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.

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 percent 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.

Diet selection and milk production and composition in Girgentana goats with different alpha s1-casein genotype.

In goats, alpha s1-casein polymorphism is related to different rates of protein synthesis. Two genetic variants, A and F, have been identified as strong and weak alleles based on a production of 3.5 and 0.45 g/l of alpha s1-casein per allele. The aim of the trial was to test whether goats can select their diet as a function of their genetic aptitude to produce milk at different casein levels and whether this selection can influence milk production or composition. Two groups of 8 animals, homozygous for strong (AA) or weak (FF) alleles were housed in individual pens. Using a manger subdivided into five separate containers, the goats were offered daily for 3 weeks: 1.5 kg of alfalfa pelleted hay, 0.7 kg of whole barley, 0.7 kg of whole maize, 0.7 kg of whole faba bean and 0.7 kg of pelleted sunflower cake. Total dry matter intake was similar between groups and resulted in nutrient inputs much higher than requirements. On average, goats selected 86% of maize plus barley and only 46% of faba bean plus sunflower. Indeed, AA goats selected less faba bean compared with FF goats (37.2 v. 56.7% of the available amount; P=0.01); during week 2 and week 3 they significantly increased maize selection (respectively for week 2 and week 3: 94.9 and 99.1% v. 85.3 and 87.3%) thus increasing the ratio between the high-energy feeds and the high-protein feeds (2.41 v. 1.81, P=0.023). As for true protein, the high soluble fraction (B1) and the indigestible fraction (C) were lower in the diet selected by AA goats (respectively in AA and FF groups: B1, 7.85 v. 9.23% CP, P<0.01; C, 6.07 v. 6.30% CP, P<0.001); these diet characteristics can be associated with lower losses of protein. Milk production, being similar in AA and FF groups when goats were fed with a mixed diet, significantly increased in AA group, when free-choice feeding was given (mean productions: 1198 v. 800 g/d, P<0.01). Casein content was higher in AA group than in FF group (2.70 v. 2.40%, P<0.01) whereas milk urea was higher in FF group (59.7 v. 48.8 mg/dl, P<0.01). In conclusion, when the animals were free to select their diet, their higher genetic aptitude to produce casein seemed to adjust their energy and protein dietary input in qualitative terms, thus leading to an increase in milk production and a decrease in milk urea. These results seem to demonstrate that interactions probably occurred between genetic polymorphism at the alpha s1-casein locus, diet selection and the efficiency of nutrient transformation into milk.