Genome-wide analysis reveals the patterns of genetic diversity and population structure of 8 Italian local chicken breeds.

The aim of this study was to conduct a genome-wide comparative analysis of 8 local Italian chicken breeds (Ermellinata di Rovigo, Millefiori di Lonigo [PML], Polverara Bianca, Polverara Nera, Padovana, Pepoi [PPP], Robusta Lionata, and Robusta Maculata), all under a conservation plan, to understand their genetic diversity and population structure. A total of 152 animals were analyzed using the Affymetrix Axiom 600 K Chicken Genotyping Array. The levels of genetic diversity were highest and lowest in PML and PPP, respectively. The results of genomic inbreeding based on runs of homozygosity (ROH; FROH) showed marked differences among breeds and ranged from 0.161 (PML) to 0.478 (PPP). Furthermore, in all breeds, short ROH (<4 Mb in length) were more frequent than long segments. Patterns of genetic differentiation, model-based clustering, and neighbor networks showed that most breeds formed nonoverlapping clusters and were clearly separate populations. The 2 Polverara breeds shared a similar genetic background and showed the lowest genetic differentiation in comparison with purebred lines; the local populations showed separated groups. PPP and PML were closer to the group of the purebred broiler lines (BRSA, BRSB, BRDA, and BRDB). Six genomic regions are presented as hotspots of autozygosity among the Italian chicken breeds, with candidate genes involved in multiple morphological phenotypes as breast muscle, muscle dry matter content, and body weight. This study is the first exhaustive genome-wide analysis of the diversity of these Italian local chickens from Veneto region. We conclude that breeds have conserved authentic genetic patterns. The results are of significant importance because they will help design and implement conservation strategies. In fact, the conservation of these breeds may also have positive impacts on the local economy, niche traditional markets, and offering a source of high-quality products to consumers. In this context, genomic information may play a crucial role in the management of local breeds.

Mitochondrial diversity of Yoruba and Fulani chickens: A biodiversity reservoir in Nigeria.

Poultry are the most widely distributed type of livestock in Nigeria. Indigenous chickens are extremely common throughout the country. Indeed, approximately 83 million chickens are raised in extensive systems and 60 million in semi-intensive systems. To provide the first comprehensive overview of the maternal lineages in Southwest Nigeria, we analyzed 96 mitochondrial DNA control region sequences from 2 indigenous chicken ecotypes: Fulani and Yoruba. All samples belonged to the most frequent haplogroup (E) in Africa and Europe and showed noticeably low haplotype diversity. Although only 11 different haplotypes were detected, with 2 of them never found before in Nigeria, the presence of unique sequences among our indigenous samples testified to their status as an important genetic resource to be preserved. Furthermore, a total of 7,868 published sequences were included in the comparative analysis, which revealed an east-west geographic pattern of haplogroup distribution and led to the conclusion that the gene flow from Southeastern Asia mainly involved one mitochondrial clade. Moreover, owing to the extensive genetic intermixing among Nigerian chickens, conservation efforts are required to safeguard the extant mitochondrial variability in these indigenous ecotypes and establish future improvement and selection programs.

The myostatin gene: an overview of mechanisms of action and its relevance to livestock animals.

Myostatin, also known as growth differentiation factor 8, a member of the transforming growth factor-beta super-family, is a negative regulator of muscle development. Myostatin acts at key points during pre- and post-natal life of amniotes that ultimately determine the overall muscle mass of an animal. Mutations have already demonstrated the impact of attenuating myostatin activity on muscle development. A number of large animals, including cattle, sheep, dogs and humans, display the 'double muscled' phenotype due to mutations in the myostatin gene. Here, we firstly give an overview of the molecular pathways regulated by myostatin that control muscle development. Then we describe the natural mutations and their associated phenotypes as well as the physiological influence of altering myostatin expression in livestock animals (cattle, sheep, goat, horse, pig, rabbit and chicken). Knowledge of null alleles and polymorphisms in the myostatin gene are of great interest in the animal breeding field, and it could be utilized to improve meat production in livestock animals.

Genetic variability of two Italian indigenous chicken breeds inferred from microsatellite marker analysis.

The objective of this study was to determine the genetic structure and variability of Bionda Piemontese and Bianca di Saluzzo (Piedmont, Northwest Italy) using an international set of microsatellite loci (AVIANDIV-FAO). Differences compared with commercial lines and other Italian breeds were verified to justify the implementation of conservation programmes. Flock contribution to genetic variability was assessed following the approach implemented in the MolKin software. Comparison was performed using the fixation index and the Reynolds genetic distance. The most likely number of different populations was estimated using the clustering procedure implemented in STRUCTURE. The molecular information suggests that management practices could have prevented random mating and produced inbreeding and heterogeneity across flocks. In this respect, Bionda and Bianca show substructuring and are more similar to British breeds than other continental European breeds. Bionda and Bianca fit into the European breeds provided with the highest number of alleles and expected heterozygosity. There is a clear distinction between the Piedmont breeds and the other populations. The Piedmont poultry differ from both commercial lines and other Italian breeds and retain a high level of genetic variability. As for other indigenous breeds, Bionda and Bianca could make an original contribution to the industry in the future. A collective planned approach to restoration is essential, because the flocks are managed with poor regulation. Enhancing connection between breeders with an efficient replacement interchange and mating plan is the right way of controlling inbreeding, preventing substructuring and increasing variability within the flocks.

Review: A review on classical and atypical scrapie in caprine: Prion protein gene polymorphisms and their role in the disease.

Scrapie is a naturally occurring transmissible spongiform encephalopathy in sheep and goat. It has been known for ~250 years and is characterised by the accumulation of an abnormal isoform of a host-encoded prion protein that leads to progressive neurodegeneration and death. Scrapie is recognised in two forms, classical and atypical scrapie. The susceptibility to both types of scrapie is influenced by polymorphisms of the prion protein gene (PRNP). Sheep susceptibility or resistance to classical scrapie is strongly regulated by the polymorphisms at codons 136, 154 and 171 of the PRNP. The genetic role in atypical scrapie in sheep has been defined by polymorphisms at codons 141, 154 and 171, which are associated with different degrees of risk in the occurrence of the ovine disease. Progress has been achieved in the prevention of scrapie in sheep due to efficient genetic breeding programmes based on eradication and control of the disease. In Europe, the success of these programmes has been verified by applying eradication and genetic selection plans. In general terms, the ovine selection plans aim to eliminate and reduce the susceptible allele and to enrich the resistant allele ARR. During outbreaks all susceptible animals are slaughtered, only ARR/ARR resistant rams and sheep and semi-resistant females are preserved. In the occurrence of scrapie positive goats a complete cull of the flock (stamping out) is performed with great economic loss and severe risk of extinction for the endangered breeds. The ability to select scrapie-resistant animals allows to define new breeding strategies aimed to boost genetic progress while reducing costs during scrapie outbreaks. Allelic variants of PRNP can be protective for caprine scrapie, and the knowledge of their distribution in goats has become very important. Over the past few years, the integration of genetic information on goat populations could be used to make selection decisions, commonly referred to as genetic selection. The objective of this review was to summarise the main findings of polymorphisms of the caprine prion protein (PrP) gene and to discuss the possible application of goat breeding schemes integrating genetic selection, with their relative advantages and limitations.

Influence of single nucleotide polymorphisms in the myostatin and myogenic factor 5 muscle growth-related genes on the performance traits of Marchigiana beef cattle.

The Marchigiana is famous for its large body size and favorable dressing percentage. A myostatin (MSTN) gene mutation (a G to T transversion) was identified in the breed. The homozygote "GG" yields a "normal" phenotype, the homozygote "TT" yields a double muscled body shape but sometimes causes survival problems, and the heterozygote genotype produces an extremely muscled body without defects. In practice, Marchigiana "TT" homozygotes are culled from reproduction, but the heterozygotes are chosen as sires. The objective of this study was to assess genes involved in Marchigiana muscle development to improve selection procedures. The effects of the MSTN and myogenic factor 5 (MYF5) genes on the growth and muscle traits in the Marchigiana breed were assessed. The effects of MSTN together with the genotype of the causative mutation (g.874G > T) and the effects of the two SNP in the promoter were studied (g.-371T > A and g.-805G > C). The SNP effects were evaluated in a comparison between the means of the several genotypes or for the average gene substitution and dominance effect. Two hundred forty-nine bullocks were evaluated using a performance test. At the beginning and end of the trial, the animals were weighed and their bodies were measured every 21 d up to 12 mo of age. In addition to these observations, morphological scores and the BLUP indices were estimated at the end of the performance test. The obtained results suggested that the MSTN g.874G > T and MYF5 SNP could be considered in the selection program of the Marchigiana breed. A MSTN g.874G > T genotyping service for the breeders could help to avoid the "TT" genotype and to select for the "GT" genotype. The "AA" MYF5 SNP genotype could also be selected for even if good muscle development yields a certain size reduction.

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.

Genetic parameters for the weights and yields of carcass cuts in Chianina cattle.

Chianina is the tallest and heaviest beef cattle breed in the world and 1 of the most appreciated breeds on the Italian meat market. A selection program focused on improving Chianina carcass quality could provide a further economic advantage to Chianina breeders. However, the current European carcass scoring system [i.e., the SEUROP (S=superior, E=excellent, U= very good, R=good, O=fair, and P=poor) grid] is not suitable for use in selective breeding programs; methods based on carcass cuts would be much more efficient. Here, the genetic parameters of weights and yields (percentage of carcass weight) of the main commercial cuts were estimated on 842 Chianina carcasses (heifers and bullocks) using a mixed model that takes into account the fixed effects of herd, year of slaughter, and sex and the random additive effect of the animal; the carcass weight was also considered in cuts yield. The average carcass weights were 492.6 ± 86.52 kg (males) and 312.1 ± 68.74 kg (females), and the largest cut was the round, with a weight of 58.6 ± 19.35 kg and yield of 24.4 ± 1.28% in males and 40.2 ± 17.59 kg and 25.3 ± 1.41% in females. The variability in cut weight was greater than that in yield percentage. The cut weight heritabilities ranged from 0.74 (chuck) to 0.21 (short plate) whereas the yield heritabilities ranged from 0.88 (loin) to 0.40 (brisket). The genetic correlations were generally high and positive between weights; correlation values with yields were lower and could be positive or negative. These findings suggest that a selection program to improve the carcass quality of Chianina beef using cuts data could potentially achieve good results.

Molecular characterization of Xp chromosome deletion in a fertile cow.

A young cow of the Marchigiana breed (central Italy) with normal body conformation and external genitalia underwent routine cytogenetic analyses prior to its use for reproduction. After normal chromosome staining, only one X chromosome was observed with a normal diploid number (2n = 60) in all 200 studied cells. Subsequent cytogenetic analyses by using both CBA- and RBA-banding techniques evidenced that almost all the p arms of the other X chromosome was lacking. Detailed FISH-mapping analyses with BAC covering this Xp arm region demonstrated that this large chromosome region was deleted. RBA-banding showed that the deleted X was late replicating. CGH array analysis evidenced that deletion involves the Xp arm from the telomere to around 39.5 Mb, referring to the BosTau6 cattle genome assembly. This abnormality deletes about 40 Mb of the X chromosome sequence, but, despite the large number of genes deleted, none of them are programmed to escape from inactivation. This can explain the normal phenotype of the female which is actually pregnant. Finally, we evidenced, by analysis of an SNP mapped to the deleted region (SNP rs29024121), that the only normal (e.g. nondeleted) X chromosome present derives from the father. Hence, the deletion has a maternal origin.

Secretion patterns and effect of prostate-derived granules on the sperm acrosome reaction of rabbit buck.

There is increasing evidence that the particulate fraction of seminal plasma plays an important role in reproduction of several mammalian species. However, the origin and role of these granules in the physiology of rabbit spermatozoa is partially unknown. The aim of this study was to investigate the implication of prostate gland in the production and secretion of granules into the rabbit semen and the role of prostate-derived granules in the sperm acrosome reaction. Light and electron microscopy of the prostate gland showed that the anterior and middle tracts of the prostate (namely the proprostate and prostate, respectively) are chiefly implicated in the secretion of granules of different size: smaller granules (SG; 0.5 µm) and large granules (LG; 4 µm). Two major patterns of secretion were identified, based on electron microscope views: storage granules (large granules) seem to empty inner smaller granules directly into the duct by exocytosis, or the storage vesicle itself is released in toto into the ducts (diacytosis). In vitro experiments using granules from vasectomized rabbits, to exclude testicular origin of granules, showed that granules reduce the acrosome reaction of Percoll-selected spermatozoa, independently of the size. Interestingly, spermatozoa incubated with heat-treated granules showed a higher sperm acrosome reaction rate, suggesting a potential role of granule-derived proteins in this process. Inhibition of the acrosome reaction is a crucial event in rabbit reproduction; ejaculated spermatozoa have to wait for a long time (8-16 h) for egg availability in the female tract after mating. Taking together, our results demonstrate that prostate granules secreted either by exocytosis or diacytosis can preserve spermatozoa fertilizing ability, by preventing sperm acrosome reaction. The type of granule-derived proteins or other macromolecules implicated in this process should be further investigated.

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.

[Considerations on the evolution of the concept of zoonoses]. / Considerazioni sull'evoluzione del concetto di zoonosi.

The existence of diseases common to humans and animals has been known since the beginning of history. The disease transmission from animals to people was first observed on rabies ("the mother of all zoonoses") and later on in occupational diseases (anthrax, glanders, "mange"); in time, also certain food-borne infections were included in this category. The microbiological era has first brought along the concept of infection, then that of zoonoses, which has extended and now numbers some 200 infections. The World Health Organization has been interested in zoonoses since its foundation. Zoonoses represent an important issue for public health, fundamental in veterinary public health, whose functions are here listed. This discipline is concerned with all health problems associated with direct and indirect relationships between humans and animals, including also non-communicable ones. It has been proposed, therefore, to extend the term zoonoses as follows: "Any detriment to the health and/or quality of human life deriving from direct or indirect relationships with (other) vertebrate, or edible or toxic invertebrate animals". Contributors (e.g. Blancou) suggest to remove "edible or toxic "from the definition. Examples of zoonoses are provided according to the extended concept.

Notes on cystic echinococcosis in the Mediterranean.

Cystic Echinococcosis (CE), caused by Echinococcus granulosus, is present from the beginning of history and in the Mediterranean it is linked to the dog-sheep cycle. The Mediterranean area possesses many features favouring CE. Positive and negative influences derived from the action of the European Community and from recent developments. The control measures of CE have political, economic, public health and environmental implications. Dog population and dog-transmitted zoonoses control, improvement of slaughtering procedures and the destruction of infected viscera, health education, interprofessional cooperation are able individually to constitute a contraposition to CE and combined to compose a control program. Epidemiological surveillance and control of CE in the Mediterranean are coordinated by the WHO Mediterranean Zoonoses Control Centre of Athens.