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..

Analysis of melanocortin 1 receptor (MC1R) gene polymorphisms in some cattle breeds: their usefulness and application for breed traceability and authentication of Parmigiano Reggiano cheese

l legame tra un prodotto di origine animale e la razza da cui questo \ue8 originato rappresenta un aspetto importante per la valorizzazione di alcune produzioni. Il maggior prezzo che questi prodotti spuntano sul mercato fa emergere l\u2019esigenza di poter autenticare o tracciare i prodotti mono-razza per smascherare e scoraggiare possibili frodi. A questo scopo sono stati proposti sistemi di analisi del DNA, alcuni dei quali utilizzano marcatori in geni che determinano il colore del mantello, che \ue8 uno dei principali caratteri che differenziano tra di loro le razze. Diverse mutazioni nel gene melanocortin 1 receptor (MC1R) sono gi\ue0 state associate a particolari effetti sul colore del mantello nella specie bovina. In questa ricerca abbiamo studiato la presenza dei principali alleli al locus MC1R, per valutare la possibilit\ue0 di utilizzare questo gene per l\u2019autenticazione e la tracciabilit\ue0 di razza dei prodotti lattiero-caseari. Le mutazioni che permettono di distinguere questi alleli sono state analizzate utilizzando protocolli di PCR-RFLP e PCR-APLP su un totale di 1360 animali appartenenti a 18 razze bovine. Per ognuna delle seguenti razze, Frisona Italiana, Bruna Italiana, Pezzata Rossa Italiana, Jersey, Rendena, Reggiana e Modenese, \ue8 stato possibile analizzare pi\uf9 di 70 animali. L\u2019allele Ed \ue8 stato identificato nella razza Frisona Italiana con una frequenza dello 0,886. L\u2019allele E (nomenclatura che include tutti gli alleli tranne che e, Ed e E1) \ue8 stato identificato con alta frequenza nella Bruna Italiana (0,591), Rendena (0,738), Jersey (0,955) e Modenese (0,961) e con bassa frequenza nella Pezzata Rossa Italiana (0,029). Inoltre, questo allele \ue8 stato osservato nella Rossa Svedese, Rossa Danese, Grigio Alpina, Piemontese, Romagnola, Marchigiana e Chianina. In alcune di queste razze (Bruna Italiana, Rendena, Grigio Alpina, Piemontese, Rossa Svedese e Rossa Danese) \ue8 stato identificato anche l\u2019allele E1. L\u2019allele e \ue8 risultato fissato nella razza Reggiana e quasi fissato nella razza Pezzata Rossa Italiana. Inoltre, con bassa frequenza, \ue8 stato identificato in tutte le altre razze analizzate, tranne che nella Marchigiana. Le differenze osservate tra razze esaminate indicano che, almeno in alcuni casi, \ue8 possibile utilizzare i polimorfismi del gene MC1R per escludere o confermare l\u2019impiego di latte di una determinata razza nella produzione di un prodotto lattiero-caseario. Il caso pi\uf9 interessante \ue8 quello del formaggio Parmigiano Reggiano prodotto con l\u2019uso esclusivo di latte di bovine di razza Reggiana. Infatti, essendo presente in questa razza soltanto l\u2019allele e il rilievo analitico di qualsiasi altro allele nel DNA estratto dal formaggio rivela l\u2019uso di latte proveniente da altre razze. La messa a punto di un metodo PCR-RFLP per l\u2019analisi del DNA estratto da prodotti lattiero caseari, incluso il Parmigiano Reggiano di oltre 24 mesi di stagionatura, rappresenta uno strumento importante per la difesa di questo prodotto mono-razza da eventuali frodi. I risultati ottenuti su 10 forme di formaggio prodotto esclusivamente con latte di bovine di razza Reggiana e su 15 forme di Parmigiano Reggiano commerciale ottenuto senza restrizione della razza di origine del latte hanno mostrato la validit\ue0 del metodo del quale \ue8 stata valutata anche la sensibilit\ue0n cattle, the MC1R gene has been the subject of several studies with the aim to elucidate the biology of coat colour. Then, polymorphisms of this gene have been proposed as tools for breed identification and animal products authentication. As a first step to identify breed specific DNA markers that can be used for the traceability of mono-breed dairy cattle products we investigated, using PCR-RFLP and PCR-APLP protocols, the presence and distribution of some alleles at the MC1R locus in 18 cattle breeds for a total of 1360 animals. For each of seven breeds (Italian Holstein, Italian Brown, Italian Simmental, Rendena, Jersey, Reggiana and Modenese) a large number of animals (>70) was genotyped so the obtained results can be considered with more confidence. Allele Ed was identified only in black pied cattle (Italian Holstein and Black Pied Valdostana). Allele E (this nomenclature includes all alleles except Ed, E1 and e) was observed in Italian Brown, Rendena, Jersey, Modenese, Italian Simmental, Grigio Alpina, Piedmontese, Chianina, Romagnola, Marchigiana, Swedish Red and White and Danish Red. Allele E1 was identified in Italian Brown, Rendena, Grigio Alpina, Piedmontese, Swedish Red and White and Danish Red. The recessive allele e, known to cause red coat colour, was fixed in Reggiana and almost fixed in Italian Simmental. This allele was observed also in Italian Holstein, Italian Brown, Rendena, Jersey and Modenese albeit with low frequency. Moreover, this allele was detected in Valdostana, Pezzata Rossa d\u2019Oropa, Piedmontese, Romagnola, Swedish Red and White, Danish Red, Charoleis and Salers. In the case of the Reggiana breed, which is fixed for allele e, the MC1R locus is highly informative with respect to breeds that carry other alleles or in which allele e is at very low frequency. In theory, using the MC1R locus it is possible to identify the presence of milk from some other breeds in Parmigiano Reggiano cheese labelled as exclusively from the Reggiana breed. This possibility was practically tested by setting up protocols to extract and analyse polymorphisms of the MC1R locus in several dairy products, including Parmigiano Reggiano cheese cured for 30 months. The lower detection limit was estimated to be 5% of non expected DNA. This test can represent a first deterrent against fraud and an important tool for the valorisation and authentication of Parmigiano Reggiano cheese obtained from only Reggiana milk

Analysis of PRKAG3 gene polymorphisms in Italian autochthonous pig breeds.

The PRKAG3 gene encodes for the regulatory gamma 3 subunit of adenosine monophosfate-activated protein kinase (AMPK) protein that acts as a regulator of carbohydrate and fat metabolism. Several single nucleotide polymorphisms (SNPs) have been identified in the porcine PRKAG3 gene. Two of them (c.595A>G or p.I199V and c.599G>A or p.R200Q) have been associated with variability of meat quality and carcass traits. In this study, we investigated the frequency of the c.595A>G and c.599G>A SNPs in 372 animals of five Italian autochthonous pig breeds (Apulo-Calabrese, Casertana, Cinta Senese, Mora Romagnola and Nero Siciliano). Genomic DNA were extracted from hair roots or blood and SNPs genotyping was performed by PCR-RFLP protocols. The c.599A (p.200Q) allele was carried by only 3 Nero Siciliano pigs. All five breeds were polymorphic at the c.595A>G site. The c.595A (p.I199) allele was the less frequent in the analysed breeds with minor allele frequency ranging from 0.144 (Nero Siciliano) to 0.464 (Casertana). Based on identified allele frequencies, the c.595A>G SNP can be useful in association studies with meat, carcass and ham quality traits in the Italian local pig breeds

A melanocortin 1 receptor (MC1R) gene polymorphism is useful for authentication of Massese sheep dairy products

Massese is an Italian sheep breed, with black or grey coat colour, mainly reared in the Tuscany and Emilia Romagna regions. Recently, the emerging interests in this breed have resulted in the production of Pecorino cheese obtained with only Massese milk. In order to be profitable, this marketing link between Massese breed and its products should be defended against fraudsters who could include milk of other sheep breeds or cow milk in Massese labelled productions. To identify the genetic factors affecting coat colour in sheep, we have recently analysed the melanocortin 1 receptor (MC1R) gene and identified several single nucleotide polymorphisms (SNPs). In this work, as a first step to set up a DNA based protocol for authentication of Massese dairy products, we further investigated the presence and distribution of one of these SNPs (c.-31G>A) in 143 Massese sheep and in another 13 sheep breeds (for a total of 351 animals). The Massese breed was fixed for allele c.-31A, whereas in all other breeds allele c.-31 G was the most frequent or with frequency of 0\ub750. At the same nucleotide position the cattle MC1R gene carries the G nucleotide. Using these data we developed a method to detect adulterating milk (from other sheep breeds or from cow) in Massese dairy products based on the analysis of the c.-31G>A SNP. We first tested the sensitivity of the protocol and then applied it to analyse DNA extracted from ricotta and Pecorino cheese obtained with only Massese milk or obtained with unrestricted sheep and cattle milk. To our knowledge, this system represents the first one that can be used for breed authentication of a sheep production and that, at the same time, can reveal frauds derived from the admixture of milk of an unreported species

Prediction of vascular aging based on smartphone acquired PPG signals

Photoplethysmography (PPG) measured by smartphone has the potential for a large scale, non-invasive, and easy-to-use screening tool. Vascular aging is linked to increased arterial stiffness, which can be measured by PPG. We investigate the feasibility of using PPG to predict healthy vascular aging (HVA) based on two approaches: machine learning (ML) and deep learning (DL). We performed data preprocessing, including detrending, demodulating, and denoising on the raw PPG signals. For ML, ridge penalized regression has been applied to 38 features extracted from PPG, whereas for DL several convolutional neural networks (CNNs) have been applied to the whole PPG signals as input. The analysis has been conducted using the crowd-sourced Heart for Heart data. The prediction performance of ML using two features (AUC of 94.7%) \u2013 the a wave of the second derivative PPG and tpr, including four covariates, sex, height, weight, and smoking \u2013 was similar to that of the best performing CNN, 12-layer ResNet (AUC of 95.3%). Without having the heavy computational cost of DL, ML might be advantageous in finding potential biomarkers for HVA prediction. The whole workflow of the procedure is clearly described, and open software has been made available to facilitate replication of the results

Genome-wide association studies for 30 haematological and blood clinical-biochemical traits in Large White pigs reveal genomic regions affecting intermediate phenotypes

Haematological and clinical-biochemical parameters are considered indicators of the physiological/health status of animals and might serve as intermediate phenotypes to link physiological aspects to production and disease resistance traits. The dissection of the genetic variability affecting these phenotypes might be useful to describe the resilience of the animals and to support the usefulness of the pig as animal model. Here, we analysed 15 haematological and 15 clinical-biochemical traits in 843 Italian Large White pigs, via three genome-wide association scan approaches (single-trait, multi-trait and Bayesian). We identified 52 quantitative trait loci (QTLs) associated with 29 out of 30 analysed blood parameters, with the most significant QTL identified on porcine chromosome 14 for basophil count. Some QTL regions harbour genes that may be the obvious candidates: QTLs for cholesterol parameters identified genes (ADCY8, APOB, ATG5, CDKAL1, PCSK5, PRL and SOX6) that are directly involved in cholesterol metabolism; other QTLs highlighted genes encoding the enzymes being measured [ALT (known also as GPT) and AST (known also as GOT)]. Moreover, the multivariate approach strengthened the association results for several candidate genes. The obtained results can contribute to define new measurable phenotypes that could be applied in breeding programs as proxies for more complex traits

Prediction of vascular aging based on smartphone acquired PPG signals

Photoplethysmography (PPG) measured by smartphone has the potential for a large scale, non-invasive, and easy-to-use screening tool. Vascular aging is linked to increased arterial stiffness, which can be measured by PPG. We investigate the feasibility of using PPG to predict healthy vascular aging (HVA) based on two approaches: machine learning (ML) and deep learning (DL). We performed data preprocessing, including detrending, demodulating, and denoising on the raw PPG signals. For ML, ridge penalized regression has been applied to 38 features extracted from PPG, whereas for DL several convolutional neural networks (CNNs) have been applied to the whole PPG signals as input. The analysis has been conducted using the crowd-sourced Heart for Heart data. The prediction performance of ML using two features (AUC of 94.7%) – the a wave of the second derivative PPG and tpr, including four covariates, sex, height, weight, and smoking – was similar to that of the best performing CNN, 12-layer ResNet (AUC of 95.3%). Without having the heavy computational cost of DL, ML might be advantageous in finding potential biomarkers for HVA prediction. The whole workflow of the procedure is clearly described, and open software has been made available to facilitate replication of the results

Targeted metabolomic profiles of piglet plasma reveal physiological changes over the suckling period

The suckling phase is a critical period for the piglets due to their incomplete immune system development and their rapid growth rates. In this study, we analysed the metabolomic profiles of piglets over this period. Eighteen piglets (nine males and nine females) from three different litters were included in the study. Body weight was recorded at birth (T0), 12 (T1) and 21 (T2) days after birth. Plasma samples were collected at two critical time points of the suckling phase (T1 and T2) and about 180 metabolites of five different biochemical classes (glycerophospholipids, amino acids, biogenic amines, hexoses and acylcarnitines) were analyzed using a target metabolomics approach based on Liquid Chromatography-Tandem Mass Spectrometry (LC-MS/MS). Metabolites whose levels could discriminate the plasma profiles at T1 and T2 were identified using the sparse version of Multilevel Partial Least Squares Discriminant Analysis (sMLPLS-DA), coupled with a stability test based on a Leave One Out (LOO) procedure. The level of twenty-three metabolites differed significantly (P < 0.1; both for stability and the effect size) between the two time points. Higher levels of six acylcarnitine (C14:1, C14:1-OH, C16-OH, C4, C5 and C5-OH), serine, threonine and tyrosine, and one phosphatidylcholine (PC ae C42:3) were observed at T1, whereas one biogenic amine (creatinine), eight phosphatidylcholines including PC aa C30:2, PC ae C30:0, PC ae C32:1, PC ae C38:4, PC ae C40:4, PC ae C42:4, PC ae C42:5 and PC ae C44:6, and four sphingomyelins, including SM (OH) C22:1, SM C16:0, SM C16:1 and SM C18:0, were more abundant at T2. The Metabolite Set Enrichment Analysis and the Pathway Analysis modules suggested a perturbation of the \u201cglycine and serine metabolism\u201d and the \u201csphingolipid metabolism\u201d. Differences of these metabolites between these two time points might be related to the rapid growth and immunological maturation phases of the piglets in this period. Our results provided new information that could describe the biological changes of the piglets over the suckling period. The identified metabolites may be useful markers of the developmental processes occurring in the piglets over this critical pre-weaned phase

A first comparative map of copy number variations in the sheep genome

We carried out a cross species cattle–sheep array comparative genome hybridization experiment to identify copy number variations (CNVs) in the sheep genome analysing ewes of Italian dairy or dual-purpose breeds (Bagnolese, Comisana, Laticauda, Massese, Sarda, and Valle del Belice) using a tiling oligonucleotide array with ~385,000 probes designed on the bovine genome. We identified 135 CNV regions (CNVRs; 24 reported in more than one animal) covering ~10.5 Mb of the virtual sheep genome referred to the bovine genome (0.398%) with a mean and a median equal to 77.6 and 55.9 kb, respectively. A comparative analysis between the identified sheep CNVRs and those reported in cattle and goat genomes indicated that overlaps between sheep and both other species CNVRs are highly significant (Pb0.0001), suggesting that several chromosome regions might contain recurrent interspecies CNVRs. Many sheep CNVRs include genes with important biological functions. Further studies are needed to evaluate their functional relevance

Single-marker and haplotype-based genome-wide association studies for the number of teats in two heavy pig breeds

The number of teats is a reproductive-related trait of great economic relevance as it affects the mothering ability of the sows and thus the number of properly weaned piglets. Moreover, genetic improvement of this trait is fundamental to parallelly help the selection for increased litter size. We present the results of single-marker and haplotypes-based genome-wide association studies for the number of teats in two large cohorts of heavy pig breeds (Italian Large White and Italian Landrace) including 3990 animals genotyped with the 70K GGP Porcine BeadChip and other 1927 animals genotyped with the Illumina PorcineSNP60 BeadChip. In the Italian Large White population, genome scans identified three genome regions (SSC7, SSC10, and SSC12) that confirmed the involvement of the VRTN gene (as we previously reported) and highlighted additional loci known to affect teat counts, including the FRMD4A and HOXB1 gene regions. A different picture emerged in the Italian Landrace population, with a total of 12 genome regions in eight chromosomes (SSC3, SSC6, SSC8, SSC11, SSC13, SSC14, SSC15, and SSC16) mainly detected via the haplotype-based genome scan. The most relevant QTL was close to the ARL4C gene on SSC15. Markers in the VRTN gene region were not significant in the Italian Landrace breed. The use of both single-marker and haplotype-based genome-wide association analyses can be helpful to exploit and dissect the genome of the pigs of different populations. Overall, the obtained results supported the polygenic nature of the investigated trait and better elucidated its genetic architecture in Italian heavy pigs