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Fontanesi L.,University of Bologna | Scotti E.,University of Bologna | Speroni C.,University of Bologna | Buttazzoni L.,Associazione Nazionale Allevatori | And 2 more authors.
Italian Journal of Animal Science | Year: 2011

Several 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=9.53E-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. ©Copyright L. Fontanesi et al., 2011.


Cardinali I.,University of Perugia | Lancioni H.,University of Perugia | Giontella A.,University of Perugia | Capodiferro M.R.,University of Pavia | And 10 more authors.
PLoS ONE | Year: 2016

Background The climatic and cultural diversity of the Italian Peninsula triggered, over time, the development of a great variety of horse breeds, whose origin and history are still unclear. To clarify this issue, analyses on phenotypic traits and genealogical data were recently coupled with molecular screening. Methodology To provide a comprehensive overview of the horse genetic variability in Italy, we produced and phylogenetically analyzed 407 mitochondrial DNA (mtDNA) control-region sequences from ten of the most important Italian riding horse and pony breeds: Bardigiano, Esperia, Giara, Lipizzan, Maremmano, Monterufolino, Murgese, Sarcidano, Sardinian Anglo-Arab, and Tolfetano. A collection of 36 Arabian horses was also evaluated to assess the genetic consequences of their common use for the improvement of some local breeds. Conclusions In Italian horses, all previously described domestic mtDNA haplogroups were detected as well as a high haplotype diversity. These findings indicate that the ancestral local mares harbored an extensive genetic diversity. Moreover, the limited haplotype sharing (11%) with the Arabian horse reveals that its impact on the autochthonous mitochondrial gene pools during the final establishment of pure breeds was marginal, if any. The only significant signs of genetic structure and differentiation were detected in the geographically most isolated contexts (i.e. Monterufolino and Sardinian breeds). Such a geographic effect was also confirmed in a wider breed setting, where the Italian pool stands in an intermediate position together with most of the other Mediterranean stocks. However, some notable exceptions and peculiar genetic proximities lend genetic support to historical theories about the origin of specific Italian breeds. © 2016 Cardinali et al.This is an open access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.


Bouallegue M.,High Agronomic Institute of Chott Mariem | Steri R.,Centro Of Ricerca Per La Produzione Delle Carni E Il Miglioramento Genetico | M'hamdi N.,National Institute of Agronomy of Tunis | Hamouda M.B.,Institution of Agricultural Research and Higher Education
Journal of Animal and Feed Sciences | Year: 2015

Different equations were employed to directly model individual lactation curves of Tunisian Holstein-Friesian cows using 260 241 test day records for milk yield, fat, and protein contents. Eleven mathematical models were compared. Parametric curves (Legendre polynomials, Ali and Schaeffer (AS), Wood, and Wilmink models) and regression splines were tested. Goodness of fit was assessed by considering the adjusted R-square ranked according to five classes, statistical criteria, and residuals analysis. Regression splines (quadratic and cubic spline models with three knots) showed better fitting performances and greater flexibility for all milk traits. The sixth-order Legendre orthogonal polynomial model and the Ali and Schaeffer model also gave the best fit for milk traits compared with the three-parameter models (Wood and Wilmink) and with the lower-order polynomial models, but the AS model was less correlated for fat content (R = 0.87), gave a moderate correlation (R = 0.90) for protein content, and had less similarity between the observed and estimated lactation curves. The performance of Legendre orthogonal polynomials and quadratic splines was strongly affected by the models' order and the number of knots.


Huws S.A.,Aberystwyth University | Chiariotti A.,Centro Of Ricerca Per La Produzione Delle Carni E Il Miglioramento Genetico | Sarubbi F.,CNR Institute for Animal Production System In Mediterranean Environment | Carfi F.,Centro Of Ricerca Per La Produzione Delle Carni E Il Miglioramento Genetico | Pace V.,Centro Of Ricerca Per La Produzione Delle Carni E Il Miglioramento Genetico
Journal of General and Applied Microbiology | Year: 2012

Sorghum presents a sustainable feedstock for Mediterranean buffaloes due to its reduced water and nitrogen requirements compared with maize, which is currently fed primarily. We investigated the effects of feeding sorghum as opposed to maize on Mediterranean buffalo rumen microbial diversity and milk fatty acid content. Four cannulated lactating Mediterranean buffalo cows were fed a basal diet for one month before switching either to maize or sorghum-silage based diets for a 3-month period. Buffaloes were then changed over to the contrasting diet for a further one month. Rumen and milk samples were collected at the end of each month. DGGE-and T-RFLP-based dendrograms generated from rumen samples did not show an effect of diet on rumen bacterial diversity. Milk samples also did not differ in terms of their fatty acid content post sorghum feeding as compared with maize feeding. Thus, sorghum provides an environmentally beneficial alternative to maize for feeding Mediterranean buffalo with little effect on rumen microbial diversity or milk fatty acid composition compared with maize feeding.


Bovo S.,University of Bologna | Schiavo G.,University of Bologna | Mazzoni G.,University of Bologna | Dall'Olio S.,University of Bologna | And 7 more authors.
Animal Genetics | Year: 2016

Calcium, magnesium and phosphorus are essential electrolytes involved in a large number of biological processes. Imbalance of these minerals in blood may indicate clinically relevant conditions and are important in inferring acute or chronic pathologies in humans and animals. In this work, we carried out a genome-wide association study (GWAS) for the level of these three electrolytes in the serum of 843 performance-tested Italian Large White pigs. All pigs were genotyped with the Illumina PorcineSNP60 BeadChip, and GWAS was carried out using genome-wide efficient mixed-model association. For the level of Ca2+, eight single nucleotide polymorphisms (SNPs) were significant, considering a false discovery rate (FDR) < 0.05, and another eight were above the moderate association threshold (Pnominal value < 5.00E-05). These SNPs are distributed in four porcine chromosomes (SSC): SSC8, SSC11, SSC12 and SSC13. In particular, a few putative different signals of association detected on SSC13 and one on SSC12 were in genes or close to genes involved in calcium metabolism (P2RY1, RAP2B, SLC9A9, C3orf58, TSC22D2, PLCH1 and CACNB1). Only one SNP (on SSC7) and six SNPs (on SSC2 and SSC7) showed moderate association with the level of magnesium and phosphorus respectively. The association signals for these two latter minerals might identify genes not known thus far for playing a role in their biological functions and regulations. In conclusion, our GWAS contributed to increased knowledge on the role that calcium, magnesium and phosphorus may play in the genetically determined physiological mechanisms affecting the natural variability of mineral levels in mammalian blood. © 2016 Stichting International Foundation for Animal Genetics


PubMed | University of Bologna and Centro Of Ricerca Per La Produzione Delle Carni E Il Miglioramento Genetico
Type: Journal Article | Journal: Animal genetics | Year: 2016

Calcium, magnesium and phosphorus are essential electrolytes involved in a large number of biological processes. Imbalance of these minerals in blood may indicate clinically relevant conditions and are important in inferring acute or chronic pathologies in humans and animals. In this work, we carried out a genome-wide association study (GWAS) for the level of these three electrolytes in the serum of 843 performance-tested Italian Large White pigs. All pigs were genotyped with the Illumina PorcineSNP60 BeadChip, and GWAS was carried out using genome-wide efficient mixed-model association. For the level of Ca(2+) , eight single nucleotide polymorphisms (SNPs) were significant, considering a false discovery rate (FDR) <0.05, and another eight were above the moderate association threshold (Pnominal value <5.00E-05). These SNPs are distributed in four porcine chromosomes (SSC): SSC8, SSC11, SSC12 and SSC13. In particular, a few putative different signals of association detected on SSC13 and one on SSC12 were in genes or close to genes involved in calcium metabolism (P2RY1, RAP2B, SLC9A9, C3orf58, TSC22D2, PLCH1 and CACNB1). Only one SNP (on SSC7) and six SNPs (on SSC2 and SSC7) showed moderate association with the level of magnesium and phosphorus respectively. The association signals for these two latter minerals might identify genes not known thus far for playing a role in their biological functions and regulations. In conclusion, our GWAS contributed to increased knowledge on the role that calcium, magnesium and phosphorus may play in the genetically determined physiological mechanisms affecting the natural variability of mineral levels in mammalian blood.


PubMed | Associazione Nazionale Allevatori Suini, University of Bologna and Centro Of Ricerca Per La Produzione Delle Carni E Il Miglioramento Genetico
Type: Journal Article | Journal: Animal genetics | Year: 2016

Protected designation of origin dry-cured hams are the most important productions of the Italian heavy pig industry. Hams capable of minimal seasoning losses produce better quality dry-cured hams. Ham weight loss during the first 7days in brine (first salting) is highly correlated with the total loss of weight up to the end of seasoning, and it has quite high heritability (0.30-0.61). For these reasons, ham weight loss at first salting has been included as a meat quality trait in the Italian heavy pig selection program. In this work, we carried out a genome-wide association study for this parameter in the Italian Large White pig breed by genotyping 1365 animals with the Illumina BeadChip PorcineSNP60 chip. Atotal of 44 single nucleotide polymorphisms (SNPs) had a P


PubMed | Associazione Nazionale Allevatori Suini, University of Bologna and Centro Of Ricerca Per La Produzione Delle Carni E Il Miglioramento Genetico
Type: Journal Article | Journal: Animal genetics | Year: 2016

In this study, we investigated at the genome-wide level if 20years of artificial directional selection based on boar genetic evaluation obtained with a classical BLUP animal model shaped the genome of the Italian Large White pig breed. The most influential boars of this breed (n=192), born from 1992 (the beginning of the selection program of this breed) to 2012, with an estimated breeding value reliability of >0.85, were genotyped with the Illumina Porcine SNP60 BeadChip. After grouping the boars in eight classes according to their year of birth, filtered single nucleotide polymorphisms (SNPs) were used to evaluate the effects of time on genotype frequency changes using multinomial logistic regression models. Of these markers, 493 had a PBonferroni <0.10. However, there was an increasing number of SNPs with a decreasing level of allele frequency changes over time, representing a continuous profile across the genome. The largest proportion of the 493 SNPs was on porcine chromosome (SSC) 7, SSC2, SSC8 and SSC18 for a total of 204 haploblocks. Functional annotations of genomic regions, including the 493 shifted SNPs, reported a few Gene Ontology terms that might underly the biological processes that contributed to increase performances of the pigs over the 20years of the selection program. The obtained results indicated that the genome of the Italian Large White pigs was shaped by a directional selection program derived by the application of methodologies assuming the infinitesimal model that captured a continuous trend of allele frequency changes in the boar population.


Pallottino F.,Consiglio per la ricerca in agricoltura e lanalisi delleconomia agraria CREA | Steri R.,Centro Of Ricerca Per La Produzione Delle Carni E Il Miglioramento Genetico | Menesatti P.,Consiglio per la ricerca in agricoltura e lanalisi delleconomia agraria CREA | Antonucci F.,Consiglio per la ricerca in agricoltura e lanalisi delleconomia agraria CREA | And 3 more authors.
Computers and Electronics in Agriculture | Year: 2015

The Lipizzan horse is one of the oldest European horse breeds, its documented origins date back to 1580 in the Imperial stud-farm at Lipizza and are currently used the high-riding school, dressage and others equestrian sports as well as recreational activities. They are also traditionally selected by their morphological characteristics. The aim of this study was to verify the accuracy between manual measurements and stereo-image ones, for the most important linear, angular and circumference measures used for breeding purposes. In this approach a dual web-camera system, in combination with an image analysis algorithm, is proposed to automatically extract the information needed. For this reason a model species such as Lipizzan horse has been chosen and the most important biometric variables (linear measurements and angles) have been selected and taken into consideration. Ten horses were analyzed manually and using a stereovision system taking into account six linear measurements and two angles. The comparison between manual and stereovision measurements showed a high total correlation (r= 0.998) and a low variability between operators (SD = 0.0004). The average error, lower than 3% and difference in magnitude of error depending by specific traits. In conclusion the stereovision system prototyped could be a good tool to improve phenotyping and enlarge the basis of population involved in breeding programs of horses as well as in other livestock species. © 2015 Elsevier B.V.

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