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A selective genotyping approach identifies single nucleotide polymorphisms in porcine chromosome 2 genes associated with production and carcass traits in Italian heavy pigs.
Full text linkSeveral studies have shown that porcine chromosome 2 (SSC2) harbors important quantitative trait loci (QTL) for production traits. In particular, an imprinted QTL for muscle mass production is determined by a mutation in the IGF2 gene (intron3-g.3072G>A). We recently identified and analysed single nucleotide polymorphisms (SNPs) in genes (cathepsin D, CTSD g.70G>A; cathepsin F, CTSF g.22G>C; lactate dehydrogenase A, LDHA g.46G>T) localized on SSC2 (including the IGF2 intron3-g.3072G>A SNP) showing association with production traits in Italian Large White pigs and/or localizing them on QTL regions. Here we analysed these markers applying a selective genotyping approach based on estimated breeding values (EBVs). Three groups of Italian Large White pigs each made by animals with the most positive (n. 50) and most negative (n. 50) EBVs for average daily gain (ADG), backfat thickness (BFT) or weight of lean cuts (LC) and one group of Italian Duroc pigs made by 50 animals with most positive and 50 animals with most negative EBV for visible intermuscular fat (VIF) were genotyped. In Italian Large White pigs, allele frequency differences for the IGF2 intron3-g.3072G>A SNP between the two extreme tails for all groups were highly significant (considering all analysed animals: P=9.85E-20 for LC; P=3.16E-15 for BFT; P=4.41E-6 for ADG). Significant allele frequency differences were also observed for the CTSD g.70G>A (P=0.0002 for ADG; P=0.00068) and LDHA g.46G>T (P=2.32E-5 for ADG) polymorphisms. These results provide further support on the effects of these polymorphisms or genes whose application on marker assisted selection programs could be envisaged
Selezione tradizionale e assistita da marcatori nei suini
No full textLa selezione italiana si distingue da quella di tutti gli altri Paesi perché è indirizzata alla produzione di un suino pesante che fornisca tagli e carne idonei per la trasformazione in salumi di alto pregio.
Il piano di selezione nazionale attivato dall’Associazione Italiana Allevatori Suini (ANAS) nei primi anni ’60 con la vigilanza dell’allora Ministero dell’Agricoltura si basa su due capisaldi: il Libro Genealogico e i centri di controllo genetico dei verri. Questa impostazione generale non è più cambiata, ma sulla base delle nuove conoscenze messe a disposizione dalla ricerca scientifica, è stata continuamente migliorata negli obiettivi e nei criteri di selezione, nei metodi di valutazione dei riproduttori, negli strumenti e nell’organizzazione per renderla sempre più adeguata alle esigenze della filiera di produzione dei salumi italiani. Al 1990 risale l’ultima revisione importante, che ha finalizzato la selezione in modo più stringente alla qualità della carne, intesa essenzialmente come attitudine alla trasformazione in prosciutto di Parma e di San Daniele. Infatti, ai classici criteri di selezione riguardanti l’economia di produzione e l’eliminazione del gene alotano, sono stati affiancati due nuovi criteri specifici per la valutazione della qualità della carne: il calo di prima salatura correlato con quello di stagionatura e il GIV (grasso inter-ed intra muscolare visibile). Inoltre per lo spessore del lardo dorsale non si persegue più una riduzione ma il mantenimento dell’attuale livello presente nelle razze per assicurare la necessaria copertura adiposa del prosciutto.
I risultati ottenuti a 15 anni dall’applicazione completa con il nuovo schema di selezione sono molto buoni, come dimostra il trend molto positivo per tutti gli obiettivi di selezione e il confronto tra le suddette caratteristiche della carne dei suini provenienti dalla selezione nazionale rispetto a quelli derivate da schemi di selezione stranieri.
L’avvento della genetica molecolare ha messo a disposizione nuovi strumenti per aumentare l’efficienza della selezione, perché può permettere il superamento dei limiti di quella tradizionale: antagonismo quantità qualità, difficoltà di rilevazione e bassa ereditabilità di alcune caratteristiche, quali, ad esempio, l’efficienza riproduttiva e la resistenza alle malattie. Inoltre può migliorare l’accuratezza della stima del valore genetico dei riproduttori e l’intensità di selezione e ridurre l’intervallo tra le generazione, aumentando e velocizzando il progresso genetico.
Con l’enorme sviluppo della genetica molecolare che ha permesso la mappatura del genoma suino sono stati messi a disposizione gli strumenti di base che hanno portato all’identificazione di un elevato numero di QTL e geni con effetto fenotipico importante, alcuni dei quali di particolare interesse per la specificità della suinicoltura italiana.
Le conoscenze acquisite hanno già dato origine ad importanti applicazioni. In futuro si attendono applicazioni ancora più importanti dall’aumento delle conoscenze, che dovrebbe portare alla completa decifrazione del DNA del genoma suino e dall’integrazione di queste con i metodi di selezione tradizionale. Bisogna tuttavia sottolineare che già adesso l’utilizzo, ai fini della selezione, delle mutazioni in molti geni con effetto rilevante sulle produzioni è molto spesso coperto da brevetti stranieri
Hereditability of same blood variables and relationship with the performance traits of Italian Simmental young bulls
No full textThe porcine fat mass and obesity associated (FTO) gene is associated with fat deposition in Italian Duroc pigs.
No full textIn humans, common variants in the fat mass and obesity associated (FTO) gene are associated with body mass index and obesity. Here we sequenced exon 4, parts of introns 3 and 4 and two portions of the 3'-untranslated region of the porcine FTO gene in a panel of nine pigs of different breeds and identified three SNPs.
Allele frequencies of the g.276T>G (AM931150) mutation were studied in seven pig breeds. This mutation was used to linkage-map FTO to SSC6. Association analyses between the g.276T>G polymorphism and several traits [pH of semimembranosus
muscle and estimated breeding values (EBV) for average daily gain, back fat thickness, lean cuts, ham weight and feed:gain ratio] were carried out in 257 sib-tested Italian Large White pigs. Only feed:gain ratio showed P<0.05. A selective genotyping approach was applied, analysing two extreme and divergent groups of Italian Large White pigs selected on the basis of back fat thickness
EBV (50 with most positive and 50 with most negative values). Fisher's exact test (two-tailed) was not significant when comparing the allele frequencies of these two groups. The same approach was used in the Italian Duroc breed for which two extreme and divergent groups of animals were selected according to visible
intermuscular fat EBV. Differences of allele frequencies between these two groups were highly significant (P<0.00001, P<0.001 and P<0.0001, considering all animals or only two- or three-generation unrelated animals respectively), indicating association between the analysed FTO marker and intermuscular fat deposition
Analysis of association between a microsatellite at intron 1 of the insulin-like growth factor 1 (IGF1) gene and fat deposition, meat production and quality traits in Italian Large White and Italian Duroc pigs
No full textIl legame tra un prodotto di origine animale e la razza da cui questo è originato rappresenta un aspetto importante per la valorizzazione di alcune produzioni. Il maggior prezzo che questi prodotti spuntano sul mercato fa emergere l’esigenza 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 è uno dei principali caratteri che differenziano tra di loro le razze. Diverse mutazioni nel gene melanocortin 1 receptor (MC1R) sono già 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 possibilità di utilizzare questo gene per l’autenticazione e la tracciabilità 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, è stato possibile analizzare più di 70 animali. L’allele Ed è stato identificato nella razza Frisona Italiana con una frequenza dello 0,886. L’allele E (nomenclatura che include tutti gli alleli tranne che e, Ed e E1) è 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 è 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) è stato identificato anche l’allele E1. L’allele e è risultato fissato nella razza Reggiana e quasi fissato nella razza Pezzata Rossa Italiana. Inoltre, con bassa frequenza, è stato identificato in tutte le altre razze analizzate, tranne che nella Marchigiana. Le differenze osservate tra razze esaminate indicano che, almeno in alcuni casi, è possibile utilizzare i polimorfismi del gene MC1R per escludere o confermare l’impiego di latte di una determinata razza nella produzione di un prodotto lattiero-caseario. Il caso più interessante è quello del formaggio Parmigiano Reggiano prodotto con l’uso esclusivo di latte di bovine di razza Reggiana. Infatti, essendo presente in questa razza soltanto l’allele e il rilievo analitico di qualsiasi altro allele nel DNA estratto dal formaggio rivela l’uso di latte proveniente da altre razze. La messa a punto di un metodo PCR-RFLP per l’analisi 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 validità del metodo del quale è stata valutata anche la sensibilitàA few studies have shown that a microsatellite at intron 1 of the insulin-like growth factor 1 (IGF.1) gene is associated with several production traits in a few pig populations. In the current work we evaluated associations between this microsatellite and production traits in Italian Large White and Italian Duroc pigs. Association studies were carried out on a total of 1120 animals using two experimental designs: i) a selective genotyping approach based on extreme and divergent Italian Large White pigs for back fat thickness (BFT) estimated breeding value (EBV) or on extreme and divergent Italian Duroc pigs for visible inter-muscular fat (VIF) EBV; and ii) analysis of unselected pigs (random groups) coming from populations of the two breeds. Allele distributions between Italian Large White and Italian Duroc pigs were different (P<0.05) with longer alleles being more frequent in Italian Large White. Results of the association analyses from two different random groups showed that this marker affects average daily gain EBV, lean cut EBV and BFT EBV in Italian Large White and BFT EBV in Italian Duroc (P<0.05). Association analysis carried out with random residuals confirmed, to some extent (P=0.096), the effects on BFT in the same animals. However, this result was not confirmed in the two extreme and divergent Italian Large White groups used in the selective genotyping exper- iment. These inconsistent results may indicate that the effect of the IGF1 microsatellite is doubtful in the investigated finishing pigs
SNP analysis in Fatty Acid Synthase and Adiponectin genes in Italian pig breeds
No full textWe investigated polymorphisms in pig Fatty Acid Synthase (FASN) and Adiponectin (ADN or ACDC, Adipocyte C1q and collagene-domain-like) genes, candidates for meat and carcass quality, analysing DNA samples of main and local pig breeds reared in Italy. FASN is an enzyme that plays a central role in fatty acid biosynthesis catalysing the production of long-chain saturated fatty acids. FASN gene has been assigned to SSC 12p1.5 and a T>C polymorphism in the fourth exon was found at position 265 of sequence AY183428. Adiponectin is a fat derived hormone involved in insulin sensitivity, in lipid and glucose metabolism. The gene was mapped on SSC 13 at 53.6 cM, in a region containing a QTL for intramuscolar fat. In this gene a G>A missense mutation within the 60th codon, determining a Val-Ile substitution in the protein, has been reported in literature. The T>C polymorphisms of FASN, and the G>A mutation of ADN genes were studied by PCR-RFLP. All analysed breeds showed the polymorphisms, except for Hampshire samples that presented only the G allele at ADN locus. In FASN locus the allele C was the most frequent in the analysed breeds and its value was higher than 0.80 in Duroc, Belgian Landrace, Pietrain and Cinta Senese samples.Two groups of Italian Large White pigs with extreme divergent genetic index (50 highest and 50 lowest) for backfat thickness were genotyped for FASN polymorphism. Significant differences of allele frequencies between the groups were found (P=0.016). In ADN locus G allele was the most frequent in the examined breeds with values ranging from 0.85 (Duroc) to 0.99 (Italian Large White). The sequencing of PCR products obtained using three different primer pairs allowed to determine the sequence of part of intron 1, exon 2, intron 2 and almost complete encoding region of 3th and last exon of ADN gene. Additional SNPs were detected in the introns of the gene by sequencing the DNA of pigs of six different breeds
Confirmation of the association between a single nucleotide polymorphism in the porcine LDHA gene and average daily gain and correlated traits in Italian Large White pigs
No full textThe lactate dehydrogenase A (LDHA) gene encodes for an enzyme predominantly expressed in skeletal muscle where it catalyses the recycling reaction of L-lactate in the final step of the anaerobic glycolysis. This gene is localized on porcine chromosome 2 (SSC2) where several reports have also localized QTLs for carcass traits and growth rate. We identified that a single nucleotide polymorphism (SNP) in exon 3 of the porcine LDHA gene (AJ557234:g.46G>T) was associated with average daily gain (ADG) in Italian Large White pigs. We herein confirm our previous results analysing this marker in a larger number of animals using a selective genotyping approach based on extreme and divergent estimated breeding values (EBV) for ADG and evaluated the effects of the g.46G>T SNP on EBV for several other traits (back fat thickness, BFT; feed:gain ratio, FGR; ham weight, HW; and lean cut content, LC)
Study of Fatty Acid Synthase and Adiponectin SNPs in the Italian Duroc breed
No full textFatty 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, in Italian Duroc
pigs. Up to now researches on these functional genes in this pig breed have not been performed.
In order to estimate allele frequencies, the FASN T>C polymorphism and the ADN G>A mutation were studied by
PCR-RFLP in 134 and 257 Italian Duroc, respectively. At the FASN locus the allele frequency was 0.041 for T allele;
at the ADN locus the frequency of the alleles A was 0.136. We investigated the effect of FASN and ADN polymorphisms
on Estimated Breeding Values (EBVs) for single traits (average daily gain, feed to gain ratio, weight of lean
cuts, ham weight, backfat thickness and visible intermuscular fat) and for selection indexes (Total Index and
Terminal Index) estimated by ANAS. The analyses were performed using the GLM procedure of SAS System and
a model with the genotype at FASN or ADN locus as fixed factor.
At the FASN locus only few pigs carried the T allele; therefore, we tried to perform the analysis comparing the pigs
with both genotypes T/T plus C/T versus those genotyped C/C at this locus. The results didn’t show any association
of the polymorphism with the examined traits.
The same model was used for the ADN locus and the G/A genotyped pigs versus the G/G ones showed a significant
higher estimated mean value for Total Index (P= 0.0114).
For both the analysed genes the obtained results should be verified on a larger sample even if the present findings
could suggest a possible role of ADN on the traits included in Total Index in the Duroc breed
Genomic selection in Italian heavy pigs: a simulation study
No full textGenomic selection is becoming a routine application in dairy cattle breeding for the advantages it gives in terms of reduced generation interval, increased accuracy and increased selection intensity. Effectiveness and practical implementation of genomic selection on pig breeds is not clear yet due to biological and technically derived differences between pig and cattle breeding (e.g. much shorter generation interval, large litter size, reduced number of semen doses produced per boar in A.I.). However, a few preliminary North European simulation studies have reported that some advantage from genomic selection might also be expected in pigs. However, studies based on North European vision of pig breeding do not take into account the peculiarities of the Italian heavy pig breeding system. Italian pig selection is based on a sib-testing scheme in which 2 full sisters and 1 full castrated brother from the same litter of the candidate boar are performance tested. This scheme opens a wide range of different genotyping strategies to be evaluated. To this aim, a pig breeding population with a 18 chromosome genome marked with 60K bi-allelic single nucleotide polymorphisms and several segregating QTLs was simulated by using the software QMSim. The population was genetically selected over 25 generations based on BLUP estimated breeding values (EBV) for a trait with heritability of 0.40. Culling was based on EBV both in sires and dams. Different genotyping strategies as well as different methods of predicting genomic breeding values (GBLUP, Bayes or Single Step) were compared. Accuracies of genetic values were calculated as correlation with true breeding values. Considering the simulated scenarios, the introduction of genomic evaluations might increase accuracy levels both in young piglets and in selected reproducers. In particular, the choice of the male candidate would be more effective. Other simulations are under way to evaluate if genomic selection could actually give economic advantages to the Italian heavy pig breeding industry
δ13C and δ15N in yellow and silver eels (Anguilla anguilla, 1758) from different Mediterranean local stocks and their variation with body size and growth
No full textThe European eel, a catadromous endangered species, displays plasticity in phenotypic traits and in trophic behaviour, features that can eventually affect growth. The aim of this study was to compare variation in carbon (delta C-13) and nitrogen (delta N-15) stable isotopes in muscle tissue of the adult eel life stages (i.e. yellow and silver eel), as function of growth. Eel samples were obtained from nine sites across the Mediterranean region, that included seven coastal lagoons of different size and ecological structure, and two freshwater habitats corresponding to one river and one lake. A large variability was found in both delta C-13 and delta N-15 values, suggesting that eels fed over a broad range of potential food sources. Eels from each location showed specific range values of delta C-13, in most sites irrespective of stage, reflecting lagoon- or freshwater-specific carbon sources. A positive correlation was found between individual delta N-15 values and annual growth rates, suggesting that eels generally seem to feed on prey of higher delta N-15 values among the trophic resources available in each foraging habitat. This allows individuals to grow faster and to attain earlier the pre-spawning phase (i.e. the silver stage). A better understanding of eel trophic ecology across different life stages and different habitats is one of the prerequisites for the effective management of local stocks
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