Piera Di Lorenzo

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.

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.

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.

Genetic diversity in four populations of Nguni (Zulu) sheep assessed by microsatellite analysis

Zulu sheep are found mainly in the rural KwaZulu-Natal province and the numbers are declining due to indiscriminate inbreeding. There is thus a need for phenotypic and genetic characterisation as a first phase for planning conservation strategies. Zulu sheep populations sampled were from Makhathini research station (MS) (n=33), University of Zululand (UZ) (n=21), a community at KwaMthethwa (KM) (n=32) and from Msinga (EM) (n=33). One European breed Appenninica (AP) was used as out group. Microsatellite analysis using 29 microsatellite loci was used in this study. Among the Zulu sheep, the mean number of alleles per locus was the lowest (3.86) in UZ and the highest (6.24) was realised in EM. The mean values of observed and expected heterozygosity were 0.57 and 0.61, respectively. Neighbour-joining tree showed two main Zulu sheep clusters: the UZ, KM and MS sheep populations clustered together and the second cluster included only representatives from the EM population. The STRUCTURE analysis showed that KM, AP and EM were founded in separate clusters, whereas UZ and MS clustered together. The study demonstrated that there was a common origin of the population from the research stations (MS and UZ populations). It also demonstrated that the EM had a different history for the other three populations. This work suggests that exchange of rams could be useful in reducing inbreeding when considering conservation breeding programmes.

Genetic differentiation between Segugio dell'Appennino and Segugio Maremmano dog breeds assessed by microsatellite markers

The domestic dog (Canis Familiaris) was the first species to be tamed and bred to occupy a variety of functions. The Segugio dell’Appennino and Segugio Maremmano are two Italian breeds used extensively as hunting dogs. Microsatellites and other genetic markers are useful tools in evaluating the within and between breed genetic variation. The aim of this study was to investigate genetic differentiation among the two breeds through the analysis of 21 microsatellite markers. The two populations share the same geographical regions but have been over time selected on different parameters to achieve specific functions. All the analysed microsatellite markers were polymorphic and the average number of alleles per locus was 8.19. The mean FIT index (0.051; P<0.05) highlights that at some point in time, the normal gene flow among the animals was disrupted, giving rise to a heterozygote deficiency in both breeds, and this is confirmed by the mean FST fixation index (0.010; P<0.05) clearly indicating an absence of a significant genetic differentiation between the two breeds. The mean FIS value was significantly different from zero (0.042) (P<0.05) reconfirming the presence of a lack of heterozygosity in the studied samples. The values of observed and expected heterozygosity were similar in the two breeds. AMOVA, PCA and STRUCTURE analysis, all emphasise the lack of significant differences among the two breeds in terms of genetic differentiation. The presence of a population substructure is probably due to a genetic introgression from different Segugio breeds, that can be confirmed with further studies.

Mitochondrial DNA variants of Podolian cattle breeds testify for a dual maternal origin

Background Over the past 15 years, 300 out of 6000 breeds of all farm animal species identified by the Food and Agriculture Organization of the United Nations (FAO) have gone extinct. Among cattle, many Podolian breeds are seriously endangered in various European areas. Podolian cattle include a group of very ancient European breeds, phenotypically close to the aurochs ancestors (Bos primigenius). The aim of the present study was to assess the genetic diversity of Podolian breeds and to reconstruct their origin. Methodology The mitochondrial DNA (mtDNA) control-regions of 18 Podolian breeds have been phylogenetically assessed. Nine non-Podolian breeds have been also included for comparison. Conclusion The overall analysis clearly highlights some peculiarities in the mtDNA gene pool of some Podolian breeds. In particular, a principal component analysis point to a genetic proximity between five breeds (Chianina, Marchigiana, Maremmana, Podolica Italiana and Romagnola) reared in Central Italy and the Turkish Grey. We here propose the suggestive hypothesis of a dual ancestral contribution to the present gene pool of Podolian breeds, one deriving from Eastern European cattle; the other arising from the arrival of Middle Eastern cattle into Central Italy through a different route, perhaps by sea, ferried by Etruscan boats. The historical migration of Podolian cattle from North Eastern Europe towards Italy has not cancelled the mtDNA footprints of this previous ancient migration.

Morphological and genetic characterisation of Pagliarola breed and its genetic relationships with other three indigenous Italian sheep breeds

Abstract Sheep are an important livestock species in the socio-economic contest around the world. In the past, exotic sheep breeds were utilised in crosses with local breeds in order to improve their production traits. The Pagliarola is an ancient sheep population spread over many areas of the central Italy, mainly in Abruzzo region. The aim of this paper was to identify this breed from other sheep breeds living in the same area trough morphological and genetic characterisation. Fifty-three Pagliarola sheep animals (two flocks) were sampled together with 30 sheep of Appenninica, Gentile di Puglia and Merinizzata Italiana. Biometrical measures and 25 microsatellite markers were studied for the characterisation. In the morphological analysis, the Pagliarola was observed to be well separated from the other breeds and the genomic results confirmed the morphological study. In the molecular approach, a total of 330 alleles were detected. In the neighbour-Net tree, each breed clustered independently and no clear cluster was observed. The expected heterozygosity was the highest in Appenninica (0.78), while Pagliarola had the lowest (0.70). Results of STRUCTURE analyses at K=5 showed Pagliarola breed splitted in two sub-clusters. Both biometric and molecular results allow to consider the residual Pagliarola as an original genotype. Moreover, the variability still remaining in this population can be useful to plan suitable conservation programs.

Comparison of four Italian beef cattle breeds by means of functional genes

Piemontese, Chianina, Marchigiana and Romagnola are the main Italian beef breeds, and the quality of their products is largely recognised all over the world. Here, 18 single nucleotide polymorphisms (SNPs) in 12 candidate genes involved on meat traits were investigated on 1055 candidates for selection in order to analyse the within- and between-breed variability with a functional marker approach. Three SNPs (GDF8-3, GH and NPY-3) were monomorphic and most of the polymorphic SNPs showed an allele distribution quite similar in the four breeds. High variability at LEP-2, LEP-3 and LEPR markers was detected across breeds and the analysis of the relationship between genetic differentiation and heterozygosity indicated significant deviation from a neutral-equilibrium model for LEP-2. The highest pairwise fixation index values (0.1189 to 0.1877) were obtained for the comparisons of Piemontese with the other breeds, while the lowest value (0.0296) was observed in Chianina and Marchigiana. The Piemontese differentiation from the other breeds could be due to its geographical isolation and selection targets. The results for breed assignment follows the genetic differentiation, in fact, Piemontese had the highest percentage of correct assignment (87.6), while Marchigiana had the lowest (47.5). These findings suggest that functional markers can be more suitable than neutral markers in discriminating breeds similar in morphology if selection plays some role in their differentiation.