Genome-wide association study identifies markers associated with carcass and meat quality traits in Italian Large White pigs

A GWAS was performed using the genotypes obtained by PorcineSNP60 v2 BeadChip and 11 phenotypic traits (carcass lean meat percentage; backfat thickness; Longissimus thoracis muscle thickness; lightness; backfat thickness measured with caliper at the midline; meat pH measured at about 1 h post mortem and 24 h post mortem; CIE L*, a* and b* color parameters; and water-holding capacity). Three markers were associated with three of the phenotypic traits considered: M1GA0009592 (SSC7) with backfat thickness and lean meat content, DIAS0002910 (SSC6) and ALGA0109856 (SSC6) with water-holding capacity. The marker M1GA0009592, associated with backfat thickness, lies in a QTL region near the gene JARID2, which is a transcription factor also involved in the regulation of adipose-derived stem cell pluripotency. The results seem to indicate a possible role of these genomic regions in the regulation of pig carcass fatness (i.e. backfat at last rib) and water-holding capacity

study of fatty acid synthase and adiponectin snps in the italian duroc breed

AbstractFatty acid synthase (FASN) is a multifunctional enzyme that plays a central role in fatty acid biosynthesis catalysing the conversion of acetyl-CoA and malonyl-CoA into long-chain saturated fatty acids and has an important role in energy homeostasis. Pig FASN gene has been assigned to chromosome 12p1.5 and a T>C polymorphism in the fourth exon was found. Adiponectin (ADN) is a fat-derived hormone involved in insulin sensitivity, in lipid and glucose metabolism. In literature is reported that the gene was mapped on chromosome 13 at 53.6 cM, in a region containing QTL for intramuscolar fat (IMF). In this gene several SNPs were identified and one of these polymorphisms (a G>A missense mutation within the 60th codon) determining the Val-Ile substitution in the protein, has been previously reported.The aim of this work is to analyse the variability of polymorphisms of fatty acid synthase described by Munoz et al., 2003 (Anim. Genet. 34:234) and adiponectin genes, candidates for meat and carcass quality..

Muscle transcriptome analysis identifies genes involved in ciliogenesis and the molecular cascade associated with intramuscular fat content in Large White heavy pigs

Intramuscular fat content (IMF) is a complex trait influencing the technological and sensorial features of meat products and determining pork quality. Thus, we aimed at analyzing through RNA-sequencing the Semimembranosus muscle transcriptome of Italian Large White pigs to study the gene networks associated with IMF deposition. Two groups of samples were used; each one was composed of six unrelated pigs with extreme and divergent IMF content (0.67 \ub1 0.09% in low IMF vs. 6.81 \ub1 1.17% in high IMF groups) that were chosen from 950 purebred individuals. Paired-end RNA sequences were aligned to Sus scrofa genome assembly 11.1 and gene counts were analyzed using WGCNA and DeSeq2 packages in R environment. Interestingly, among the 58 differentially expressed genes (DEGs), several were related to primary cilia organelles (such as Lebercilin 5 gene), in addition to the genes involved in the regulation of cell differentiation, in the control of RNA-processing, and G-protein and ERK signaling pathways. Together with cilia-related genes, we also found in high IMF pigs an over-expression of the Fibroblast Growth Factor 2 (FGF2) gene, which in other animal species was found to be a regulator of ciliogenesis. Four WGCNA gene modules resulted significantly associated with IMF deposition: grey60 (P = 0.003), darkturquoise (P = 0.022), skyblue1 (P = 0.022), and lavenderblush3 (P = 0.030). The genes in the significant modules confirmed the results obtained for the DEGs, and the analysis with "cyto- Hubba" indicated genes controlling RNA splicing and cell differentiation as hub genes. Among the complex molecular processes affecting muscle fat depots, genes involved in primary cilia may have an important role, and the transcriptional reprogramming observed in high IMF pigs may be related to an FGF-related molecular cascade and to ciliogenesis, which in the literature have been associated with fibro-adipogenic precursor differentiation

Characterisation of wine yeasts isolated at different temperatures using the enrichment technique

Research NoteSaccharomyces cerevisiae strains isolated from fermenting grape must incubated at extreme fermentation temperatures (40 and 5 degrees C) were oenologically characterised. These cultures compared with S. cerevisiae wine strains, show a wider optimum temperature for growth and can ferment vigorously in a wider temperature range (27 to 35 degrees C)

Identification of differentially expressed small RNAs and prediction of target genes in Italian Large White pigs with divergent backfat deposition

The identification of the molecular mechanisms regulating pathways associated with the potential for fat deposition in pigs can lead to the detection of key genes and markers for the genetic improvement of fat traits. Interactions of microRNAs (miRNAs) with target RNAs regulate gene expression and modulate pathway activation in cells and tissues. In pigs, miRNA discovery is far from saturation, and the knowledge of miRNA expression in backfat tissue and particularly of the impact of miRNA variations is still fragmentary. Using RNA-seq, we characterized the small RNA (sRNA) expression profiles in Italian Large White pig backfat tissue. Comparing two groups of pigs divergent for backfat deposition, we detected 31 significant differentially expressed (DE) sRNAs: 14 up-regulated (including ssc-miR-132, ssc-miR-146b, ssc-miR-221-5p, ssc-miR-365-5p and the moRNA ssc-moR-21-5p) and 17 down-regulated (including ssc-miR-136, ssc-miR-195, ssc-miR-199a-5p and ssc-miR-335). To understand the biological impact of the observed miRNA expression variations, we used the expression correlation of DE miRNA target transcripts expressed in the same samples to define a regulatory network of 193 interactions between DE miRNAs and 40 DE target transcripts showing opposite expression profiles and being involved in specific pathways. Several miRNAs and mRNAs in the network were found to be expressed from backfat-related pig QTL. These results are informative for the complex mechanisms influencing fat traits, shed light on a new aspect of the genetic regulation of fat deposition in pigs and facilitate the prospective implementation of innovative strategies of pig genetic improvement based on genomic markers

Is Tuber brumale a threat to T. melanosporum and T. aestivum plantations?

True truffles in the genus Tuber are the most valuable ectomycorrhizal fungiand their cultivation has become widespread around the world. Competition with other ectomycorrhizal fungi and especially with undesired Tuber species, like T. brumale, can threaten the success of a truffle plantation. In this work, the competitiveness of T. brumale towards T. melanosporum and T. aestivum was assessed in a 14 year-old plantation carried out planting seedlings inoculated with these three truffle species in adjacent plots. Analyses of both truffle ectomycorrhizas and extra-radical mycelium were carried out in the transects separating the T. brumale plot from T. melanosporum and T. aestivum plots. The results confirm the competitiveness of T. brumale against T. aestivum and T. melanosporum due to its major ability to colonize the soil around its ectomycorrhizas. However, its competitiveness is limited to the transect areas and it was never found inside T. melanosporum plot. These results remark that, in presence of optimal conditions for T. melanosporum and T. aestivum, the greatest risk of contamination with T. brumale is due to wrong greenhouse activity

Investigating the features of PDO green hams during salting: Insights for new markers and genomic regions in commercial hybrid pigs

Protected Designation of Origin (PDO) dry-cured hams production is greatly dependent on raw meat quality. This study was performed to identify genetic markers associated with the quality of dry-cured ham. Carcass traits of 229 heavy pigs belonging to three commercial genetic lines were registered (weight, EUROP classification). Phenotypic traits (Semimembranosus muscle ultimate pH, ham weight and lean meat content, adsorbed salt) of the corresponding thighs, undergone PDO ham process in three different plants, were measured, using a fast and non-invasive technology. Green ham weight and lean meat percentage influenced the estimated salt content and the weight loss during salting, even if the processing plant greatly affected the variability of the measured ham traits. The genomic data were obtained with the GeneSeek Genomic Profiler (GGP) 70k HD Porcine Array, using the slaughter day and the sex of the animals in the statistical analyses. The phenotypic traits were associated with the genotypes through GenAbel software. The results showed that 18 SNPs located on nine porcine chromosomes were found to be associated with nine phenotypic traits, mainly related to ham weight loss during salting. New associations were found between markers in the genes Neural Precursor Cell Expressed Developmentally Down-Regulated 9 (NEDD9, SSC7), T-Cell Lymphoma Invasion and Metastasis 2 (TIAM2, SSC1), and the ham quality traits. After validation, these SNPs may be useful to improve the quality of thighs for the production of PDO dry-cured hams

Lidar And Hyperspectral Data Integration For Landslide Monitoring: The Test Case Of Valoria Landslide

In the framework of the WISELAND project, funded by MIUR, we tested the integration between Lidar and hyperspectral methodologies in the Valoria landslide (Modena province, Italy), a high risk area with vulnerable elements, subjected to periodic and abrupt reactivations. Multitemporal Lidar Digital Terrain Models (DTMs) allowed the calculation of a differential surface, highlighting absolute height variations, recognizing the main landslide components and identifying depletion and accumulation zones. Hyperspectral data helped in the landslide terrain roughness characterization, performing the Principal Component Analysis (PCA) and correlating the results with Flatness and Organization geomorphometric parameters derived from Lidar DTM

Mitochondrial DNA diversity of five Italian autochtonous donkey breeds

AbstractTo investigate the mitochondrial DNA diversity of five Italian donkey breeds (Amiata, Martinafranca, Romagnolo, Asinara, and Ragusano), we sequenced the HVR I region (D-loop, 288 bp) and cytochrome b gene (274 bp) in 121 individuals. In the D-loop we found nineteen mutations corresponding to fourteen different haplotypes, while in cyt b coding gene only six mutations were found, originating five different haplotypes. In particular, three mutations out of six were non-synonymous, causing an aminoacidic substitution. About the D-loop region, the value of nucleotide diversity (π) observed within breeds was relatively low, but not far from values detected in other European breeds. Phylogenetic and network analyses disclosed the presence of two divergent maternal lineages within Italian donkeys. These haplogroups correspond to the well known lineages of ancestors (Equus asinus somaliensis and E. a. africanus), as donkeys were domesticated from distinct wild subspecies living in Eastern Africa regions. ..