA and UFA were found, compared to SI cows. The lower, more favorable atherogenic index of milk from EX system was coherent with the improved healthy characteristics of milk from animals fed almost exclusively on pasture. A significant interaction genotype x feeding system was evident for 18:1, higher in the LL cows only in the EX system, but not in the SI system.

Genome-Wide SNP Analysis Reveals the Population Structure and the Conservation Status of 23 Italian Chicken Breeds.

The genomic variability of local Italian chicken breeds, which were monitored under a conservation plan, was studied using single nucleotide polymorphisms (SNPs) to understand their genetic diversity and population structure. A total of 582 samples from 23 local breeds and four commercial stocks were genotyped using the Affymetrix 600 K Chicken SNP Array. In general, the levels of genetic diversity, investigated through different approaches, were lowest in the local chicken breeds compared to those in the commercial stocks. The level of genomic inbreeding, based on runs of homozygosity (FROH), was markedly different among the breeds and ranged from 0.121 (Valdarnese) to 0.607 (Siciliana). In all breeds, short runs of homozygosity (ROH) (<4 Mb in length) were more frequent than long segments. The patterns of genetic differentiation, model-based clustering, and neighbor networks showed that most breeds formed non-overlapping clusters and were clearly separate populations, which indicated the presence of gene flow, especially among breeds that originated from the same geographical area. Four genomic regions were identified as hotspots of autozygosity (islands) among the breeds, where the candidate genes are involved in morphological traits, such as body weight and feed conversion ratio. We conclude that the investigated breeds have conserved authentic genetic patterns, and these results can improve conservation strategies; moreover, the conservation of local breeds may play an important role in the local economy as a source of high-quality products for consumers.

Casein haplotype diversity in seven dairy goat breeds.

Selection, drift, gene flow and breeding have extensively shaped the genomic variability of domestic animals. In goat species, several mutations identified within the casein genes have been shown to affect the level of gene expression of milk production traits. The four casein genes - CSN1S1, CSN2, CSN1S2 and CSN3 - are organized in a cluster of 250 kb located in chromosome 6, and due to tight linkage, their genetic variability is well depicted by haplotypes which are transmitted to the progeny. Thirty single nucleotide polymorphisms (SNPs) located within the casein gene cluster were used to characterize the haplotype variability of six southern Italian goat breeds (Girgentana, Maltese, Rossa Mediterranea, Argentata dell'Etna, Messinese, Capra dell'Aspromonte). A representative sample of the Norwegian dairy goat breed (Norsk melkegeit) has been used as an out-group to obtain a weighted measure of genetic diversity in the metapopulation. A total of 54 haplotypes were detected among the seven breeds: 26, 9, 8 and 11 haplotypes were found at CSN1S1, CSN2, CSN1S2 and CSN3 respectively. The number of haplotypes per breed was 14 (Norwegian), 26 (Messinese), 27 (Rossa Mediterranea and Girgentana) and 31 (Maltese, Argentata dell'Etna and Capra dell'Aspromonte). The Maltese breed showed the highest number of private haplotypes, whereas the Norwegian goat recorded the highest number of shared haplotypes. The linkage disequilibrium analysis showed higher levels of association for the SNP pairs within casein loci than SNP pairs between casein loci, likely reflecting low levels of intra-genic recombination. The highest linkage disequilibrium values were found in CSN1S1 and CSN2 genes in all the breeds, except for Argentata dell'Etna and Rossa Mediterranea. The resolution of the haplotype diversity at the casein cluster can be exploited both for selective and conservative plans.

New Insights into Chemical and Mineral Composition of Donkey Milk throughout Nine Months of Lactation.

Donkey milk is increasingly being proposed as a natural alternative milk for various categories of consumers, especially infants and the elderly population. However, its potential production, gross, and mineral composition have not been deeply investigated yet. Sixty-two individual milk samples were collected monthly from nine Ragusano donkeys reared in a specialized dairy farm. Milk yield as well as chemical and mineral composition, including macro and micro elements, were investigated over an entire lactation, from the second to the ninth month of milking. Milk yield averaged 1.64 kg/day, which highlights good aptitude of the Ragusano breed for the production of milk. Gross composition was characterized by low content of dry matter (8.19%), a high amount of lactose (6.07%), low protein (1.34%), and very low-fat content (0.16%). Whey proteins represented 58% of the total protein, and proteose-peptones accounted for 0.35 ± 0.07 g per 100 g. Total ash content was 0.36 g per 100 g and represented 4.40% of the dry matter. The most abundant element was K, which was followed by Ca, Na, and P. As expected, the micro elements Fe, Zn, and Cu were found in low amounts or in traces. Dry matter, fat, whey proteins. The total ash, Ca, P, Mg, and mineral ratios were significantly affected by the lactation stage.

Leptin Gene Polymorphism in Goats Fed with Diet at Different Energy Level: Effects on Feed Intake, Milk Traits, Milk Fatty Acids Composition, and Metabolic State.

The study investigated the effects of a polymorphism at the LEP gene intron 1 microsatellite region and its interaction with diet energy level on feed intake, milk traits, milk fatty acid composition, and metabolic state in goats. Sixteen Girgentana lactating goats at mid-lactation, selected on the basis of their genotype (8 goats homozygous 266 bp/266 bp, L genotype; 8 goats heterozygous 266 bp/264 bp, H genotype), were fed ad libitum according to a change-over design, with two diets at different energy levels reached with different hay inclusion: low energy diet (LE)-100% of hay; and high energy diet (HE)-65% of hay. No differences in milk yield and composition or in dry matter intake were found between leptin genotypes or between diets. Leptin genotype had no effect on plasma metabolite concentrations. The differences between diets were recorded for plasma ß-hydroxybutyric acid (BHBA) concentrations with higher (p = 0.01) values for the HE compared to the LE diet (0.44 vs. 0.24 mmol/L, respectively). Nonesterified fatty acid (NEFA) values seem to indicate a positive energy balance in goats. No interaction genotype per diet was evident for most of the studied parameters. Fatty acid composition was strongly influenced by LEP genotype: L goats, compared to H goats, showed higher levels of monounsaturated fatty acids (MUFA), polyunsaturated fatty acids (PUFA), and 14:1/14:0 desaturation index; lower levels of saturated fatty acids (SFA); and a more favorable atherogenic index. These results seem to suggest an improvement of health characteristics of milk with the L genotype.

Polymorphism at donkey ß-lactoglobulin II locus: identification and characterization of a new genetic variant with a very low expression.

In the last years, donkey milk had evidenced a renewed interest as a potential functional food and a breast milk substitute. In this light, the study of the protein composition assumes an important role. In particular, ß-lactoglobulin (ß-LG), which is considered as one of the main allergenic milk protein, in donkey species consists of two molecular forms, namely ß-LG I and ß-LG II. In the present research, a genetic analysis coupled with a proteomic approach showed the presence of a new allele, here named F, which is apparently associated with a null or a severely reduced expression of ß-LG II protein. The new ß-LG II F genetic variant shows a theoretical average mass (Mav) of 18,310.64 Da, a value practically corresponding with that of the variant D (∆mass < 0.07 Da), but differs from ß-LG II D for two amino acid substitutions: Thr100 (variant F) → Ala100 (variant D) and Thr118 (variant F) → Met118 (variant D). Proteomic investigation of the whey protein fraction of an individual milk sample, homozygous FF at ß-LG II locus, allowed to identify, as very minor component, the new ß-LG II F genetic variant. By MS/MS analysis of enzymatic digests, the sequence of the ß-LG II F was characterized, and the predicted genomic data confirmed.

Herbage intake and milk yield in Comisana ewes as effect of 4 vs 7 h of grazing during late lactation.

Thirty-two Comisana ewes at late lactation were used in two trials carried out during late spring in 2 consecutive years, with the aim to evaluate the effect of the duration of grazing on herbage intake and performance. In each trial, 16 pluriparous Comisana lactating ewes were equally divided into two groups which grazed in two separate areas of natural pasture from 11:00 to 15:00 h (group 4H) or from 10:00 to 17:00 (group 7H). A concentrate mixture (500 g/day) was also offered to each ewe. The mean maximum temperature was, respectively, 23.5 ± 3.8 °C during experiment 1 and 27.0 ± 3.1 °C during experiment 2. Probably as a consequence of the differences in climatic conditions, the results on herbage intake and milk production were different during the two trials. Herbage dry matter intake was not affected by the duration of grazing during trial 1, whereas it was significantly lower in 4H group compared to that in 7H group (0.67 vs 1.02 kg/day; P < 0.001) during trial 2. It could be hypothesised that while with lower environmental temperature (trial 1), the 4H ewes were able to reach good intake levels despite grazing during the hottest hours; with higher temperatures throughout the trial (trial 2), the 4H ewes reduced ingestion. Milk production was higher in 4H group during trial 1 (778 vs 707 g/day; P = 0.006), whereas it was not affected by the number of hours of grazing during trial 2, despite the higher intake levels reached by the 7H group. In conclusion, 3 extra hours of grazing for ewes at late lactation on a low quality pasture could be nullified in terms of yield response.

Genetic diversity of Italian goat breeds assessed with a medium-density SNP chip.

BACKGROUND: Among the European countries, Italy counts the largest number of local goat breeds. Thanks to the recent availability of a medium-density SNP (single nucleotide polymorphism) chip for goat, the genetic diversity of Italian goat populations was characterized by genotyping samples from 14 Italian goat breeds that originate from different geographical areas with more than 50 000 SNPs evenly distributed on the genome. RESULTS: Analysis of the genotyping data revealed high levels of genetic polymorphism and an underlying North-south geographic pattern of genetic diversity that was highlighted by both the first dimension of the multi-dimensional scaling plot and the Neighbour network reconstruction. We observed a moderate and weak population structure in Northern and Central-Southern breeds, respectively, with pairwise FST values between breeds ranging from 0.013 to 0.164 and 7.49 % of the total variance assigned to the between-breed level. Only 2.11 % of the variance explained the clustering of breeds into geographical groups (Northern, Central and Southern Italy and Islands). CONCLUSIONS: Our results indicate that the present-day genetic diversity of Italian goat populations was shaped by the combined effects of drift, presence or lack of gene flow and, to some extent, by the consequences of traditional management systems and recent demographic history. Our findings may constitute the starting point for the development of marker-assisted approaches, to better address future breeding and management policies in a species that is particularly relevant for the medium- and long-term sustainability of marginal regions.

Genetic diversity and variability in endangered Pantesco and two other Sicilian donkey breeds assessed by microsatellite markers.

The genetic variability of Pantesco and other two Sicilian autochthonous donkey breeds (Ragusano and Grigio Siciliano) was assessed using a set of 14 microsatellites. The main goals were to describe the current differentiation among the breeds and to provide genetic information useful to safeguard the Pantesco breed as well as to manage Ragusano and Grigio Siciliano. In the whole sample, that included 108 donkeys representative of the three populations, a total of 85 alleles were detected. The mean number of alleles was lower in Pantesco (3.7), than in Grigio Siciliano and Ragusano (4.4 and 5.9, resp.). The three breeds showed a quite low level of gene diversity (He) ranging from 0.471 in Pantesco to 0.589 in Grigio. The overall genetic differentiation index (Fst) was quite high; more than 10% of the diversity was found among breeds. Reynolds' (D(R)) genetic distances, correspondence, and population structure analysis reproduced the same picture, revealing that, (a) Pantesco breed is the most differentiated in the context of the Sicilian indigenous breeds, (b) within Ragusano breed, two well-defined subgroups were observed. This information is worth of further investigation in order to provide suitable data for conservation strategies.

Genetic analysis of Sicilian autochthonous horse breeds using nuclear and mitochondrial DNA markers.

Genetic diversity and relationship among 3 Sicilian horse breeds were investigated using 16 microsatellite markers and a 397-bp length mitochondrial D-loop sequence. The analysis of autosomal DNA was performed on 191 horses (80 Siciliano [SIC], 61 Sanfratellano [SAN], and 50 Sicilian Oriental Purebred [SOP]). SIC and SAN breeds were notably higher in genetic variability than the SOP. Genetic distances and cluster analysis showed a close relationship between SIC and SAN breeds, as expected according to the breeds' history. Sequencing of hypervariable mitochondrial DNA region was performed on a subset of 60 mares (20 for each breed). Overall, 20 haplotypes with 31 polymorphic sites were identified: A higher haplotype diversity was detected in SIC and SAN breeds, with 13 and 11 haplotypes respectively, whereas only one haplotype was found in SOP. These were compared with 118 sequences from GenBank. BLAST showed that 17 of the 20 haplotypes had been reported previously in other breeds. One haplotype, found in SIC, traces back to a Bronze Age archaeological site (Inner Mongolia). The 3 Sicilian breeds are now rare, and 2 of them are officially endangered. Our results represent a valuable tool for management strategies as well as for conservation purposes.

Molecular characterization and genetic structure of the Nero Siciliano pig breed.

Nero Siciliano is an autochthonous pig breed that is reared mainly in semi-extensive systems in northeastern Sicily. Despite its economic importance and well-appreciated meat products, this breed is currently endangered. Consequently, an analysis of intra-breed variability is a fundamental step in preserving this genetic resource and its breeding system. In this work, we used 25 microsatellite markers to examine the genetic composition of 147 unrelated Nero Siciliano pigs. The total number of alleles detected (249, 9.96 per locus) and the expected heterozygosity (0.708) indicated that this breed had a high level of genetic variability. Bayesian cluster analysis showed that the most likely number of groups into which the sample could be partitioned was nine. Based on the proportion of each individuals genome derived from ancestry, pigs with at least 70% of their genome belonging to one cluster were assigned to that cluster. The cluster size ranged from 7 to 17 (n = 108). Genetic variability in this sub-population was slightly lower than in the whole sample, genetic differentiation among clusters was moderate (F(ST) 0.125) and the F(IS) value was 0.011. NeighborNet and correspondence analysis revealed two clusters as the most divergent. Molecular coancestry analysis confirmed the good within-breed variability and highlighted the clusters that retained the highest genetic diversity.