DALLA DOMESTICAZIONE ALLA GENOMICA, COME L’UOMO MODIFICA LE SPECIE ANIMALI CHE ALLEVA

The paper briefly reviews the main steps of animal breeding starting from livestock domestication. The major cultural changes in biology comprehension during XIX and XX centuries are reported with some emphasis on the meaning of the infinitesimal model interpreting quantitative phenotypes. Genomic analysis, dominant on the scenes since the beginning of this century, is explored in a wider way. Genomic selection, production traceability and association between economic traits and specific regions of genome are briefly discussed

Detection of selection signatures for ear carriage in Maltese goat breed

Selection and breeding practices in goats have led to the fixation of several traits. This is probably due to the standardization of several peculiar morphological characteristics that have always been one of the major exclusion criteria of individuals from selection. Among these, ear carriage is one of the most ancient and considered a signature of domestication in several species, such as the dog, pig, sheep and goat (Boyko et al., 2010). The availability of improved genomic analyses tools for goats may provide useful information on genes involved in this trait. By studying, for example, the homozygosity decay of haplotypes (contiguous length of alleles) such information can be detected. In the current study, we focused on the Maltese goat, a breed showing floppy ears, in comparison with other Italian breeds using a goat medium density SNP chip (Nicoloso et al., 2015). A total 48,767 SNP markers for 369 animals belonging to 16 breeds or populations were analyzed. Genotypes were imputed within population excluding markers without known position on the current genome assembly (ARS1, Bickhart et al., 2017). Population analysis using MDS, ADMIXTURE and fastSTRUCTURE confirmed the good differentiation among the populations. Integrated Haplotype Score (iHS, Sabeti et al., 2007) was performed for each population, comparing the regions detected on the Maltese breed with the others considered to detect genes that may be involved into shaping ear morphology. These results may provide new insights into ear carriage phenotype by detecting genes that play a pivotal role in shaping the goat phenotypic diversity

Selection Signatures in Italian Livestock Guardian and Herding Shepherd Dogs

Simple Summary Livestock guardian and herding shepherd dogs are morphologically and behaviourally different, due to the long selection for different tasks made by farmers and breeders. This study aimed to identify genomic regions that best distinguish and characterise four livestock guardian and five herding Italian dog breeds. Genomic SNP data of 158 dogs were compared using two analyses, allowing for the identification of regions harbouring 29 genes. Sixteen runs of homozygosity islands were found in livestock guardians, four of which were partially shared with the fifteen found in herding shepherd dogs. The identified genes were related to dog domestication and behaviour, including herding behaviour, body size and muscle development, the prick or drop ear phenotype, and eye development and functionality. These results contribute to a better understanding of how human selection shaped the genome of dogs selected for different tasks, even considering a limited geographic area. 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

Electronic Instability in a Zero-Gap Semiconductor: The Charge-DensityWave in (TaSe4)(2)I

We report a comprehensive study of the paradigmatic quasi-1D compound (TaSe4)(2)I performed by means of angle-resolved photoemission spectroscopy (ARPES) and first-principles electronic structure calculations. We find it to be a zero-gap semiconductor in the nondistorted structure, with non-negligible interchain coupling. Theory and experiment support a Peierls-like scenario for the charge-density wave formation below T-CDW = 263 K, where the incommensurability is a direct consequence of the finite interchain coupling. The formation of small polarons, strongly suggested by the ARPES data, explains the puzzling semiconductor-to-semiconductor transition observed in transport at T-CDW.open114sciescopu

MC1R gene: comparison between different farm animal species

Il gene MC1R: confronto fra diverse specie animali di interesse zootecnico. Negli animali di interesse zootecnico, il polimorfismo del gene MC1R coinvolto nella pigmentazione \ue8 stato studiato a livello molecolare soltanto nell\u2019ultimo decennio. Si sono confrontate descrizioni fenotipiche e polimorfismi del gene MC1R in alcune razze bovine (Rendena, Bruna, Cabannina, Ottonese-Varzese e Pezzata Rossa) e nel cavallo (62 animali). Tutti gli animali feomelanici sono portatori delle mutazioni recessive allo stato omozigote indipendentemente dalla tonalit\ue0 del mantello. I cavalli neri sono portatori dell\u2019allele selvatico del gene MC1R e della mutazione recessiva del gene ASIP allo stato omozigote. Nei cavalli bai e nelle altre razze bovine studiate \ue8 presente, almeno allo stato eterozigote, l\u2019allele selvatico. Nella Bruna e nella Cabannina \ue8 presente anche l\u2019allele E1. Nel gene MC1R, sequenziato in capre di razza Bionda dell\u2019Adamello e Nera di Verzasca, si \ue8 evidenziata l\u2019unica mutazione descritta in letteratura. I risultati sono stati confrontati con le informazioni disponibili nella specie murina e umana.Coat colour genes in farm animals have only been studied at molecular level over the last ten years, starting with Klungland et al. in 1995. Among the genes involved in pigmentation, MC1R, previously known as Extension locus, revealed polymorphisms related to red and black coat colour in different farm animal species. More exactly, the MelanoCortin-1 Receptor (MC1R) gene, specifically expressed in melanocytes, encodes for the homonymous G-protein coupled receptor involved in the regulation of the type of melanin synthesized. Melanocytes produce in fact two different types of melanins: the black or brown eumelanin and the yellow or red pheomelanin. The hair distribution of eu- and pheomelanins depends on the activity of MC1R, which is normally modulated by response to the melanocortin hormone, antagonized by the action of Agouti protein encoded by the ASIP gene. We previously studied the MC1R polymorphisms in some cattle reared in Italy (Crepaldi et al., 2003) and we now present the data on MC1R in other Italian cattle breeds, horses and goats. The aim of this work is to compare the pigmentary phenotypes and causative MC1R mutations in different farm animals and model species, such as mouse and human, in order to highlight differences and similarities between phenotypes and MC1R polymorphisms. The relationship between phenotypes and Agouti locus is also discussed

Stearoyl CoA desaturase gene polymorphism in Italian cattle breeds

AbstractStearoyl COA desaturase (SCD) is a rate-limiting enzyme in the biosynthesis of monounsaturated fatty acids. In cattle, a number of studies support the hypothesis that SCD gene regulation and polymorphism may affect fatty acid composition and fat quality in meat and milk. In ruminant-derived food products, SCD activity has been correlated to the content of conjugated linoleic acid (CLA), a mixture of geometrical and positional isomers of linoleic acid C18:2 having several positive effects on human health (i.e. anticarginogenic, antiatherogenic and immunomodulating effects).Aim of this study was to assess the polymorphism of 3 previously reported Single Nucleotide Polymorphisms (SNPs) in exon 5 of SCD gene in 12 cattle breeds raised in Italy, to evaluate the genetic variability and the genetic differences due to breed and/or selection purpose. Breeds sampled cover the whole geographic area of Italian peninsula and represent different selective purposes: 6 meat-purpose or meat-prevalence breeds (Pied..

The long-lasting protective effect of HGF in cardiomyoblasts exposed to doxorubicin requires a positive feed-forward loop mediated by ERK1,2-TIMP1-STAT3

Previous studies showed that the hepatocyte growth factor (HGF)–Met receptor axis plays long-lasting cardioprotection against doxorubicin anti-cancer therapy. Here, we explored the mechanism(s) underlying the HGF protective effect. DNA damage was monitored by histone H2AX phosphorylation and apoptosis by proteolytic cleavage of caspase 3. In doxorubicin-treated H9c2 cardiomyoblasts, the long-lasting cardioprotection is mediated by activation of the Ras/Raf/Mek/Erk (extracellular signal-regulated kinase 1,2) signaling pathway and requires Stat3 (signal transducer and activator of transcription 3) activation. The HGF protection was abrogated by the Erk1,2 inhibitor, PD98059. This translated into reduced Y705 phosphorylation and impaired nuclear translocation of Stat3, showing crosstalk between Erk1,2 and Stat3 signaling. An array of 29 cytokines, known to activate Stat3, was interrogated to identify the molecule(s) linking the two pathways. The analysis showed a selective increase in expression of the tissue inhibitor of metalloproteinases-1 (Timp1). Consistently, inhibition in cardiomyoblasts of Timp1 translation by siRNAs blunted both Stat3 activation and the cardioprotective effect of HGF. Thus, Timp1 is responsible for the generation of a feed-forward loop of Stat3 activation and helps cardiomyocytes to survive during the genotoxic stress induced by anthracyclines

Molecular cloning, promoter analysis and SNP identification of Italian Nicastrese and Saanen lactoferrin gene

Lactoferrin (Lf) is an iron-binding glycoprotein found in exocrine secretions including milk. High levels of lactoferrin may have a role in the prevention of microbial infection of the mammary gland. In this report we sequenced and characterized goat lactoferrin cDNA and its promoter region in two different breeds of goat. The complete cDNA comprised 2356 nucleotides, including 38bp at the 5'-UTR and 194bp at the 3'-UTR. The open reading frame is 2127bp long and it encodes a mature protein of 689 aminoacids. A total of 19 nucleotide differences, 11 of them being responsible for 8 aminoacid changes, were identified through the comparison with French, Korean and Tibetan goat lactoferrin cDNAs. About 1700bp of the lactoferrin gene promoter were sequenced. Sequence analysis revealed a non-canonical TATA box, multiple SP1/GC elements, and other putative binding sites for transcription factors, such as NF-kappaB, STAT3 and AP2. Two SNPs were identified, one of which would seem to create a new putative AP2 consensus sequence. The presence of an additional AP2 binding site could be associated with quantitative differences of such protein fraction, which could enhance all the activities related to such protein, and improve mammary gland defence against bacterial infections