Francesca Maria Sarti

Phylogenetic Relationships of Three Italian Merino-Derived Sheep Breeds Evaluated through a Complete Mitogenome Analysis

In Italy, the crisis of the wool industry triggered the necessity to reconvert the two traditional Merino-derived breeds, Gentile di Puglia and Sopravissana, to meat production, by creating the Merinizzata Italiana. The aim of the present study was to assess the genetic diversity of these three Italian Merino-derived (IMd) breeds by examining the molecular information encoded in the maternally-inherited mitochondrial DNA (mtDNA). A parallel molecular investigation was performed on the putative paternal and maternal breeds, the Merino from Spain and the Appenninica from Italy, respectively, as well as on three unrelated dairy breeds (Sarda and Comisana from Italy, and Lacaune from France). Firstly, the mtDNA control region of 291 samples was analyzed. When comparing the overall genetic distances among the eight stocks, the three IMd breeds clustered together close to the Appenninica, thus confirming its parental role. Among the 90 IMd samples, 82 different haplotypes were observed, almost all belonging to haplogroup B, and only one to A. For 23 mtDNAs, including nine IMd, the analysis was then brought to the level of entire mitogenomes. Three distinct sub-haplogroups within B were found to encompass the IMd samples, with one clade (B1a2a1) apparently restricted to those sheep. Thus, despite experiencing a drastic reduction in number (mainly due to changes in breeding practices driven by the economy), the IMd breeds still represent a reservoir of distinctive mitochondrial variants, which could potentially contribute to the development of conservation and management programs of Italian sheep breeds.

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.

Phylogeny, genetic relationships and population structure of five Italian local chicken breeds

Number and population size of local chicken breeds in Italy is considered to be critical. Molecular data can be used to provide reliable insight into the diversity of chicken breeds. The first aim of this study was to investigate the maternal genetic origin of five Italian local chicken breeds (Ancona, Livorno, Modenese, Romagnola and Valdarnese bianca) based on mitochondrial DNA (mtDNA) information. Secondly, the extent of the genetic diversity, population structure and the genetic relationships among these chicken populations, by using 27 microsatellite markers, were assessed. To achieve these targets, a 506 bp fragment of the D-loop region was sequenced in 50 chickens of the five breeds. Eighteen variable sites were observed which defined 12 haplotypes. They were assigned to three clades and two maternal lineages. Results indicated that 90% of the haplotypes are related to clade E, which has been described to originate from the Indian subcontinent. For the microsatellite analysis, 137 individual blood samples from the five Italian breeds were included. A total of 147 alleles were detected at 27 microsatellite loci. The five Italian breeds showed a slightly higher degree of inbreeding (FIS=0.08) than the commercial populations that served as reference. Structure analysis showed a separation of the Italian breeds from the reference populations. A further sub-clustering allowed discriminating among the five different Italian breeds. This research provides insight into population structure, relatedness and variability of the five studied breeds.

The measurement of chest girth as an alternative to weight determination in the performance recording of meat sheep

Abstract The aim of this study was to assess, for two Italian meat sheep breeds (Appenninica and Merinizzata italiana), the relationship between an easily recorded measurement (girth of chest) and the character used for selection purposes (weight), and to define the most appropriate mathematical methods to infer the second from the first. For the Appenninica 1392 lambs were measured, for the Merinizzata italiana 1559 lambs were measured. The possibility of estimating weight through chest girth (CG) measurement was evaluated, separately for each breed, by taking the most suitable model between those including different kinds of regression effect. The model was chosen in relation to the value of the determination coefficient and the sum of square residuals. The prediction accuracy of the model was assessed by comparing the expected values with the observed ones through a number of statistical tests. A further prediction analysis was carried out using the mean values of the observed weights that fell in each 1 cm class of girth, in order to reduce the error derived by the varying numbers of observations per unit of chest girth. The model including the square regression nested within the sex effect and the flock random effect nested within the sex effect was observed to be the most suitable one to predict the weight from the chest girth; the determination coefficients ranged between 0.944 (Appenninica) and 0.955 (Merinizzata). The prediction parameters were: -10.458+ 0.241 (CG) + 0.004 (CG2) for the Appenninica males; -6.121 + 0.093 (CG) + 0.005 (CG2) for the Appenninica females; -6.325 + 0.189 (CG) + 0.004 (CG2) for the Merinizzata males; -4.676 + 0.078 (CG) + 0.005 (CG2) for the Merinizzata females. The correlation between the observed and expected values was always higher than 0.97. The equations estimated using the mean weights for each girth showed extremely high determination coefficients (≅ 0.99) due to the reduction of variability implied by this method. Choosing between the equations calculated on the entire data set or on the mean weights will only be possible after a period of field tests.

Gene Expression of Hepatic Glucocorticoid Receptor NR3C1 and Correlation with Plasmatic Corticosterone in Italian Chickens

This study examined breed-specific stress-related hormonal and gene expression profiles in three Italian chicken breeds (Valdarnese Bianca, Bionda Piemontese, Robusta Maculata) reared in controlled conditions. Glucocorticoids work through the glucocorticoid receptor (GR), which modulates target genes transcription. We investigated breed-specific changes in corticosterone (ELISA) and GR expression. GR mRNA levels were analyzed using one-tube, two-temperature real-time PCR for absolute quantification of the gene expression by the standard curve method. Our results show high expression of GR in hepatic tissue. Significant effect of the breed was recorded for plasma corticosterone concentration: Valdarnese Bianca 3.35 ng/mL, Bionda Piemontese 1.73 ng/mL, Robusta Maculata 2.02 ng/mL. Breed specific gene expression has been recorded with a GR ranging from 1.12E+04 (Robusta Maculata) to 1.00E+05 (Bionda Piemontese) mRNA copy number/100 ng total RNA. Negative correlation was found between gene expression and blood corticosterone level.

A microsatellites-based survey on the genetic structure of two Italian local chicken breeds

The biodiversity safeguard is an important goal of poultry production in every developed country. Nowadays, the high chicken meat demand from the world market has been leading to a large spread of strongly producing commercial chicken lines. The creation of these standard types is causing a progressive loss of genetic variability. Ancona and Livorno are two Italian autochthonous chicken breeds which represent a great resource in terms of specific genetic richness. Aim of this study is to investigate the genetic diversity of these breeds as potential valuable genetic variability source. In fact, in spite of their endangered status, these chicken breeds are very appreciated for their ability to adapt themselves to extensive organic rearing systems. Blood samples from 131 individuals were collected and genotyped through a thirty microsatellitesbased analysis. All the observed descriptive statistical indexes suggested a heterozygosity deficiency and an inbreeding level (mean observed heterozygosity = 0.46, mean expected heterozygosity = 0.53, Fis in Ancona and Livorno = 0.251 and 0.086). The tree from inter-individual DAS distance using Neighbour-Joining algorithm and the FCA analysis showed a higher internal variability in Livorno than in Ancona. STRUCTURE analysis showed the genetic uniqueness of the breeds and the presence of sub-groups in Ancona originating from a possible genetic isolation. This research could be a suitable starting point to set up improved selection schemes and a potential preliminary genotypic test for all the cocks to be used in the selection.

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.

The Hypertrophic Marchigiana: physical and biochemical parameters for meat quality evaluation

Abstract The aim of this study was to evaluate the meat quality of double muscled Marchigiana young bulls characterized by different genotypes for the hypertrophy: normal and mutated (heterozygous). Calpain and calpastatin activities were determined to verify the state of aging meat on a sample of Longissimus thoracis muscle (XIII thoracic rib) taken at slaughtering (0h) and after 24 hours (24h). After 14 days of aging, another sample of muscle was taken to evaluate physical and chemical parameters of meat quality. The results showed a better meat quality of mutated animals respect normal animals. Another interesting result was the correlation between the biochemical parameters and some physical parameters, such as WBS (Warner Bratzler Shear Force), CL (Cooking loss). These results showed the relationship between the proteolytic activity of calpain system and meat tenderness.

Wool quality in Gentile di Puglia sheep breed as measure of genetic integrity

Abstract The Gentile di Puglia is a breed created in the 15th century by crossing Merino Spanish rams and “gentile” ewes reared in some areas of Southern Italy, mainly Apulia and Basilicata. The crisis of the wool industry, the poor quantity of milk, the inadequacy of Gentile di Puglia to be milked by machine and the passage from transhumant to permanent rearing caused a dramatic reduction of this population, which was largely crossed with other breeds and declined from about one million heads in the sixties to 5,000 at the present time. In order to save the ancient typical Gentile di Puglia breed, the aim of this work was to estimate the “genetic integrity” of the remaining Gentile di Puglia population by means of an analysis of wool quality measured through the diameter of the fibre and the homogeneity of the fleece. Our hypothesis was that the animals originated from outcrosses to other Merino derived breeds specialised for meat would show larger diameters of the fibres and a reduced homogeneity of the fleece. The research was carried out using Herd Book registered animals from 9 farms: 1 from Isernia, 2 from Campobasso and 6 from Foggia province. The statistical analysis on the diameter of the fibre was carried out on a dataset of 38,200 observations (200 records x 191 animals) divided in four classes (ultrafine, fine, croisè, ordinary). The high frequencies of ultrafine and fine fibre classes show that the quality of the wool is still good in the population. This consideration can be extended to all the farms involved in the study that could therefore be suitable in the conservation programs for this breed. The homogeneity of the fleece was also good in providing further evidence of the genetic integrity of the population. Other analysis carried out on the quality of the wool in relation to the body size confirmed that the observed Gentile di Puglia is well representative of the ancient breed.

Suitability of linear scoring in meat sheep: the practical case of Merinizzata Italiana breed

Linear scoring is widely applied in domestic animal species, mainly in cattle and horses. There are only few cases of linear scoring in sheep, probably because the small body size and the narrow range of the classes make difficult to correctly evaluate the measures. In this paper the results of a linear scoring test carried out on Merinizzata Italiana sheep breed in order to verify the feasibility of this method in sheep, are reported. Twenty untrained people, with three different levels of scoring experience in meat sheep morphology, evaluated 52 pluriparous ewes for body length, chest circumference, chest width, rump height, rump width, and withers height; to check for misclassification, their scores were compared with a reference score, previously obtained measuring the same animals by the suitable tools (measuring tape and a Lydtin stick). The percentage of correct scoring ranged from 44.4% for body length to 61.8% for withers height, and was not affected by the experience of the judge. In all characters, the distance of the class from the trait mean had a significant effect in increasing the intensity of misclassifications; the judge’s experience showed a positive effect in reducing the intensity of the misclassification for body length, that was the hardest trait to score. These results encourage to further verifying in practice the linear scoring in the Merinizzata Italiana sheep and in other meat breeds.