The Experts below are selected from a list of 6474 Experts worldwide ranked by ideXlab platform

Luca Fontanesi - One of the best experts on this subject based on the ideXlab platform.

  • genome wide association analyses for coat colour patterns in the autochthonous nero siciliano Pig Breed
    Livestock Science, 2020
    Co-Authors: Giuseppina Schiavo, Maurizio Gallo, Samuele Bovo, Silvia Tinarelli, S Dallolio, Luca Fontanesi
    Abstract:

    Abstract Nero Siciliano (or Sicilian Black) is an Italian autochthonous Pig Breed reared in the Sicily island, mainly under extensive management systems. Nero Siciliano Pigs are black (with black skin and black hair), but animals with white face or partially white face ("suino facciolo") can be registered to the Breed herd book. Sometimes, other white patterns on extreme portions of legs could appear in this population. This study took advantage from the rare occurrence of Pigs with white patterns in the Nero Siciliano population to carry out a genome-wide association study and comparative genome-wide Fixation index (FST) analysis to identify genomic regions that could affect coat colour variability (solid black vs white patterns over black) in this autochthonous Pig Breed. Analyses have been conducted on 66 Nero Siciliano Pigs: 30 completely black and 36 black with white patterns. All samples have been genotyped for the KIT gene duplication and MC1R mutations, two genes well known to affect coat colours in Pigs. Only Pigs that did not carry any duplication of the KIT gene and were homozygous for the ED2 black dominant MC1R gene allele (n = 26 completely black and n. 22 with white patterns) were genotyped with the Illumina PorcineSNP60 BeadChip. The genome-wide analyzes identified on chromosome 2 a significant marker (rs81329493) associated with the coat colour white patterns in this Breed. The homologous chromosome region in felids contains the gene responsible for the blotched tabby and striped coat colour patterns. Further studies, including a larger number of Pigs, are needed to confirm this result and identify the causative mutation(s) affecting this coat colour diversity, which might be used to design a conservation programme in this Breed aiming to maintain phenotypic homogeneity (i.e. solid black) that is typically associated with Nero Siciliano Pigs. This study demonstrated how genetic diversity segregating in an autochthonous genetic resource can be explored to understand the genetic mechanisms affecting phenotypic traits in a livestock species.

  • genome wide association analyses for several exterior traits in the autochthonous casertana Pig Breed
    Livestock Science, 2019
    Co-Authors: Giuseppina Schiavo, Francesca Bertolini, Maurizio Gallo, Samuele Bovo, Silvia Tinarelli, S Dallolio, Luca Fontanesi
    Abstract:

    Abstract Casertana is an autochthonous Pig Breed reared in the Central-South of Italy, mainly in extensive or semi-extensive production systems. A small number of animals are registered to the Breed herd-book. The population of this Breed is not completely fixed for several exterior traits, including ear size (small vs large), ear bearing (forward vs floppy), presence or absence of wattles and coat colour (black vs slate-grey) that we recorded in a total of 101 Pigs from six different farms. All these Pigs were also genotyped with the Illumina PorcineSNP60 BeadChip. Then, with the aim to identify DNA markers associated with these traits, we run four genome-wide association studies (GWAS) comparing Pigs having different phenotypes for each of the four external traits. Genome-wide fixation index (FST) analyses were run to confirm the results. GEMMA software was used in the GWAS. Single nucleotide polymorphisms (SNPs) associated to the wattle trait were identified on porcine chromosome (SSC) 1 and SSC11. Markers associated to the coat colour trait were located on SSC6, SSC8, SSC14 and SSC15. These chromosome regions were confirmed by the independent FST analyses. FST did not confirm the signals detected for the two ear conformation traits. Candidate genes were identified according to the function of the annotated genes in the detected genome regions. Despite the small number of Pigs that could be investigated, this study showed that autochthonous animal genetic resources might be useful to disclose genetic factors affecting traits that are not fixed in a population.

  • exploiting phenotype diversity in a local animal genetic resource identification of a single nucleotide polymorphism associated with the tail shape phenotype in the autochthonous casertana Pig Breed
    Livestock Science, 2018
    Co-Authors: Francesca Bertolini, Maurizio Gallo, Giuseppina Schiavo, Silvia Tinarelli, S Dallolio, Laura Santoro, Valerio Joe Utzeri, Leonardo Nanni Costa, Luca Fontanesi
    Abstract:

    Abstract Casertana is a local Pig Breed mainly raised in Central-South regions of Italy. Pigs of this Breed are considered the descendants of the ancient Neapolitan population that largely influenced the constitution of the modern commercial Pigs. The Pigs of this Breed are usually curly-tailed, like several other domestic Pig populations. However, Casertana population shows some variability for this trait, including animals having straight tail as observed in wild boars. In this study, we run, for the first time, a genome wide association study (GWAS) comparing the curly tailed (no. = 53) and straight tailed (no. = 19) Casertana Pigs to identify genomic regions associated with the tail shape phenotype in Sus scrofa. All animals were genotyped with the Illumina PorcineSNP60 BeadChip v.2. GEMMA software was used in the GWAS for which we were able to correct for stratification in the analysed cohort. A single nucleotide polymorphism (rs81439488), located on porcine chromosome 12, was significantly associated with the investigated trait. This marker is close to the SRY-box 9 (SOX9) gene that encodes for a transcription factor that is required during sequential steps of the chondrocyte differentiation pathway, notochord maintenance and skeletogenesis. As the shape of the tail could be important in relation to the problem of tail biting in Pigs, the obtained results might open new perspectives for defining selection programs answering indirectly animal welfare issues. This work demonstrated that autochthonous animal genetic resources might be used to disclose genetic factors affecting peculiar traits by exploiting segregating phenotypes and genetic variability.

  • twenty years of artificial directional selection have shaped the genome of the italian large white Pig Breed
    Animal Genetics, 2016
    Co-Authors: Giampietro Schiavo, Giuliano Galimberti, D G Calo, A B Samore, Francesca Bertolini, Maurizio Gallo, Luca Buttazzoni, Vincenzo Russo, Luca Fontanesi
    Abstract:

    Summary In this study, we investigated at the genome-wide level if 20 years 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 20 years 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.

  • Twenty years of artificial directional selection have shaped the genome of the Italian Large White Pig Breed.
    Animal Genetics, 2015
    Co-Authors: Giampietro Schiavo, Giuliano Galimberti, D G Calo, A B Samore, Francesca Bertolini, Maurizio Gallo, Luca Buttazzoni, Vincenzo Russo, Luca Fontanesi
    Abstract:

    Summary In this study, we investigated at the genome-wide level if 20 years 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 

Jose M Lorenzo - One of the best experts on this subject based on the ideXlab platform.

  • effect of chestnuts level in the formulation of the commercial feed on carcass characteristics and meat quality of celta Pig Breed
    Spanish Journal of Agricultural Research, 2016
    Co-Authors: C De Jesus, Ruben Dominguez, J Cantalapiedra, Antonio Iglesias, Jose M Lorenzo
    Abstract:

    The effect of including chestnuts in the formulation of the feed on carcass characteristics and meat quality from 24 castrated males Celta Pigs was studied. The inclusion of 15% of chestnut (CH15) improved ( p 0.05) differences except for the carcass length and ham length, for which the CH15 group proved to be the group with the longest sizes. The diet did not affect the physicochemical properties (colour parameters, water holding capacity and shear force) of longissimus dorsi muscle. The composition of some fatty acids of the longissimus dorsi muscle was affected by diet. The total saturated (35-38%) and total polyunsaturated fatty acids (8-10%) did not present differences. However, the increase of chestnut in the diet increased ( p <0.05) the monounsaturated fatty acids in intramuscular fat (57% in CH25 vs . 53% in control and CH15). Within monounsaturated fatty acids, the C18:1n9 was the most influenced by the diet. The expression of the enzyme that synthesizes C18:1n9 depend on the composition of the diet. Therefore, the lower content of protein and the higher amounts of C18:1n9 and C18:2n6 in the chestnut could be explaining the greater content of C18:1n9 in muscle of chestnut-fed animals. The main conclusion is that including chestnuts in the diet would allow reduce production costs with no effect or even improving carcass measurements and meat quality.

  • effect of genotype on fatty acid composition of intramuscular and subcutaneous fat of celta Pig Breed
    Grasas Y Aceites, 2014
    Co-Authors: Ruben Dominguez, Jose M Lorenzo
    Abstract:

    A total of 45 Celta Breed Pigs were used to investigate the effect of genotype (Barcina, Carballina and Santiaguesa lines) on the fatty acid composition of intramuscular (IMF) and subcutaneous fat (SF). The total IMF content was influenced by genotype (P < 0.05), since the Barcina line had the highest levels (5.21% vs 1.99 and 3.59% for Santiaguesa and Carballina lines, respectively). The total and neutral lipids from the IMF of the Santiaguesa line displayed higher contents of PUFA than the other two lines. The nutritional indices were also affected by genotype, since the Santiaguesa line presented the lowest atherogenic (AI) and thrombogenic (TI) indices and the highest hypocholesterolemic/hypercholesterolemic ratio (h/H) (P < 0.05). The IMF total and neutral lipids presented higher (P < 0.05) values of MUFA than SF, while the PUFA content was greatest in SF (P < 0.05). Regarding the polar fraction, samples from IMF presented the highest values of PUFA (between 37–44%). Finally, SF showed higher percentages of MUFA and SFA than IMF (P < 0.05). The differences in IMF content and back fat thickness imply that the deposition of IMF and SF may be regulated by different mechanism among the three lines.

  • effect of the inclusion of chestnut in the finishing diet on volatile compounds during the manufacture of dry cured lacon from celta Pig Breed
    Meat Science, 2014
    Co-Authors: Jose M Lorenzo, Daniel Franco, Javier Carballo
    Abstract:

    The effect of the finishing diet on the volatile compounds throughout the manufacture of dry-cured "lacon" (a Spanish traditional meat product), from the Celta Pig Breed was studied. Thirty-six Pigs were separated into three groups according to the type of feeding during the finish-fattening period of three months (concentrate, mixed diet and chestnut). From the Pigs of each diet, four batches of dry-cured "lacon" were manufactured. From each batch, samples of fresh meat, meat after salting, after post-salting, and after 14, 28, 56 and 84 days of drying-ripening were taken. Volatiles were extracted by a purge-and-trap method and analyzed by gas chromatographic/mass spectrometry (GC/MS). Seventy-six volatile compounds were identified and quantified from dry-cured "lacon" samples in Pigs finished with chestnut, eighty-two for concentrate fed Pigs and eighty in Pigs fed with the mixed diet. The number of identified volatile compounds increased during the manufacturing process; at 84 days of drying-ripening, in the dry-cured "lacon" samples from Pigs finished with concentrate, mixed diet and chestnut, 54, 58 and 62 volatile compounds were detected, respectively. The most abundant group of flavour compounds at the end of the manufacturing process was hydrocarbons in the three feeding systems, followed by aldehydes, ketones and alcohols. Discriminant analysis selected six variables (dodecane, butadienol, pentenol, 2-pentenal, decen-3-ona and pyridine-2-methyl) and calculated two discriminating functions which allowed verification of chestnut in the finishing diet.

  • effect of fat level on physicochemical volatile compounds and sensory characteristics of dry ripened chorizo from celta Pig Breed
    Meat Science, 2013
    Co-Authors: Maria Gomez, Jose M Lorenzo
    Abstract:

    Abstract A traditional Spanish dry-ripened sausage “chorizo” from Celta Pig Breed was formulated with 10, 20 and 30% of back fat (LF, MF and HF, respectively). An increase in fat content significantly affected the chemical composition of the sausages at the end of ripening (higher fat content and lower protein content and moisture) and physico-chemical parameters (lower pH, aw, hardness, springiness and chewiness and higher TBARS index, L*, a* and b* values). With the increase of fat in the sausage formulation a higher total content of free fatty acids (FFA) was also obtained, showing a greater lipolysis than in LF sausages. All these parameters were significantly affected by ripening time. A lower total content of volatile compounds were found in HF sausages, being detected 3 alcohols, 4 aldehydes, 12 esters, 3 ketones, 7 aliphatic and 4 aromatic hydrocarbons. Sensorial analysis showed differences for fat level and fat-lean cohesiveness within appearance attributes; odour intensity and spices odour within odour attributes and hardness within texture attributes.

  • effect of the inclusion of chestnut in the finishing diet on volatile compounds of dry cured ham from celta Pig Breed
    Journal of Integrative Agriculture, 2013
    Co-Authors: Jose M Lorenzo, Javier Carballo, Daniel Franco
    Abstract:

    Abstract The effect of the inclusion of chestnut in Pigs finishing diet on volatile compounds of dry-cured Celta ham was studied. Twelve hams of each type (from three different Pigs finishing diets: concentrate (CO), mixed (MI) and chestnut (CH)) were used. Volatiles were extracted using a purge-and-trap method and analyzed by gas chromatography/mass spectrometry (GC/MS). Thirty-nine volatile compounds were identified in dry-cured Celta ham samples. Most abundant volatiles in ham samples were aldehydes, which represented respectively, 53% (CO), 51% (MI) and 46% (CH) of the total volatile composition. With the exception of 2-butenal, 2-methyl, all aldehydes were affected by feeding system. On the other hand, hydrocarbons n-alkanes were the second major group in the volatile profile of dry-cured Celta hams and represented 28.9, 35.7 and 32.4% of the total volatile composition for CO, MI and CH groups, respectively. Ham samples from chestnut group showed a higher content of alcohols and this result could be related with the inclusion of chestnut in the finishing diet of Pigs. Principal component analysis showed a good separation among groups. The discriminant analysis selected eight variables (butanoic acid, hexanal, octanal, nonenal (E), decenal (E), tetradecane, decane trimethyl and pyridine 2-methyl) and calculated two discriminating functions to predict if chestnut has been included in the finishing diet. Thus, it was possible to discriminate between groups fed with finishing diets containing chestnuts in their composition (mixed and chestnut group).

Vincenzo Russo - One of the best experts on this subject based on the ideXlab platform.

  • twenty years of artificial directional selection have shaped the genome of the italian large white Pig Breed
    Animal Genetics, 2016
    Co-Authors: Giampietro Schiavo, Giuliano Galimberti, D G Calo, A B Samore, Francesca Bertolini, Maurizio Gallo, Luca Buttazzoni, Vincenzo Russo, Luca Fontanesi
    Abstract:

    Summary In this study, we investigated at the genome-wide level if 20 years 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 20 years 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.

  • Twenty years of artificial directional selection have shaped the genome of the Italian Large White Pig Breed.
    Animal Genetics, 2015
    Co-Authors: Giampietro Schiavo, Giuliano Galimberti, D G Calo, A B Samore, Francesca Bertolini, Maurizio Gallo, Luca Buttazzoni, Vincenzo Russo, Luca Fontanesi
    Abstract:

    Summary In this study, we investigated at the genome-wide level if 20 years 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 

  • Genome-wide study on intramuscular fat in Italian Large White Pig Breed using the PorcineSNP60 BeadChip.
    Journal of Animal Breeding and Genetics, 2015
    Co-Authors: Roberta Davoli, Diana Luise, V. Mingazzini, Silvia Braglia, Paolo Zambonelli, Andrea Serra, Vincenzo Russo
    Abstract:

    Summary Genome-wide association study results are presented for intramuscular fat in Italian Large White Pig Breed. A total of 886 individuals were genotyped with PorcineSNP60 BeadChip. After quality control performed with plink software and in R environment, 49 208 markers remained for the association analysis. The genome-wide association studies was conducted using linear mixed model implemented in GenABEL. We detected seven new SNPs of genes till now not found associated to intramuscular fat (IMF). Three markers map in a wide intergenic region rich of QTL linked to fat traits, one map 388 kb upstream the gene SDK1, one map inside PPP3CA gene, one inside SCPEP1 gene and the last is not mapped in the porcine genome yet. Associations here presented indicate a moderate effect of these genes on IMF. In particular, PPP3CA, that is involved in the oxidative metabolism of skeletal muscle, could be considerated as an interesting candidate gene for IMF content in Pigs. However, further studies are needed to clarify the role of these genes on the physiological processes involved in IMF regulation. These results may be useful to control this trait that is important in terms of nutritional, technological and organoleptic characteristics of fresh meat and processed products.

  • Analysis of the MC1R gene in the Nero Siciliano Pig Breed and usefulness of this locus for Breed traceability.
    Veterinary Research Communications, 2007
    Co-Authors: Enrico D'alessandro, Roberta Davoli, Luca Fontanesi, Luigi Liotta, Vincenzo Chiofalo, Vincenzo Russo
    Abstract:

    D’Alessandro, E., Fontanesi, L., Liotta, L., Davoli, R., Chiofalo, V., and Russo, V., 2007. Analysis of the MC1R Gene in the Nero Siciliano Pig Breed and Usefulness of this Locus for Breed Traceability. Veterinary Research Communications, 31(Suppl. 1), 389–392

Maurizio Gallo - One of the best experts on this subject based on the ideXlab platform.

  • redefinition of the mora romagnola Pig Breed herd book standard based on dna markers useful to authenticate its mono Breed products an example of sustainable conservation of a livestock genetic resource
    Open Access Journal, 2021
    Co-Authors: Silvia Tinarelli, Giuseppina Schiavo, Samuele Bovo, Valerio Joe Utzeri, Anisa Ribani, Valeria Taurisano, Claudio Bovo, S Dallolio, Francesco Nen, Maurizio Gallo
    Abstract:

    Mora Romagnola is an autochthonous Pig Breed, raised in the north of Italy. Mono-Breed pork products of this Breed are part of important niche value chain that is intrinsically linked to the conservation of this local genetic resources that can only survive due to the premium price that these products can obtain on the market. However, the added value attracts fraudsters that unscrupulously sell mis-labelled Mora Romagnola products, causing consumer distrust that, in turn, undermines the conservation strategy of this Breed. To monitor and better characterise this local Breed, we phenotyped 826 Mora Romagnola Pigs for three Breed-specific traits. Then, we genotyped almost all living sows and boars registered to the Herd Book (n. = 357 animals) for polymorphisms in the MC1R and NR6A1 genes (affecting coat colour and vertebral number, respectively). The results were used to re-define the Breed descriptors of the Mora Romagnala Breed that included information on the allowed genotypes at these two genes. A few Pigs that did not carry the allowed genotypes were excluded from its Herd Book. Finally, we evaluated the usefulness of these DNA markers to authenticate Mora Romagnola meat against meat derived from other 11 Pig Breeds and wild boars. To our knowledge, the Mora Romagnola Herd Book is one of the first examples that established a direct link between a genetic standard of a Breed with the possibility to authenticate mono-Breed products using DNA markers with the specific purpose to combat frauds and, indirectly, support the conservation of a livestock genetic resource.

  • genome wide association analyses for coat colour patterns in the autochthonous nero siciliano Pig Breed
    Livestock Science, 2020
    Co-Authors: Giuseppina Schiavo, Maurizio Gallo, Samuele Bovo, Silvia Tinarelli, S Dallolio, Luca Fontanesi
    Abstract:

    Abstract Nero Siciliano (or Sicilian Black) is an Italian autochthonous Pig Breed reared in the Sicily island, mainly under extensive management systems. Nero Siciliano Pigs are black (with black skin and black hair), but animals with white face or partially white face ("suino facciolo") can be registered to the Breed herd book. Sometimes, other white patterns on extreme portions of legs could appear in this population. This study took advantage from the rare occurrence of Pigs with white patterns in the Nero Siciliano population to carry out a genome-wide association study and comparative genome-wide Fixation index (FST) analysis to identify genomic regions that could affect coat colour variability (solid black vs white patterns over black) in this autochthonous Pig Breed. Analyses have been conducted on 66 Nero Siciliano Pigs: 30 completely black and 36 black with white patterns. All samples have been genotyped for the KIT gene duplication and MC1R mutations, two genes well known to affect coat colours in Pigs. Only Pigs that did not carry any duplication of the KIT gene and were homozygous for the ED2 black dominant MC1R gene allele (n = 26 completely black and n. 22 with white patterns) were genotyped with the Illumina PorcineSNP60 BeadChip. The genome-wide analyzes identified on chromosome 2 a significant marker (rs81329493) associated with the coat colour white patterns in this Breed. The homologous chromosome region in felids contains the gene responsible for the blotched tabby and striped coat colour patterns. Further studies, including a larger number of Pigs, are needed to confirm this result and identify the causative mutation(s) affecting this coat colour diversity, which might be used to design a conservation programme in this Breed aiming to maintain phenotypic homogeneity (i.e. solid black) that is typically associated with Nero Siciliano Pigs. This study demonstrated how genetic diversity segregating in an autochthonous genetic resource can be explored to understand the genetic mechanisms affecting phenotypic traits in a livestock species.

  • genome wide association analyses for several exterior traits in the autochthonous casertana Pig Breed
    Livestock Science, 2019
    Co-Authors: Giuseppina Schiavo, Francesca Bertolini, Maurizio Gallo, Samuele Bovo, Silvia Tinarelli, S Dallolio, Luca Fontanesi
    Abstract:

    Abstract Casertana is an autochthonous Pig Breed reared in the Central-South of Italy, mainly in extensive or semi-extensive production systems. A small number of animals are registered to the Breed herd-book. The population of this Breed is not completely fixed for several exterior traits, including ear size (small vs large), ear bearing (forward vs floppy), presence or absence of wattles and coat colour (black vs slate-grey) that we recorded in a total of 101 Pigs from six different farms. All these Pigs were also genotyped with the Illumina PorcineSNP60 BeadChip. Then, with the aim to identify DNA markers associated with these traits, we run four genome-wide association studies (GWAS) comparing Pigs having different phenotypes for each of the four external traits. Genome-wide fixation index (FST) analyses were run to confirm the results. GEMMA software was used in the GWAS. Single nucleotide polymorphisms (SNPs) associated to the wattle trait were identified on porcine chromosome (SSC) 1 and SSC11. Markers associated to the coat colour trait were located on SSC6, SSC8, SSC14 and SSC15. These chromosome regions were confirmed by the independent FST analyses. FST did not confirm the signals detected for the two ear conformation traits. Candidate genes were identified according to the function of the annotated genes in the detected genome regions. Despite the small number of Pigs that could be investigated, this study showed that autochthonous animal genetic resources might be useful to disclose genetic factors affecting traits that are not fixed in a population.

  • exploiting phenotype diversity in a local animal genetic resource identification of a single nucleotide polymorphism associated with the tail shape phenotype in the autochthonous casertana Pig Breed
    Livestock Science, 2018
    Co-Authors: Francesca Bertolini, Maurizio Gallo, Giuseppina Schiavo, Silvia Tinarelli, S Dallolio, Laura Santoro, Valerio Joe Utzeri, Leonardo Nanni Costa, Luca Fontanesi
    Abstract:

    Abstract Casertana is a local Pig Breed mainly raised in Central-South regions of Italy. Pigs of this Breed are considered the descendants of the ancient Neapolitan population that largely influenced the constitution of the modern commercial Pigs. The Pigs of this Breed are usually curly-tailed, like several other domestic Pig populations. However, Casertana population shows some variability for this trait, including animals having straight tail as observed in wild boars. In this study, we run, for the first time, a genome wide association study (GWAS) comparing the curly tailed (no. = 53) and straight tailed (no. = 19) Casertana Pigs to identify genomic regions associated with the tail shape phenotype in Sus scrofa. All animals were genotyped with the Illumina PorcineSNP60 BeadChip v.2. GEMMA software was used in the GWAS for which we were able to correct for stratification in the analysed cohort. A single nucleotide polymorphism (rs81439488), located on porcine chromosome 12, was significantly associated with the investigated trait. This marker is close to the SRY-box 9 (SOX9) gene that encodes for a transcription factor that is required during sequential steps of the chondrocyte differentiation pathway, notochord maintenance and skeletogenesis. As the shape of the tail could be important in relation to the problem of tail biting in Pigs, the obtained results might open new perspectives for defining selection programs answering indirectly animal welfare issues. This work demonstrated that autochthonous animal genetic resources might be used to disclose genetic factors affecting peculiar traits by exploiting segregating phenotypes and genetic variability.

  • twenty years of artificial directional selection have shaped the genome of the italian large white Pig Breed
    Animal Genetics, 2016
    Co-Authors: Giampietro Schiavo, Giuliano Galimberti, D G Calo, A B Samore, Francesca Bertolini, Maurizio Gallo, Luca Buttazzoni, Vincenzo Russo, Luca Fontanesi
    Abstract:

    Summary In this study, we investigated at the genome-wide level if 20 years 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 20 years 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.

Javier Carballo - One of the best experts on this subject based on the ideXlab platform.

  • fatty acid profile and cholesterol and retinol contents in different locations of celta Pig Breed
    Grasas Y Aceites, 2014
    Co-Authors: Ruben Dominguez, Sidonia Martinez, Javier Carballo, Inmaculada Franco
    Abstract:

    The fatty acid profile (total, neutral and polar lipids) and cholesterol and retinol contents of the intramuscular -Longissimus dorsi (LD) and Psoas major (PM)-, adipose -rump, covering Biceps femoris muscle, ventral and dorsal-, perirenal and hepatic fat of the Celta Pig Breed (Galicia, northwest Spain) were evaluated. Oleic acid was the most abundant fatty acid, except in the polar lipids of the intramuscular fat, where the most abundant fatty acid was linoleic acid. The fatty acid composition of total and neutral lipids was influenced more by the location than the fatty acids of polar lipids. There were some differences only in minor fatty acids of intramuscular and subcutaneous fat between castrated females and castrated males. The fatty acids of neutral lipids were also more influenced by sex than the fatty acids of polar lipids. The cholesterol and retinol contents showed no significant differences by sex. The LD muscle showed a higher content of intramuscular fat than the PM muscle. The greatest cholesterol values were described in the liver. Subcutaneous locations showed higher cholesterol levels than muscles.

  • effect of the inclusion of chestnut in the finishing diet on volatile compounds during the manufacture of dry cured lacon from celta Pig Breed
    Meat Science, 2014
    Co-Authors: Jose M Lorenzo, Daniel Franco, Javier Carballo
    Abstract:

    The effect of the finishing diet on the volatile compounds throughout the manufacture of dry-cured "lacon" (a Spanish traditional meat product), from the Celta Pig Breed was studied. Thirty-six Pigs were separated into three groups according to the type of feeding during the finish-fattening period of three months (concentrate, mixed diet and chestnut). From the Pigs of each diet, four batches of dry-cured "lacon" were manufactured. From each batch, samples of fresh meat, meat after salting, after post-salting, and after 14, 28, 56 and 84 days of drying-ripening were taken. Volatiles were extracted by a purge-and-trap method and analyzed by gas chromatographic/mass spectrometry (GC/MS). Seventy-six volatile compounds were identified and quantified from dry-cured "lacon" samples in Pigs finished with chestnut, eighty-two for concentrate fed Pigs and eighty in Pigs fed with the mixed diet. The number of identified volatile compounds increased during the manufacturing process; at 84 days of drying-ripening, in the dry-cured "lacon" samples from Pigs finished with concentrate, mixed diet and chestnut, 54, 58 and 62 volatile compounds were detected, respectively. The most abundant group of flavour compounds at the end of the manufacturing process was hydrocarbons in the three feeding systems, followed by aldehydes, ketones and alcohols. Discriminant analysis selected six variables (dodecane, butadienol, pentenol, 2-pentenal, decen-3-ona and pyridine-2-methyl) and calculated two discriminating functions which allowed verification of chestnut in the finishing diet.

  • effect of the inclusion of chestnut in the finishing diet on volatile compounds of dry cured ham from celta Pig Breed
    Journal of Integrative Agriculture, 2013
    Co-Authors: Jose M Lorenzo, Javier Carballo, Daniel Franco
    Abstract:

    Abstract The effect of the inclusion of chestnut in Pigs finishing diet on volatile compounds of dry-cured Celta ham was studied. Twelve hams of each type (from three different Pigs finishing diets: concentrate (CO), mixed (MI) and chestnut (CH)) were used. Volatiles were extracted using a purge-and-trap method and analyzed by gas chromatography/mass spectrometry (GC/MS). Thirty-nine volatile compounds were identified in dry-cured Celta ham samples. Most abundant volatiles in ham samples were aldehydes, which represented respectively, 53% (CO), 51% (MI) and 46% (CH) of the total volatile composition. With the exception of 2-butenal, 2-methyl, all aldehydes were affected by feeding system. On the other hand, hydrocarbons n-alkanes were the second major group in the volatile profile of dry-cured Celta hams and represented 28.9, 35.7 and 32.4% of the total volatile composition for CO, MI and CH groups, respectively. Ham samples from chestnut group showed a higher content of alcohols and this result could be related with the inclusion of chestnut in the finishing diet of Pigs. Principal component analysis showed a good separation among groups. The discriminant analysis selected eight variables (butanoic acid, hexanal, octanal, nonenal (E), decenal (E), tetradecane, decane trimethyl and pyridine 2-methyl) and calculated two discriminating functions to predict if chestnut has been included in the finishing diet. Thus, it was possible to discriminate between groups fed with finishing diets containing chestnuts in their composition (mixed and chestnut group).

  • influence of inclusion of chestnut in the finishing diet on fatty acid profile of dry cured ham from celta Pig Breed
    Meat Science, 2012
    Co-Authors: Roberto Bermudez, Inmaculada Franco, Javier Carballo, Daniel Franco, Jose M Lorenzo
    Abstract:

    The effect of the inclusion of chestnut in the finishing diet on fatty acid profile of dry-cured Celta ham was studied. Twelve hams of each type (from three different diets: concentrate, mixed and chestnut) were used. Significant differences between treatments (P<0.001) were found regarding total saturated fatty acids (SFA), monounsaturated fatty acids (MUFA) and polyunsaturated fatty acids (PUFA). Ham samples from the mixed and chestnut groups had less SFA (35.57% and 35.63%, respectively) with respect to ham samples from the concentrate group (40.33%), while hams from the mixed and chestnut batches showed higher values of MUFA than hams from the concentrate group (50.70 vs. 49.79 vs. 43.85, P<0.001, respectively). From a nutritional point of view, Celta hams from chestnut diets could be considered as healthier regarding their fatty acid profiles (low n-6/n-3 ratio and high hypocholesterolemic/Hypercholesterolemic ratio). Discriminant analysis selected five variables (C(16:0), C(16:1cis-9), C(20:2), C(20:3n-6) and C(20:4n-6)) and calculated two discriminating functions which verifies the presence of chestnut in the finishing diet.

  • fatty acid profile of the fat from celta Pig Breed fattened using a traditional feed effect of the location in the carcass
    Journal of Food Composition and Analysis, 2006
    Co-Authors: Inmaculada Franco, Cristina M Escamilla, Jose Santiago Garcia, Camino Garcia M Fontan, Javier Carballo
    Abstract:

    Abstract The Celta Breed of Pig is an autochthonous Breed raised in Galicia (northwest Spain), whose numbers are presently increasing. In this work, the content of 22 fatty acids was studied in samples of fat taken from three different deposits on the dressed carcasses (intramuscular, subcutaneous ventral and subcutaneous dorsal) of 14 Celta castrated male hogs. These were slaughtered at the age of 15 months after being fed a traditional diet mainly consisting, during the last three months of fattening, of chestnuts (fruit of Castanea sativa). The intramuscular fat showed higher (37.93±1.27%) statistically significant values ( P 0.05 ) of saturated fatty acids than the subcutaneous ventral fat (34.84±2.41%) and the subcutaneous dorsal fat (31.89±1.49%). Stearic acid showed the largest difference among the three locations. The unsaturated fatty acids showed a significantly higher percentage in the subcutaneous dorsal fat (68.11±1.49%) than in the subcutaneous ventral fat (65.16±2.41%) and in the intramuscular fat (62.07±1.27%). The percentage of polyunsaturated fatty acids was also significantly higher in the subcutaneous dorsal fat (15.51±0.72%) than in the subcutaneous ventral fat (14.13±1.02%) and in the intramuscular fat (11.29±1.72%). Linoleic and eicosadienoic fatty acids showed the highest variation in their percentages when compared in the three locations of the fat in the carcass. The contents of monounsaturated fatty acids were similar in all three locations and no significant differences were observed linked to the location of the fat in the carcass. Using statistical techniques of discriminant analysis, it has been possible to correctly differentiate the fat of the three locations on the basis of their content (%) of the C18, C18:2 and C20:2 fatty acids. The profile of fatty acids that we observed in the fat of the Celta hogs does not differ greatly from those described by other authors in other Pig Breeds and crosses.