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Focusing on the late Miocene succession stratigraphic successions including the evaporite deposits from the Messinian salinity crisis (MSC) of the Adriatic foreland basin, a revision of available boreholes and seismic data allowed us to recognize the presence of reservoirs and seals systems that can be considered of potential interest for the storage of natural and synthetic gas. Potentially good reservoir sites can be found where porous rocks referable to siliciclastic turbiditites (Marnoso‐arenacea and Laga Fms) or shallow‐water carbonates (Bolognano Fm) preferentially involved in anticlinal structures and covered by thick MSC evaporites, which may represent effective reservoir seals. The integrated reconstruction of porous rocks distribution and facies, thickness, and lateral continuity of the overlying evaporites, allows the identification and zonation of geological settings in the Adriatic foredeep, backbulge and foreland with peculiar stratigraphy and deformations, only partially considered before, that may deserve consideration in the research of potential gas storage sites. [ABSTRACT FROM AUTHOR]

The paleosalinity of water from which the gypsum precipitated during the Messinian salinity crisis is a controversial issue. Recent microthermometry studies on primary fluid inclusions in gypsum provided very low salinity values not compatible with precipitation from seawater, and suggested strong mixing between seawater and nonmarine waters enriched in calcium sulfate. We applied a new microthermometric protocol on gypsum crystals from nine Mediterranean sections that were experimentally stretched to measure a larger population of fluid inclusions. The results show salinities ranging from 9 to 238 wt? NaCl equivalent, largely falling within the evaporation path of normal seawater. The data from previous studies were obtained mostly from those fluid inclusions capable of nucleating a stable bubble after a weak stretching, which probably correspond to those having a lower salinity acquired through post-depositional crack-and-seal processes. Our data suggest instead that the primary gypsum precipitated from a marine brine, later modified by post-trapping processes during tectonics and exhumation. [ABSTRACT FROM AUTHOR]

In this study, we aimed to characterise the genetic diversity of Italian pigeon breeds and describe the relationships among them and other European lineages, conjecturing which processes have led to actual breeds. We analysed the eight most diffused Italian pigeon breeds in addition to 11 foreign lineages that could have shared common ancestors or have been used in the creation of the Italian breeds. We analysed 12 autosomal microsatellite loci in 427 samples collected from 19 breeds belonging to six main groups of domestic pigeons (tumblers and highflyers, structure, owls, wattle, utility and hen). Genetic variability did not differ considerably among breeds, with an average observed heterozygosity (HO) of 0.550 ± 0.072 (max = 0.661 in breed Sottobanca; min = 0.411 in breed Frillback). The 21.34% of total genetic variation found was partitioned among breeds. Italian pigeon breeds were assigned coherently to their respective groups of origin. The analysis supports the origin of homing pigeons from English Carrier and the existence of a close relationship between Old Dutch Capuchine and Italian Owl. Despite the differences in body size, pigeons of the breeds belonging to the hen group are genetically very similar. The sub-populations recognised by breeders inside Italian Owl and Triganino are not genetically supported and their identification as new breeds ought not to be yet proposed, although they are morphologically distinguishable. Consequently, it could also be discussed how the genetic characterisation of domestic lineages could give useful information in breeding and selection processes. [ABSTRACT FROM AUTHOR]

Derives the expressed sequence tags (EST) from porcine skeletal muscle by somatic cell hybrid analysis. Presence of the three'-untranslated region in the EST sequences selected for mapping; Comparison of the observed localization with the locations predicted from heterologous chromosome painting data; Establishment of EST from clones in a porcine skeletal muscle cDNA library.

Donkeys (Equus asinus) have been used extensively in agriculture and transportations since their domestication, ca. 5000-7000 years ago, but the increased mechanization of the last century has largely spoiled their role as burden animals, particularly in developed countries. Consequently, donkey breeds and population sizes have been declining for decades, and the diversity contributed by autochthonous gene pools has been eroded. Here, we examined coding-region data extracted from 164 complete mitogenomes and 1392 donkey mitochondrial DNA (mtDNA) control-region sequences to (i) assess worldwide diversity, (ii) evaluate geographical patterns of variation, and (iii) provide a new nomenclature of mtDNA haplogroups. The topology of the Maximum Parsimony tree confirmed the two previously identified major clades, i.e. Clades 1 and 2, but also highlighted the occurrence of a deep-diverging lineage within Clade 2 that left a marginal trace in modern donkeys. Thanks to the identification of stable and highly diagnostic coding-region mutational motifs, the two lineages were renamed as haplogroup A and haplogroup B, respectively, to harmonize clade nomenclature with the standard currently adopted for other livestock species. Control-region diversity and population expansion metrics varied considerably between geographical areas but confirmed North-eastern Africa as the likely domestication center. The patterns of geographical distribution of variation analyzed through phylogenetic networks and AMOVA confirmed the co-occurrence of both haplogroups in all sampled populations, while differences at the regional level point to the joint effects of demography, past human migrations and trade following the spread of donkeys out of the domestication center. Despite the strong decline that donkey populations have undergone for decades in many areas of the world, the sizeable mtDNA variability we scored, and the possible identification of a new early radiating lineage further stress the need for an extensive and large-scale characterization of donkey nuclear genome diversity to identify hotspots of variation and aid the conservation of local breeds worldwide., Competing Interests: The authors have declared that no competing interests exist., (Copyright: © 2024 Migliore et al. This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.)

With more than 150 recognized breeds, donkeys assume relevant economic importance, especially in developing countries. Even if the estimated number of heads worldwide is 53M, this species received less attention than other livestock species. Italy has traditionally been considered one of the cradles of European donkey breeding, and despite a considerable loss of biodiversity, today still counts nine autochthonous populations. A total of 220 animals belonging to nine different populations were genotyped using the double-digest restriction site associated DNA (ddRAD) sequencing to investigate the pattern of diversity using a multi-technique approach. A total of 418,602,730 reads were generated and successfully demultiplexed to obtain a medium-density SNP genotypes panel with about 27K markers. The diversity indices showed moderate levels of variability. The genetic distances and relationships, largely agree with the breeding history of the donkey populations under investigation. The results highlighted the separation of populations based on their genetic origin or geographical proximity between breeding areas, showed low to moderate levels of admixture, and indicated a clear genetic difference in some cases. For some breeds, the results also validate the success of proper management conservation plans. Identified runs of homozygosity islands, mapped within genomic regions related to immune response and local adaptation, are consistent with the characteristics of the species known for its rusticity and adaptability. This study is the first exhaustive genome-wide analysis of the diversity of Italian donkey populations. The results emphasized the high informativeness of genome-wide markers retrieved through the ddRAD approach. The findings take on great significance in designing and implementing conservation strategies. Standardized genotype arrays for donkey species would make it possible to combine worldwide datasets to provide further insights into the evolution of the genomic structure and origin of this important genetic resource., (© The Author(s) 2024. Published by Oxford University Press on behalf of the American Society of Animal Science.)

Livestock guardian (LGD) and herding shepherd (HSD) dogs have distinct morphological and behavioural characteristics, long selected by farmers and breeders, to accomplish different tasks. This study aimed to find the genomic regions that best differentiate and characterise Italian LGD and HSD. Genomic data of 158 dogs of four LGD and five HSD breeds, obtained with the 170K canine SNPchip, were collected. The two groups were compared using F ST and XP-EHH analyses, identifying regions containing 29 genes. Moreover, 16 islands of runs of homozygosity were found in LGD, and 15 in HSD; 4 of them were partially shared. Among the genes found that better differentiated HSD and LGD, several were associated with dog domestication and behavioural aspects; particularly, MSRB3 and LLPH were linked to herding behaviour in previous studies. Others, DYSK , MAP2K5 , and RYR , were related to body size and muscle development. Prick ears prevailed in sampled HSD, and drop ears in LGD; this explains the identification of WIF1 and MSRB3 genes. Unexpectedly, a number of genes were also associated with eye development and functionality. These results shed further light on the differences that human selection introduced in dogs aimed at different duties, even in a limited geographic area such as Italy.

In the course of evolution, pecorans (i.e., higher ruminants) developed a remarkable diversity of osseous cranial appendages, collectively referred to as "headgear," which likely share the same origin and genetic basis. However, the nature and function of the genetic determinants underlying their number and position remain elusive. Jacob and other rare populations of sheep and goats are characterized by polyceraty, the presence of more than two horns. Here, we characterize distinct POLYCERATE alleles in each species, both associated with defective HOXD1 function. We show that haploinsufficiency at this locus results in the splitting of horn bud primordia, likely following the abnormal extension of an initial morphogenetic field. These results highlight the key role played by this gene in headgear patterning and illustrate the evolutionary co-option of a gene involved in the early development of bilateria to properly fix the position and number of these distinctive organs of Bovidae., (© The Author(s) 2021. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.)

Columba livia is a wild bird whose domestication has led to a large number of pigeon breeds. The occasional loss or straying of domestic birds determined the origin of feral pigeons, which are now widespread all around the world. In this study, we assumed that the main contribution to feral populations is provided by domestic breeds reared in the same areas. We tested this hypothesis by analysing the variability of 12 microsatellite loci in nine Italian feral populations sampled in areas with different intensities of breeding and selecting domestic breeds. We included in the analysis samples belonging to ten domestic lineages commonly bred in Italy. The pattern of geographic differentiation of feral populations turned out to be rather complex and only partially explained by the geographic distance between populations. This pattern can be understood only when the domestic breeds were included in the analysis. In particular, feral populations located in regions with a long-lasting tradition of pigeon breeding showed a high level of admixture with domestic breeds, in particular with Racing Homer and Piacentino. Ferals from Bolzano, Venice and Sassari were characterized by unique genetic components, mostly not shared by other feral populations and by the considered domestic breeds. Our results further emphasize the complex genetic structure of feral populations whose origin can be properly investigated by taking into account the pool of domestic pigeons bred in the considered area., (Copyright © 2020 Elsevier GmbH. All rights reserved.)

According to recent archeological evidence, turkey (Meleagris gallopavo gallopavo) domestication may have occurred in Mexico around 2000 years ago. However, little is known about the phylogenetic and genealogical background underlying domestic turkey populations. This study aimed to further understand the domestication process and identify inter- or intraspecific connections between turkey populations to determine their origins, trace their global expansion, and define the species' genetic value. Ninety-three domestic turkeys (local breeds) were sampled from populations in Brazil, Mexico, USA, Spain, Italy, Iran, and Egypt. Publicly available sequences from previous studies were also included. Standard mitochondrial DNA, genetic diversity, and haplotype network analyses were performed. Seventy-six polymorphic sites were identified. Turkeys from Mexico showed the greatest number of polymorphic sites (40), while turkeys from Italy and Brazil reported only one site each. Nucleotide diversity was also highest in Mexico and the USA (π = 0.0175 and 0.0102, respectively) and lowest in Brazil and Italy. Of the six major haplogroups defined, the Mexican and USA populations appeared to have remained more stable and diverse than the other populations. This may be due to conservative husbandry policies in the rural areas of other populations, which have prevented the introduction of commercial turkey lines.

Through thousands of years of breeding and strong human selection, the dog ( Canis lupus familiaris ) exists today within hundreds of closed populations throughout the world, each with defined phenotypes. A singular geographic region with broad diversity in dog breeds presents an interesting opportunity to observe potential mechanisms of breed formation. Italy claims 14 internationally recognized dog breeds, with numerous additional local varieties. To determine the relationship among Italian dog populations, we integrated genetic data from 263 dogs representing 23 closed dog populations from Italy, seven Apennine gray wolves, and an established dataset of 161 globally recognized dog breeds, applying multiple genetic methods to characterize the modes by which breeds are formed within a single geographic region. Our consideration of each of five genetic analyses reveals a series of development events that mirror historical modes of breed formation, but with variations unique to the codevelopment of early dog and human populations. Using 142,840 genome-wide SNPs and a dataset of 1,609 canines, representing 182 breeds and 16 wild canids, we identified breed development routes for the Italian breeds that included divergence from common populations for a specific purpose, admixture of regional stock with that from other regions, and isolated selection of local stock with specific attributes.

Hybridization and introgression can impact the evolution of natural populations. Several wild canid species hybridize in nature, sometimes originating new taxa. However, hybridization with free-ranging dogs is threatening the genetic integrity of grey wolf populations (Canis lupus), or even the survival of endangered species (e.g., the Ethiopian wolf C. simensis). Efficient molecular tools to assess hybridization rates are essential in wolf conservation strategies. We evaluated the power of biparental and uniparental markers (39 autosomal and 4 Y-linked microsatellites, a melanistic deletion at the β-defensin CBD103 gene, the hypervariable domain of the mtDNA control-region) to identify the multilocus admixture patterns in wolf x dog hybrids. We used empirical data from 2 hybrid groups with different histories: 30 presumptive natural hybrids from Italy and 73 Czechoslovakian wolfdogs of known hybrid origin, as well as simulated data. We assessed the efficiency of various marker combinations and reference samples in admixture analyses using 69 dogs of different breeds and 99 wolves from Italy, Balkans and Carpathian Mountains. Results confirmed the occurrence of hybrids in Italy, some of them showing anomalous phenotypic traits and exogenous mtDNA or Y-chromosome introgression. Hybridization was mostly attributable to village dogs and not strictly patrilineal. The melanistic β-defensin deletion was found only in Italian dogs and in putative hybrids. The 24 most divergent microsatellites (largest wolf-dog FST values) were equally or more informative than the entire panel of 39 loci. A smaller panel of 12 microsatellites increased risks to identify false admixed individuals. The frequency of F1 and F2 was lower than backcrosses or introgressed individuals, suggesting hybridization already occurred some generations in the past, during early phases of wolf expansion from their historical core areas. Empirical and simulated data indicated the identification of the past generation backcrosses is always uncertain, and a larger number of ancestry-informative markers is needed.

Catria is 1 of the 22 native Italian horse breeds that now survive from a larger number. Thirty individuals, representative of the Catria horse, were analyzed for 11 microsatellites and compared with data of 10 breeds reared in Italy. Three different approaches, genetic distances, correspondence analysis, and clustering methods, were considered to study genetic relationships among Catria and the other horse populations. Genetic differentiation among breeds was highly significant (P < 0.01) for all loci. Average F(ST) values indicate that around 10% of the total genetic variation was explained by the between-breed differences and the 3 approaches utilized gave similar results. Italian native breeds are clearly separated from the other examined breeds. However, by the correspondence analysis, the Catria appears closer to Maremmano and Murgese. The results of Bayesian approaches give further information showing for Catria a common origin with Maremmano and Italian Heavy Draught. Genetic relationships among Catria and the other breeds are consistent with the breed's documented history. The data and information found here can be utilized in the organization of conservation programmes planned to reduce inbreeding and to minimize loss of genetic variability.

The GENETPIG database has been established for storing and disseminating the results of the European project: 'GENETPIG: identification of genes controlling economic traits in pig'. The partners of this project have mapped about 630 porcine and human ESTs onto the pig genome. The database collects the mapping results and links them to other sources of mapping data; this includes pig maps as well as available comparative mapping information. Functional annotation of the mapped ESTs is also given when a significant similarity to cognate genes was established. The database is accessible for consultation via the Internet at http://www.infobiogen.fr/services/Genetpig/.

Porcine skeletal muscle genes play a major role in determining muscle growth and meat quality. Therefore, to progress towards a better understanding of the genetic factors influencing these traits, the first step is to characterize the genes expressed in skeletal muscle tissue in pig. To this aim, we constructed a porcine biceps femoris muscle cDNA library and sequenced 111 randomly isolated clones. By FASTA analysis, we identified 72 unique clones: 47 showed homology to previously identified genes in human or other mammals, 20 matched uncharacterized expressed sequence tags (ESTs), two showed no significant matches to sequences already present in DNA databases, and three other clones containing only repetitive elements were excluded from further analysis. Mitochondrial genes (16.2%), myosin heavy chain genes (9%) and the actin alpha skeletal muscle gene (9%) were the most abundant transcripts. Among the 47 identified genes several muscle-specific or predominant sequences expressed in skeletal muscle were found. The sequences of the clones matching uncharacterized human, mouse or porcine ESTs were tested by GRAIL in order to identify putative coding regions. The results of our analysis allowed the establishment of a first list of genes expressed in porcine skeletal muscle.

Evidence was provided for a new erythrocyte ADA allele (Aw) in the Swedish Landrace breed of pigs. The enzyme activity of Aw variant was considerably less than that of the previously reported erythrocyte ADA variants A and B. The mobility of the Aw variant was identical to that of the A variant, both by electrophoresis and by isoelectric focusing. The in vitro heat stability (at 56 degrees C) of the Aw variant was similar to that of A and B variants. The leucocyte ADA activity was normal in pigs with the erythrocyte ADA Aw variant. The frequencies of the erythrocyte ADA alleles, A, B, Aw, and O (silent allele) in four breeds of pigs in Sweden were: Landrace--0.51, 0.19, 0.11, 0.19; Large White--0.91, 0.03, 0.0, 0.06; Duroc--0.95, 0.05, 0.0, 0.0; Hampshire--0.12, 0.14, 0.0, 0.74.