TY  - RPRT
AU  - Dadousis, Christos
AU  - Munoz, Maria
AU  - Ovilo, Cristina
AU  - Fabbri, Maria Chiara
AU  - Araujo, Jose Pedro
AU  - Bovo, Samuele
AU  - Čandek Potokar, Marjeta
AU  - Charneca, Rui
AU  - Crovetti, Alessandro
AU  - Gallo, Maurizio
AU  - Garcia-Casco, Juan Maria
AU  - Karolyi, Danijel
AU  - Kušec, Goran
AU  - Martins, Jose Manuel
AU  - Mercat, Marie-Jose
AU  - Pugliese, Carolina
AU  - Quintanilla, Raquel
AU  - Radović, Čedomir
AU  - Razmaite, Violeta
AU  - Ribani, Anisa
AU  - Raquet, Juliet
AU  - Savić, Radomir
AU  - Schiavo, Giuseppina
AU  - Škrlep, Martin
AU  - Tinarelli, Silvia
AU  - Usai, Graziano
AU  - Zimmer, Christoph
AU  - Fontanesi, Luca
AU  - Bozzi, Riccardo
PY  - 2022
UR  - http://r.istocar.bg.ac.rs/handle/123456789/819
AB  - Preserving diversity of indigenous pig (Sus scrofa) breeds is a key factor to (i) sustain the pork chain
(both at local and global scales) including the production of high-quality branded products, (ii) enrich
the animal biobanking and (iii) progress conservation policies. Single nucleotide polymorphism (SNP)
chips ofer the opportunity for whole-genome comparisons among individuals and breeds. Animals
from twenty European local pigs breeds, reared in nine countries (Croatia: Black Slavonian, Turopolje;
France: Basque, Gascon; Germany: Schwabisch-Hällisches Schwein; Italy: Apulo Calabrese, Casertana,
Cinta Senese, Mora Romagnola, Nero Siciliano, Sarda; Lithuania: Indigenous Wattle, White Old Type;
Portugal: Alentejana, Bísara; Serbia: Moravka, Swallow-Bellied Mangalitsa; Slovenia: Krškopolje pig;
Spain: Iberian, Majorcan Black), and three commercial breeds (Duroc, Landrace and Large White) were
sampled and genotyped with the GeneSeek Genomic Profler (GGP) 70 K HD porcine genotyping chip.
A dataset of 51 Wild Boars from nine countries was also added, summing up to 1186 pigs (~49 pigs/
breed). The aim was to: (i) investigate individual admixture ancestries and (ii) assess breed traceability
via discriminant analysis on principal components (DAPC). Albeit the mosaic of shared ancestries
found for Nero Siciliano, Sarda and Moravka, admixture analysis indicated independent evolvement
PB  - Nature Portfolio
T2  - Scientifc Reports
T1  - Admixture and breed traceability in European indigenous pig breeds and wild boar using genome‑wide SNP data
VL  - 12
IS  - 7146
DO  - https://doi.org/10.1038/s41598-022-10698-8
ER  - 

@techreport{
author = "Dadousis, Christos and Munoz, Maria and Ovilo, Cristina and Fabbri, Maria Chiara and Araujo, Jose Pedro and Bovo, Samuele and Čandek Potokar, Marjeta and Charneca, Rui and Crovetti, Alessandro and Gallo, Maurizio and Garcia-Casco, Juan Maria and Karolyi, Danijel and Kušec, Goran and Martins, Jose Manuel and Mercat, Marie-Jose and Pugliese, Carolina and Quintanilla, Raquel and Radović, Čedomir and Razmaite, Violeta and Ribani, Anisa and Raquet, Juliet and Savić, Radomir and Schiavo, Giuseppina and Škrlep, Martin and Tinarelli, Silvia and Usai, Graziano and Zimmer, Christoph and Fontanesi, Luca and Bozzi, Riccardo",
year = "2022",
abstract = "Preserving diversity of indigenous pig (Sus scrofa) breeds is a key factor to (i) sustain the pork chain
(both at local and global scales) including the production of high-quality branded products, (ii) enrich
the animal biobanking and (iii) progress conservation policies. Single nucleotide polymorphism (SNP)
chips ofer the opportunity for whole-genome comparisons among individuals and breeds. Animals
from twenty European local pigs breeds, reared in nine countries (Croatia: Black Slavonian, Turopolje;
France: Basque, Gascon; Germany: Schwabisch-Hällisches Schwein; Italy: Apulo Calabrese, Casertana,
Cinta Senese, Mora Romagnola, Nero Siciliano, Sarda; Lithuania: Indigenous Wattle, White Old Type;
Portugal: Alentejana, Bísara; Serbia: Moravka, Swallow-Bellied Mangalitsa; Slovenia: Krškopolje pig;
Spain: Iberian, Majorcan Black), and three commercial breeds (Duroc, Landrace and Large White) were
sampled and genotyped with the GeneSeek Genomic Profler (GGP) 70 K HD porcine genotyping chip.
A dataset of 51 Wild Boars from nine countries was also added, summing up to 1186 pigs (~49 pigs/
breed). The aim was to: (i) investigate individual admixture ancestries and (ii) assess breed traceability
via discriminant analysis on principal components (DAPC). Albeit the mosaic of shared ancestries
found for Nero Siciliano, Sarda and Moravka, admixture analysis indicated independent evolvement",
publisher = "Nature Portfolio",
journal = "Scientifc Reports",
title = "Admixture and breed traceability in European indigenous pig breeds and wild boar using genome‑wide SNP data",
volume = "12",
number = "7146",
doi = "https://doi.org/10.1038/s41598-022-10698-8"
}

Dadousis, C., Munoz, M., Ovilo, C., Fabbri, M. C., Araujo, J. P., Bovo, S., Čandek Potokar, M., Charneca, R., Crovetti, A., Gallo, M., Garcia-Casco, J. M., Karolyi, D., Kušec, G., Martins, J. M., Mercat, M., Pugliese, C., Quintanilla, R., Radović, Č., Razmaite, V., Ribani, A., Raquet, J., Savić, R., Schiavo, G., Škrlep, M., Tinarelli, S., Usai, G., Zimmer, C., Fontanesi, L.,& Bozzi, R.. (2022). Admixture and breed traceability in European indigenous pig breeds and wild boar using genome‑wide SNP data. in Scientifc Reports
Nature Portfolio., 12(7146).
https://doi.org/https://doi.org/10.1038/s41598-022-10698-8

Dadousis C, Munoz M, Ovilo C, Fabbri MC, Araujo JP, Bovo S, Čandek Potokar M, Charneca R, Crovetti A, Gallo M, Garcia-Casco JM, Karolyi D, Kušec G, Martins JM, Mercat M, Pugliese C, Quintanilla R, Radović Č, Razmaite V, Ribani A, Raquet J, Savić R, Schiavo G, Škrlep M, Tinarelli S, Usai G, Zimmer C, Fontanesi L, Bozzi R. Admixture and breed traceability in European indigenous pig breeds and wild boar using genome‑wide SNP data. in Scientifc Reports. 2022;12(7146).
doi:https://doi.org/10.1038/s41598-022-10698-8 .

Dadousis, Christos, Munoz, Maria, Ovilo, Cristina, Fabbri, Maria Chiara, Araujo, Jose Pedro, Bovo, Samuele, Čandek Potokar, Marjeta, Charneca, Rui, Crovetti, Alessandro, Gallo, Maurizio, Garcia-Casco, Juan Maria, Karolyi, Danijel, Kušec, Goran, Martins, Jose Manuel, Mercat, Marie-Jose, Pugliese, Carolina, Quintanilla, Raquel, Radović, Čedomir, Razmaite, Violeta, Ribani, Anisa, Raquet, Juliet, Savić, Radomir, Schiavo, Giuseppina, Škrlep, Martin, Tinarelli, Silvia, Usai, Graziano, Zimmer, Christoph, Fontanesi, Luca, Bozzi, Riccardo, "Admixture and breed traceability in European indigenous pig breeds and wild boar using genome‑wide SNP data" in Scientifc Reports, 12, no. 7146 (2022),
https://doi.org/https://doi.org/10.1038/s41598-022-10698-8 . .

TY  - JOUR
AU  - Schiavo, Giussepina
AU  - Bovo, Samuele
AU  - Munoz, Maria
AU  - Ribani, Anisa
AU  - Alves, Estefania
AU  - Araujo, Jose P.
AU  - Bozzi, Riccardo
AU  - Čandek-Potokar, Marjeta
AU  - Charneca, Rui
AU  - Fernandez, Ana I.
AU  - Gallo, Maurizio
AU  - Garcia, Fabian
AU  - Karolyi, Danijel
AU  - Kušec, Goran
AU  - Martins, Jose Manuel
AU  - Mercat, Marie-Jose
AU  - Nunez, Yolanda
AU  - Quintanilla, Raquel
AU  - Radović, Čedomir
AU  - Razmaite, Violeta
AU  - Riquet, Juliette
AU  - Savić, Radomir
AU  - Usai, Graziano
AU  - Utzeri, Valerio J.
AU  - Zimmer, Christoph
AU  - Ovilo, Cristina
AU  - Fontanesi, Luca
PY  - 2021-04
UR  - http://r.istocar.bg.ac.rs/handle/123456789/925
AB  - ROHs are long stretches of DNA homozygous at each polymorphic position. The proportion of
genome covered by ROHs and their length are indicators of the level and origin of inbreeding.
Frequent common ROHs within the same population define ROH islands and indicate hotspots of
selection. In this work, we investigated ROHs in a total of 1131 pigs from 20 European local pig
breeds and in three cosmopolitan breeds, genotyped with the GGP Porcine HD Genomic Profiler.
PLINK software was used to identify ROHs. Size classes and genomic inbreeding parameters were evaluated. ROH islands were defined by evaluating different thresholds of homozygous SNP
frequency. A functional overview of breed-specific ROH islands was obtained via overrepresentation analyses of GO biological processes. Mora Romagnola and Turopolje breeds had the largest proportions of genome covered with ROH (~1003 and ~955 Mb respectively),
whereas Nero Siciliano and Sarda breeds had the lowest proportions (~207 and 247 Mb
respectively). The highest proportion of long ROH (>16 Mb) was in Apulo-Calabrese, Mora
Romagnola and Casertana. The largest number of ROH islands was identified in the Italian
Landrace (n=32), Cinta Senese (n=26) and LithuanianWhite Old Type (n=22) breeds. Several
ROH islands were in regions encompassing genes known to affect morphological traits.
Comparative ROH structure analysis among breeds indicated the similar genetic structure of
local breeds across Europe. This study contributed to understanding of the genetic history of the
investigated pig breeds and provided information to manage these pig genetic resources.
PB  - Blackwell Publishing Ltd
T2  - Animal Genetics
T1  - Runs of homozygosity provide a genome landscape picture of inbreeding and genetic history of European autochthonous and commercial pig breeds
VL  - 52
SP  - 155
EP  - 170
DO  - 10.1111/age.13045
ER  - 

@article{
author = "Schiavo, Giussepina and Bovo, Samuele and Munoz, Maria and Ribani, Anisa and Alves, Estefania and Araujo, Jose P. and Bozzi, Riccardo and Čandek-Potokar, Marjeta and Charneca, Rui and Fernandez, Ana I. and Gallo, Maurizio and Garcia, Fabian and Karolyi, Danijel and Kušec, Goran and Martins, Jose Manuel and Mercat, Marie-Jose and Nunez, Yolanda and Quintanilla, Raquel and Radović, Čedomir and Razmaite, Violeta and Riquet, Juliette and Savić, Radomir and Usai, Graziano and Utzeri, Valerio J. and Zimmer, Christoph and Ovilo, Cristina and Fontanesi, Luca",
year = "2021-04",
abstract = "ROHs are long stretches of DNA homozygous at each polymorphic position. The proportion of
genome covered by ROHs and their length are indicators of the level and origin of inbreeding.
Frequent common ROHs within the same population define ROH islands and indicate hotspots of
selection. In this work, we investigated ROHs in a total of 1131 pigs from 20 European local pig
breeds and in three cosmopolitan breeds, genotyped with the GGP Porcine HD Genomic Profiler.
PLINK software was used to identify ROHs. Size classes and genomic inbreeding parameters were evaluated. ROH islands were defined by evaluating different thresholds of homozygous SNP
frequency. A functional overview of breed-specific ROH islands was obtained via overrepresentation analyses of GO biological processes. Mora Romagnola and Turopolje breeds had the largest proportions of genome covered with ROH (~1003 and ~955 Mb respectively),
whereas Nero Siciliano and Sarda breeds had the lowest proportions (~207 and 247 Mb
respectively). The highest proportion of long ROH (>16 Mb) was in Apulo-Calabrese, Mora
Romagnola and Casertana. The largest number of ROH islands was identified in the Italian
Landrace (n=32), Cinta Senese (n=26) and LithuanianWhite Old Type (n=22) breeds. Several
ROH islands were in regions encompassing genes known to affect morphological traits.
Comparative ROH structure analysis among breeds indicated the similar genetic structure of
local breeds across Europe. This study contributed to understanding of the genetic history of the
investigated pig breeds and provided information to manage these pig genetic resources.",
publisher = "Blackwell Publishing Ltd",
journal = "Animal Genetics",
title = "Runs of homozygosity provide a genome landscape picture of inbreeding and genetic history of European autochthonous and commercial pig breeds",
volume = "52",
pages = "155-170",
doi = "10.1111/age.13045"
}

Schiavo, G., Bovo, S., Munoz, M., Ribani, A., Alves, E., Araujo, J. P., Bozzi, R., Čandek-Potokar, M., Charneca, R., Fernandez, A. I., Gallo, M., Garcia, F., Karolyi, D., Kušec, G., Martins, J. M., Mercat, M., Nunez, Y., Quintanilla, R., Radović, Č., Razmaite, V., Riquet, J., Savić, R., Usai, G., Utzeri, V. J., Zimmer, C., Ovilo, C.,& Fontanesi, L.. (2021-04). Runs of homozygosity provide a genome landscape picture of inbreeding and genetic history of European autochthonous and commercial pig breeds. in Animal Genetics
Blackwell Publishing Ltd., 52, 155-170.
https://doi.org/10.1111/age.13045

Schiavo G, Bovo S, Munoz M, Ribani A, Alves E, Araujo JP, Bozzi R, Čandek-Potokar M, Charneca R, Fernandez AI, Gallo M, Garcia F, Karolyi D, Kušec G, Martins JM, Mercat M, Nunez Y, Quintanilla R, Radović Č, Razmaite V, Riquet J, Savić R, Usai G, Utzeri VJ, Zimmer C, Ovilo C, Fontanesi L. Runs of homozygosity provide a genome landscape picture of inbreeding and genetic history of European autochthonous and commercial pig breeds. in Animal Genetics. 2021;52:155-170.
doi:10.1111/age.13045 .

Schiavo, Giussepina, Bovo, Samuele, Munoz, Maria, Ribani, Anisa, Alves, Estefania, Araujo, Jose P., Bozzi, Riccardo, Čandek-Potokar, Marjeta, Charneca, Rui, Fernandez, Ana I., Gallo, Maurizio, Garcia, Fabian, Karolyi, Danijel, Kušec, Goran, Martins, Jose Manuel, Mercat, Marie-Jose, Nunez, Yolanda, Quintanilla, Raquel, Radović, Čedomir, Razmaite, Violeta, Riquet, Juliette, Savić, Radomir, Usai, Graziano, Utzeri, Valerio J., Zimmer, Christoph, Ovilo, Cristina, Fontanesi, Luca, "Runs of homozygosity provide a genome landscape picture of inbreeding and genetic history of European autochthonous and commercial pig breeds" in Animal Genetics, 52 (2021-04):155-170,
https://doi.org/10.1111/age.13045 . .

TY  - JOUR
AU  - Nunez, Yolanda
AU  - Radović, Čedomir
AU  - Savić, Radomir
AU  - Garcia-Casco, M. Juan
AU  - Čandek-Potokar, Marjeta
AU  - Benitez, Rita
AU  - Radojković, Dragan
AU  - Lukić, Miloš
AU  - Gogić, Marija
AU  - Munoz, Maria
AU  - Fontanesi, Luca
AU  - Ovilo, Cristina
PY  - 2021-03-16
UR  - http://r.istocar.bg.ac.rs/handle/123456789/772
AB  - This work was aimed at evaluating loin transcriptome and metabolic pathway differences between the two main Serbian local pig breeds with divergent characteristics regarding muscle growth and fatness, as well as exploring nutrigenomic effects of tannin supplementation in Mangalitsa (MA) pigs. The study comprised 24 Mangalitsa and 10 Moravka (MO) males, which were kept under
identical management conditions. Mangalitsa animals were divided in two nutritional groups (n = 12) receiving a standard (control) or tannin–supplemented diet (1.5%; MAT). Moravka pigs were fed the standard mixture. All animals were slaughtered at a similar age; 120 kg of average live weight (LW) and loin tissue was used for RNA-seq analysis. Results showed 306 differentially expressed genes (DEGs) according to breed, enriched in genes involved in growth, lipid metabolism, protein metabolism and muscle development, such as PDK4, FABP4, MYOD1 and STAT3, as well as a relevant number of genes involved in mitochondrial respiratory activity (MT- Ds, NDUFAs among others). Oxidative phosphorylation was the most significantly affected pathway, activated in Mangalitsa muscle, revealing the basis of a different muscle metabolism. Also, many other relevant pathways were affected by breed and involved in oxidative stress response, fat accumulation and development of skeletal muscle. Results also allowed the identification of potential regulators and causal networks such as those controlled by FLCN, PPARGC1A or PRKAB1 with relevant regulatory roles on DEGs involved in mitochondrial and lipid metabolism, or IL3 and TRAF2 potentially controlling DEGs involved in muscle development. The Tannin effect on transcriptome was small, with only 23 DEGs, but included interesting ones involved in lipid deposition such as PPARGC1B. The results indicate a significant effect of the breed on muscle tissue gene expression, affecting relevant biological pathways and allowing the identification of strong regulatory candidate genes to underlie the gene expression and phenotypic differences between the compared groups.
PB  - MDPI
T2  - Animals
T1  - Muscle transcriptome analysis reveals molecular pathways related to oxidative phosphorylation, antioxidant defense, fatness and growth in mangalitsa and moravka pigs
VL  - 11
IS  - 844
DO  - 10.3390/ani11030844
ER  - 

@article{
author = "Nunez, Yolanda and Radović, Čedomir and Savić, Radomir and Garcia-Casco, M. Juan and Čandek-Potokar, Marjeta and Benitez, Rita and Radojković, Dragan and Lukić, Miloš and Gogić, Marija and Munoz, Maria and Fontanesi, Luca and Ovilo, Cristina",
year = "2021-03-16",
abstract = "This work was aimed at evaluating loin transcriptome and metabolic pathway differences between the two main Serbian local pig breeds with divergent characteristics regarding muscle growth and fatness, as well as exploring nutrigenomic effects of tannin supplementation in Mangalitsa (MA) pigs. The study comprised 24 Mangalitsa and 10 Moravka (MO) males, which were kept under
identical management conditions. Mangalitsa animals were divided in two nutritional groups (n = 12) receiving a standard (control) or tannin–supplemented diet (1.5%; MAT). Moravka pigs were fed the standard mixture. All animals were slaughtered at a similar age; 120 kg of average live weight (LW) and loin tissue was used for RNA-seq analysis. Results showed 306 differentially expressed genes (DEGs) according to breed, enriched in genes involved in growth, lipid metabolism, protein metabolism and muscle development, such as PDK4, FABP4, MYOD1 and STAT3, as well as a relevant number of genes involved in mitochondrial respiratory activity (MT- Ds, NDUFAs among others). Oxidative phosphorylation was the most significantly affected pathway, activated in Mangalitsa muscle, revealing the basis of a different muscle metabolism. Also, many other relevant pathways were affected by breed and involved in oxidative stress response, fat accumulation and development of skeletal muscle. Results also allowed the identification of potential regulators and causal networks such as those controlled by FLCN, PPARGC1A or PRKAB1 with relevant regulatory roles on DEGs involved in mitochondrial and lipid metabolism, or IL3 and TRAF2 potentially controlling DEGs involved in muscle development. The Tannin effect on transcriptome was small, with only 23 DEGs, but included interesting ones involved in lipid deposition such as PPARGC1B. The results indicate a significant effect of the breed on muscle tissue gene expression, affecting relevant biological pathways and allowing the identification of strong regulatory candidate genes to underlie the gene expression and phenotypic differences between the compared groups.",
publisher = "MDPI",
journal = "Animals",
title = "Muscle transcriptome analysis reveals molecular pathways related to oxidative phosphorylation, antioxidant defense, fatness and growth in mangalitsa and moravka pigs",
volume = "11",
number = "844",
doi = "10.3390/ani11030844"
}

Nunez, Y., Radović, Č., Savić, R., Garcia-Casco, M. J., Čandek-Potokar, M., Benitez, R., Radojković, D., Lukić, M., Gogić, M., Munoz, M., Fontanesi, L.,& Ovilo, C.. (2021-03-16). Muscle transcriptome analysis reveals molecular pathways related to oxidative phosphorylation, antioxidant defense, fatness and growth in mangalitsa and moravka pigs. in Animals
MDPI., 11(844).
https://doi.org/10.3390/ani11030844

Nunez Y, Radović Č, Savić R, Garcia-Casco MJ, Čandek-Potokar M, Benitez R, Radojković D, Lukić M, Gogić M, Munoz M, Fontanesi L, Ovilo C. Muscle transcriptome analysis reveals molecular pathways related to oxidative phosphorylation, antioxidant defense, fatness and growth in mangalitsa and moravka pigs. in Animals. 2021;11(844).
doi:10.3390/ani11030844 .

Nunez, Yolanda, Radović, Čedomir, Savić, Radomir, Garcia-Casco, M. Juan, Čandek-Potokar, Marjeta, Benitez, Rita, Radojković, Dragan, Lukić, Miloš, Gogić, Marija, Munoz, Maria, Fontanesi, Luca, Ovilo, Cristina, "Muscle transcriptome analysis reveals molecular pathways related to oxidative phosphorylation, antioxidant defense, fatness and growth in mangalitsa and moravka pigs" in Animals, 11, no. 844 (2021-03-16),
https://doi.org/10.3390/ani11030844 . .

TY  - JOUR
AU  - Bovo, Samuele
AU  - Ribani, Anisa
AU  - Munoz, Maria
AU  - Alves, Estefania
AU  - Araujo, Jose P.
AU  - Bozzi, Riccardo
AU  - Charneca, Rui
AU  - Di Palma, Federica
AU  - Etherington, Graham
AU  - Fernandez, Ana I.
AU  - Garcia, Fabian
AU  - Garcia-Casco, Juan
AU  - Karolyi, Danijel
AU  - Gallo, Maurizio
AU  - Gvozdanović, Katarina
AU  - Martins, Jose Manuel
AU  - Mercat, Marie J.
AU  - Nunez, Yolanda
AU  - Quintailla, Raquel
AU  - Radović, Čedomir
AU  - Razmaite, Violeta
AU  - Riquet, Juliette
AU  - Savić, Radomir
AU  - Schiavo, Giuseppina
AU  - Škrlep, Martin
AU  - Usai, Graziano
AU  - Utzeri, Valerio J.
AU  - Zimmer, Christoph
AU  - Ovilo, Cristina
AU  - Fontanesi, Luca
PY  - 2020
UR  - http://r.istocar.bg.ac.rs/handle/123456789/719
AB  - In this study, we identified copy number variants (CNVs) in 19 European autochthonous pig
breeds and in two commercial breeds (Italian Large White and Italian Duroc) that represent
important genetic resources for this species. The genome of 725 pigs was sequenced using a
breed-specific DNA pooling approach (30–35 animals per pool) obtaining an average depth
per pool of 429. This approach maximised CNV discovery as well as the related copy
number states characterising, on average, the analysed breeds. By mining more than
17.5 billion reads, we identified a total of 9592 CNVs (~683 CNVs per breed) and 3710
CNV regions (CNVRs; 1.15% of the reference pig genome), with an average of 77 CNVRs per
breed that were considered as private. A few CNVRs were analysed in more detail, together
with other information derived from sequencing data. For example, the CNVR encompassing the KIT gene was associated with coat colour phenotypes in the analysed breeds,
confirming the role of the multiple copies in determining breed-specific coat colours. The
CNVR covering the MSRB3 gene was associated with ear size in most breeds. The CNVRs
affecting the ELOVL6 and ZNF622 genes were private features observed in the Lithuanian
Indigenous Wattle and in the Turopolje pig breeds respectively. Overall, the genome
variability unravelled here can explain part of the genetic diversity among breeds and might
contribute to explain their origin, history and adaptation to a variety of production systems
PB  - International Foundation for Animal Genetics
T2  - Animal Genetics
T1  - Genome-wide detection of copy number variants in European autochthonous and commercial pig breeds by whole-genome sequencing of DNA pools identified breed-characterising copy number states
DO  - doi:10.1111/age.12954
ER  - 

@article{
author = "Bovo, Samuele and Ribani, Anisa and Munoz, Maria and Alves, Estefania and Araujo, Jose P. and Bozzi, Riccardo and Charneca, Rui and Di Palma, Federica and Etherington, Graham and Fernandez, Ana I. and Garcia, Fabian and Garcia-Casco, Juan and Karolyi, Danijel and Gallo, Maurizio and Gvozdanović, Katarina and Martins, Jose Manuel and Mercat, Marie J. and Nunez, Yolanda and Quintailla, Raquel and Radović, Čedomir and Razmaite, Violeta and Riquet, Juliette and Savić, Radomir and Schiavo, Giuseppina and Škrlep, Martin and Usai, Graziano and Utzeri, Valerio J. and Zimmer, Christoph and Ovilo, Cristina and Fontanesi, Luca",
year = "2020",
abstract = "In this study, we identified copy number variants (CNVs) in 19 European autochthonous pig
breeds and in two commercial breeds (Italian Large White and Italian Duroc) that represent
important genetic resources for this species. The genome of 725 pigs was sequenced using a
breed-specific DNA pooling approach (30–35 animals per pool) obtaining an average depth
per pool of 429. This approach maximised CNV discovery as well as the related copy
number states characterising, on average, the analysed breeds. By mining more than
17.5 billion reads, we identified a total of 9592 CNVs (~683 CNVs per breed) and 3710
CNV regions (CNVRs; 1.15% of the reference pig genome), with an average of 77 CNVRs per
breed that were considered as private. A few CNVRs were analysed in more detail, together
with other information derived from sequencing data. For example, the CNVR encompassing the KIT gene was associated with coat colour phenotypes in the analysed breeds,
confirming the role of the multiple copies in determining breed-specific coat colours. The
CNVR covering the MSRB3 gene was associated with ear size in most breeds. The CNVRs
affecting the ELOVL6 and ZNF622 genes were private features observed in the Lithuanian
Indigenous Wattle and in the Turopolje pig breeds respectively. Overall, the genome
variability unravelled here can explain part of the genetic diversity among breeds and might
contribute to explain their origin, history and adaptation to a variety of production systems",
publisher = "International Foundation for Animal Genetics",
journal = "Animal Genetics",
title = "Genome-wide detection of copy number variants in European autochthonous and commercial pig breeds by whole-genome sequencing of DNA pools identified breed-characterising copy number states",
doi = "doi:10.1111/age.12954"
}

Bovo, S., Ribani, A., Munoz, M., Alves, E., Araujo, J. P., Bozzi, R., Charneca, R., Di Palma, F., Etherington, G., Fernandez, A. I., Garcia, F., Garcia-Casco, J., Karolyi, D., Gallo, M., Gvozdanović, K., Martins, J. M., Mercat, M. J., Nunez, Y., Quintailla, R., Radović, Č., Razmaite, V., Riquet, J., Savić, R., Schiavo, G., Škrlep, M., Usai, G., Utzeri, V. J., Zimmer, C., Ovilo, C.,& Fontanesi, L.. (2020). Genome-wide detection of copy number variants in European autochthonous and commercial pig breeds by whole-genome sequencing of DNA pools identified breed-characterising copy number states. in Animal Genetics
International Foundation for Animal Genetics..
https://doi.org/doi:10.1111/age.12954

Bovo S, Ribani A, Munoz M, Alves E, Araujo JP, Bozzi R, Charneca R, Di Palma F, Etherington G, Fernandez AI, Garcia F, Garcia-Casco J, Karolyi D, Gallo M, Gvozdanović K, Martins JM, Mercat MJ, Nunez Y, Quintailla R, Radović Č, Razmaite V, Riquet J, Savić R, Schiavo G, Škrlep M, Usai G, Utzeri VJ, Zimmer C, Ovilo C, Fontanesi L. Genome-wide detection of copy number variants in European autochthonous and commercial pig breeds by whole-genome sequencing of DNA pools identified breed-characterising copy number states. in Animal Genetics. 2020;.
doi:doi:10.1111/age.12954 .

Bovo, Samuele, Ribani, Anisa, Munoz, Maria, Alves, Estefania, Araujo, Jose P., Bozzi, Riccardo, Charneca, Rui, Di Palma, Federica, Etherington, Graham, Fernandez, Ana I., Garcia, Fabian, Garcia-Casco, Juan, Karolyi, Danijel, Gallo, Maurizio, Gvozdanović, Katarina, Martins, Jose Manuel, Mercat, Marie J., Nunez, Yolanda, Quintailla, Raquel, Radović, Čedomir, Razmaite, Violeta, Riquet, Juliette, Savić, Radomir, Schiavo, Giuseppina, Škrlep, Martin, Usai, Graziano, Utzeri, Valerio J., Zimmer, Christoph, Ovilo, Cristina, Fontanesi, Luca, "Genome-wide detection of copy number variants in European autochthonous and commercial pig breeds by whole-genome sequencing of DNA pools identified breed-characterising copy number states" in Animal Genetics (2020),
https://doi.org/doi:10.1111/age.12954 . .

TY  - JOUR
AU  - Bovo, Samuele
AU  - Ribani, Anisa
AU  - Munoz, Maria
AU  - Alves, Estefania
AU  - Araujo, Jose P.
AU  - Bozzi, Riccardo
AU  - Čandek-Potokar, Marjeta
AU  - Charneca, Rui
AU  - Di Palma, Federica
AU  - Etherington, Graham
AU  - Fernandez, Ana I.
AU  - Garcia, Fabian
AU  - Garcia-Casco, Juan
AU  - Karolyi, Danijel
AU  - Gallo, Maurizio
AU  - Margeta, Vladimir
AU  - Martins, Jose Manuel
AU  - Mercat, Marie J.
AU  - Moscatelli, Giulia
AU  - Nunaz, Yolanda
AU  - Quintailla, Raquel
AU  - Radović, Čedomir
AU  - Razmaite, Violeta
AU  - Riquet, Juliette
AU  - Savić, Radomir
AU  - Schiavo, Giuseppina
AU  - Usai, Graziano
AU  - Utzeri, Valerio J.
AU  - Zimmer, Christoph
AU  - Ovilo, Cristina
AU  - Fontanesi, Luca
PY  - 2020
UR  - http://r.istocar.bg.ac.rs/handle/123456789/718
AB  - Background: Natural and artificial directional selection in cosmopolitan and autochthonous pig breeds and wild boars have shaped their genomes and resulted in a reservoir of animal genetic diversity. Signatures of selection are the result of these selection events that have contributed to the adaptation of breeds to different environments and production systems. In this study, we analysed the genome variability of 19 European autochthonous pig breeds (Alentejana, Bísara, Majorcan Black, Basque, Gascon, Apulo‑Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano, Sarda, Krškopolje pig, Black Slavonian, Turopolje, Moravka, Swallow‑Bellied Mangalitsa, Schwäbisch‑Hällisches Schwein, Lithuanian indigenous wattle and Lithuanian White old type) from nine countries, three European commercial breeds (Italian Large White, Italian Landrace and Italian Duroc), and European wild boars, by mining whole‑genome sequencing data obtained by using a DNA‑pool sequencing approach. Signatures of selection were identified by using a single‑breed approach with two statistics [within‑breed pooled heterozygosity (HP) and fixation index (FST)] and group‑based FST approaches, which compare groups of breeds defined according to external traits and use/specialization/type. Results: We detected more than 22 million single nucleotide polymorphisms (SNPs) across the 23 compared populations and identified 359 chromosome regions showing signatures of selection. These regions harbour genes that are already known or new genes that are under selection and relevant for the domestication process in this species, and that affect several morphological and physiological traits (e.g. coat colours and patterns, body size, number of vertebrae and teats, ear size and conformation, reproductive traits, growth and fat deposition traits). Wild boar related signatures of selection were detected across all the genome of several autochthonous breeds, which suggests that crossbreeding (accidental or deliberate) occurred with wild boars.
Conclusions: Our findings provide a catalogue of genetic variants of many European pig populations and identify genome regions that can explain, at least in part, the phenotypic diversity of these genetic resources.
PB  - BMC Publishing
T2  - Genetics Selection Evolution
T1  - Whole-genome sequencing of European autochthonous and commercial pig breeds allows the detection of signatures of selection for adaptation of genetic resources to different breeding and production systems
VL  - 52
IS  - 33
DO  - doi.org/10.1186/s12711-020-00553-7
ER  - 

@article{
author = "Bovo, Samuele and Ribani, Anisa and Munoz, Maria and Alves, Estefania and Araujo, Jose P. and Bozzi, Riccardo and Čandek-Potokar, Marjeta and Charneca, Rui and Di Palma, Federica and Etherington, Graham and Fernandez, Ana I. and Garcia, Fabian and Garcia-Casco, Juan and Karolyi, Danijel and Gallo, Maurizio and Margeta, Vladimir and Martins, Jose Manuel and Mercat, Marie J. and Moscatelli, Giulia and Nunaz, Yolanda and Quintailla, Raquel and Radović, Čedomir and Razmaite, Violeta and Riquet, Juliette and Savić, Radomir and Schiavo, Giuseppina and Usai, Graziano and Utzeri, Valerio J. and Zimmer, Christoph and Ovilo, Cristina and Fontanesi, Luca",
year = "2020",
abstract = "Background: Natural and artificial directional selection in cosmopolitan and autochthonous pig breeds and wild boars have shaped their genomes and resulted in a reservoir of animal genetic diversity. Signatures of selection are the result of these selection events that have contributed to the adaptation of breeds to different environments and production systems. In this study, we analysed the genome variability of 19 European autochthonous pig breeds (Alentejana, Bísara, Majorcan Black, Basque, Gascon, Apulo‑Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano, Sarda, Krškopolje pig, Black Slavonian, Turopolje, Moravka, Swallow‑Bellied Mangalitsa, Schwäbisch‑Hällisches Schwein, Lithuanian indigenous wattle and Lithuanian White old type) from nine countries, three European commercial breeds (Italian Large White, Italian Landrace and Italian Duroc), and European wild boars, by mining whole‑genome sequencing data obtained by using a DNA‑pool sequencing approach. Signatures of selection were identified by using a single‑breed approach with two statistics [within‑breed pooled heterozygosity (HP) and fixation index (FST)] and group‑based FST approaches, which compare groups of breeds defined according to external traits and use/specialization/type. Results: We detected more than 22 million single nucleotide polymorphisms (SNPs) across the 23 compared populations and identified 359 chromosome regions showing signatures of selection. These regions harbour genes that are already known or new genes that are under selection and relevant for the domestication process in this species, and that affect several morphological and physiological traits (e.g. coat colours and patterns, body size, number of vertebrae and teats, ear size and conformation, reproductive traits, growth and fat deposition traits). Wild boar related signatures of selection were detected across all the genome of several autochthonous breeds, which suggests that crossbreeding (accidental or deliberate) occurred with wild boars.
Conclusions: Our findings provide a catalogue of genetic variants of many European pig populations and identify genome regions that can explain, at least in part, the phenotypic diversity of these genetic resources.",
publisher = "BMC Publishing",
journal = "Genetics Selection Evolution",
title = "Whole-genome sequencing of European autochthonous and commercial pig breeds allows the detection of signatures of selection for adaptation of genetic resources to different breeding and production systems",
volume = "52",
number = "33",
doi = "doi.org/10.1186/s12711-020-00553-7"
}

Bovo, S., Ribani, A., Munoz, M., Alves, E., Araujo, J. P., Bozzi, R., Čandek-Potokar, M., Charneca, R., Di Palma, F., Etherington, G., Fernandez, A. I., Garcia, F., Garcia-Casco, J., Karolyi, D., Gallo, M., Margeta, V., Martins, J. M., Mercat, M. J., Moscatelli, G., Nunaz, Y., Quintailla, R., Radović, Č., Razmaite, V., Riquet, J., Savić, R., Schiavo, G., Usai, G., Utzeri, V. J., Zimmer, C., Ovilo, C.,& Fontanesi, L.. (2020). Whole-genome sequencing of European autochthonous and commercial pig breeds allows the detection of signatures of selection for adaptation of genetic resources to different breeding and production systems. in Genetics Selection Evolution
BMC Publishing., 52(33).
https://doi.org/doi.org/10.1186/s12711-020-00553-7

Bovo S, Ribani A, Munoz M, Alves E, Araujo JP, Bozzi R, Čandek-Potokar M, Charneca R, Di Palma F, Etherington G, Fernandez AI, Garcia F, Garcia-Casco J, Karolyi D, Gallo M, Margeta V, Martins JM, Mercat MJ, Moscatelli G, Nunaz Y, Quintailla R, Radović Č, Razmaite V, Riquet J, Savić R, Schiavo G, Usai G, Utzeri VJ, Zimmer C, Ovilo C, Fontanesi L. Whole-genome sequencing of European autochthonous and commercial pig breeds allows the detection of signatures of selection for adaptation of genetic resources to different breeding and production systems. in Genetics Selection Evolution. 2020;52(33).
doi:doi.org/10.1186/s12711-020-00553-7 .

Bovo, Samuele, Ribani, Anisa, Munoz, Maria, Alves, Estefania, Araujo, Jose P., Bozzi, Riccardo, Čandek-Potokar, Marjeta, Charneca, Rui, Di Palma, Federica, Etherington, Graham, Fernandez, Ana I., Garcia, Fabian, Garcia-Casco, Juan, Karolyi, Danijel, Gallo, Maurizio, Margeta, Vladimir, Martins, Jose Manuel, Mercat, Marie J., Moscatelli, Giulia, Nunaz, Yolanda, Quintailla, Raquel, Radović, Čedomir, Razmaite, Violeta, Riquet, Juliette, Savić, Radomir, Schiavo, Giuseppina, Usai, Graziano, Utzeri, Valerio J., Zimmer, Christoph, Ovilo, Cristina, Fontanesi, Luca, "Whole-genome sequencing of European autochthonous and commercial pig breeds allows the detection of signatures of selection for adaptation of genetic resources to different breeding and production systems" in Genetics Selection Evolution, 52, no. 33 (2020),
https://doi.org/doi.org/10.1186/s12711-020-00553-7 . .

TY  - JOUR
AU  - Muñoz, M.
AU  - Bozzi, Riccardo
AU  - García, F.
AU  - Nuñez, Yolanda
AU  - Geraci, Claudia
AU  - Crovetti, Alessandro
AU  - Garcia Casco, Juan Maria
AU  - Alves, Estefânia
AU  - Škrlep, M.
AU  - Charneca, Rui
AU  - Martins, J.M.
AU  - Quintanilla, R.
AU  - Tibau, J.
AU  - Kušec, Goran
AU  - Djurkin-Kušec, I.
AU  - Mercat, Marie-José
AU  - Riquet, J.
AU  - Estellé, J.
AU  - Zimmer, C.
AU  - Razmaite, V.
AU  - Araujo, José Pedro
AU  - Radović, Čedomir
AU  - Savić, Radomir
AU  - Karolyi, Danijel
AU  - Gallo, Maurizio
AU  - Čandek-Potokar, Marjeta
AU  - Fontanesi, Luca
AU  - Fernández, A.I.
AU  - Óvilo, C.
PY  - 2018
UR  - http://r.istocar.bg.ac.rs/handle/123456789/551
UR  - http://hdl.handle.net/20.500.12327/251
AB  - The aim of this work was to analyse the distribution of causal and candidate mutations associated to relevant productive traits in twenty local European pig breeds. Also, the potential of the SNP panel employed for elucidating the genetic structure and relationships among breeds was evaluated. Most relevant genes and mutations associated with pig morphological, productive, meat quality, reproductive and disease resistance traits were prioritized and analyzed in a maximum of 47 blood samples from each of the breeds (Alentejana, Apulo-Calabrese, Basque, Bísara, Majorcan Black, Black Slavonian (Crna slavonska), Casertana, Cinta Senese, Gascon, Iberian, Krškopolje (Krškopoljski), Lithuanian indigenous wattle, Lithuanian White Old Type, Mora Romagnola, Moravka, Nero Siciliano, Sarda, Schwäbisch-Hällisches Schwein (Swabian Hall pig), Swallow-Bellied Mangalitsa and Turopolje). We successfully analyzed allelic variation in 39 polymorphisms, located in 33 candidate genes. Results provide relevant information regarding genetic diversity and segregation of SNPs associated to production and quality traits. Coat color and morphological trait-genes that show low level of segregation, and fixed SNPs may be useful for traceability. On the other hand, we detected SNPs which may be useful for association studies as well as breeding programs. For instance, we observed predominance of alleles that might be unfavorable for disease resistance and boar taint in most breeds and segregation of many alleles involved in meat quality, fatness and growth traits. Overall, these findings provide a detailed catalogue of segregating candidate SNPs in 20 European local pig breeds that may be useful for traceability purposes, for association studies and for breeding schemes. Population genetic analyses based on these candidate genes are able to uncover some clues regarding the hidden genetic substructure of these populations, as the extreme genetic closeness between Iberian and Alentejana breeds and an uneven admixture of the breeds studied. The results are in agreement with available knowledge regarding breed history and management, although largest panels of neutral markers should be employed to get a deeper understanding of the population's structure and relationships.
PB  - Public Library of Science (PLoS)
T2  - PloS one
T1  - Diversity across major and candidate genes in European local pig breeds
VL  - 13
IS  - 11
DO  - 10.1371/journal.pone.0207475
ER  - 

@article{
author = "Muñoz, M. and Bozzi, Riccardo and García, F. and Nuñez, Yolanda and Geraci, Claudia and Crovetti, Alessandro and Garcia Casco, Juan Maria and Alves, Estefânia and Škrlep, M. and Charneca, Rui and Martins, J.M. and Quintanilla, R. and Tibau, J. and Kušec, Goran and Djurkin-Kušec, I. and Mercat, Marie-José and Riquet, J. and Estellé, J. and Zimmer, C. and Razmaite, V. and Araujo, José Pedro and Radović, Čedomir and Savić, Radomir and Karolyi, Danijel and Gallo, Maurizio and Čandek-Potokar, Marjeta and Fontanesi, Luca and Fernández, A.I. and Óvilo, C.",
year = "2018",
abstract = "The aim of this work was to analyse the distribution of causal and candidate mutations associated to relevant productive traits in twenty local European pig breeds. Also, the potential of the SNP panel employed for elucidating the genetic structure and relationships among breeds was evaluated. Most relevant genes and mutations associated with pig morphological, productive, meat quality, reproductive and disease resistance traits were prioritized and analyzed in a maximum of 47 blood samples from each of the breeds (Alentejana, Apulo-Calabrese, Basque, Bísara, Majorcan Black, Black Slavonian (Crna slavonska), Casertana, Cinta Senese, Gascon, Iberian, Krškopolje (Krškopoljski), Lithuanian indigenous wattle, Lithuanian White Old Type, Mora Romagnola, Moravka, Nero Siciliano, Sarda, Schwäbisch-Hällisches Schwein (Swabian Hall pig), Swallow-Bellied Mangalitsa and Turopolje). We successfully analyzed allelic variation in 39 polymorphisms, located in 33 candidate genes. Results provide relevant information regarding genetic diversity and segregation of SNPs associated to production and quality traits. Coat color and morphological trait-genes that show low level of segregation, and fixed SNPs may be useful for traceability. On the other hand, we detected SNPs which may be useful for association studies as well as breeding programs. For instance, we observed predominance of alleles that might be unfavorable for disease resistance and boar taint in most breeds and segregation of many alleles involved in meat quality, fatness and growth traits. Overall, these findings provide a detailed catalogue of segregating candidate SNPs in 20 European local pig breeds that may be useful for traceability purposes, for association studies and for breeding schemes. Population genetic analyses based on these candidate genes are able to uncover some clues regarding the hidden genetic substructure of these populations, as the extreme genetic closeness between Iberian and Alentejana breeds and an uneven admixture of the breeds studied. The results are in agreement with available knowledge regarding breed history and management, although largest panels of neutral markers should be employed to get a deeper understanding of the population's structure and relationships.",
publisher = "Public Library of Science (PLoS)",
journal = "PloS one",
title = "Diversity across major and candidate genes in European local pig breeds",
volume = "13",
number = "11",
doi = "10.1371/journal.pone.0207475"
}

Muñoz, M., Bozzi, R., García, F., Nuñez, Y., Geraci, C., Crovetti, A., Garcia Casco, J. M., Alves, E., Škrlep, M., Charneca, R., Martins, J.M., Quintanilla, R., Tibau, J., Kušec, G., Djurkin-Kušec, I., Mercat, M., Riquet, J., Estellé, J., Zimmer, C., Razmaite, V., Araujo, J. P., Radović, Č., Savić, R., Karolyi, D., Gallo, M., Čandek-Potokar, M., Fontanesi, L., Fernández, A.I.,& Óvilo, C.. (2018). Diversity across major and candidate genes in European local pig breeds. in PloS one
Public Library of Science (PLoS)., 13(11).
https://doi.org/10.1371/journal.pone.0207475

Muñoz M, Bozzi R, García F, Nuñez Y, Geraci C, Crovetti A, Garcia Casco JM, Alves E, Škrlep M, Charneca R, Martins J, Quintanilla R, Tibau J, Kušec G, Djurkin-Kušec I, Mercat M, Riquet J, Estellé J, Zimmer C, Razmaite V, Araujo JP, Radović Č, Savić R, Karolyi D, Gallo M, Čandek-Potokar M, Fontanesi L, Fernández A, Óvilo C. Diversity across major and candidate genes in European local pig breeds. in PloS one. 2018;13(11).
doi:10.1371/journal.pone.0207475 .

Muñoz, M., Bozzi, Riccardo, García, F., Nuñez, Yolanda, Geraci, Claudia, Crovetti, Alessandro, Garcia Casco, Juan Maria, Alves, Estefânia, Škrlep, M., Charneca, Rui, Martins, J.M., Quintanilla, R., Tibau, J., Kušec, Goran, Djurkin-Kušec, I., Mercat, Marie-José, Riquet, J., Estellé, J., Zimmer, C., Razmaite, V., Araujo, José Pedro, Radović, Čedomir, Savić, Radomir, Karolyi, Danijel, Gallo, Maurizio, Čandek-Potokar, Marjeta, Fontanesi, Luca, Fernández, A.I., Óvilo, C., "Diversity across major and candidate genes in European local pig breeds" in PloS one, 13, no. 11 (2018),
https://doi.org/10.1371/journal.pone.0207475 . .

TY  - CONF
AU  - Óvilo, Cristina
AU  - Bozzi, Riccardo
AU  - García, F.
AU  - Nuñez, Yolanda
AU  - Geraci, Claudia
AU  - Crovetti, Alessandro
AU  - Garcia Casco, Juan Maria
AU  - Alves, Estefânia
AU  - Škrlep, Martin
AU  - Charneca, Rui
AU  - Quintanilla, Raquel
AU  - Kušec, Goran
AU  - Riquet, Juliette
AU  - Mercat, Marie-José
AU  - Zimmer, Christoph
AU  - Razmaitė, Violeta
AU  - Araujo, José Pedro
AU  - Radović, Čedomir
AU  - Savić, Radomir
AU  - Čandek-Potokar, Marjeta
AU  - Fontanesi, Luca
AU  - Fernández, Ana
AU  - Muñoz, Maria
PY  - 2017
UR  - https://zenodo.org/record/1135160
UR  - http://epserbia.open.ac.rs/123456789/196
UR  - http://r.istocar.bg.ac.rs/handle/123456789/572
AB  - In the frame of the European TREASURE* project, the genetic characterization of 20 local pig breeds is being performed with genetic and genomic tools. The objectives are the study of genetic diversity in these populations and the identification of useful markers for authentication, traceability, conservation and breeding programs. In first place, a candidate gene approach has been applied and the most relevant genes and mutations associated with pig productive, meat quality, reproductive and disease resistance traits have  been prioritized and analyzed. Two OpenArray® chips of 32 and 16 SNPs were designed and genotyped in 48 animals from each one of 20 breeds included in the project (Alentejana, Apulo Calabrese, Basque, Bísaro, Black Majorcan, Black Sicilian, Black Slavonian, Casertana, Cinta Senese, Gascon, Iberian, Krskopolje, Lithuanian indigenous wattle, Mangalitsa, Mora Romagnola, Moravka, Old Lithuanian White, Sarda, Schwäbisch Hällisches, Turopolje). Forty SNPs located in 34 genes were successfully genotyped (MC1R, TYRP1, NR6A, PCK1, RYR1, IGF2, MC4R, PHKG1, SCD, GBP5, TAS2R39, TAS2R4, MUC4, ESR1, CYP2E1, LEP, CAST, MTTP, CYB5A, FTO, PPARGC1A, CAPN1, PPARD, CTSL, LEPR, PRKAG3, ACACA, KIT, ACSL4, ADIPOQ, FASN, AHR, FUT1, MSTN). Results provide relevant information regarding genetic diversity and segregation of SNPs responsible for specific production and quality traits. Coat color and morphological trait-genes, showing low level of segregation, and fixed SNPs may be useful for traceability. On the other hand, we detected SNPs which may be useful for breeding programs. For instance, we observed predominance of unfavorable alleles for disease resistance and boar taint genes in most breeds, and segregation of many genes involved in meat quality, fatness and growth. These results joint with ongoing genomic assays, will provide essential information regarding genetic diversity, structure, selective signatures and biological processes responsible for specific production and quality traits.
PB  - Badajoz : CICYTEX
C3  - Book of Abstracts of the 4th Fatty Pig Science and Utilization International Conference
T1  - Diversity across Major and Candidate Genes in European Local Pig Breeds
SP  - 51
EP  - 52
DO  - 10.5281/zenodo.1135160
ER  - 

@conference{
author = "Óvilo, Cristina and Bozzi, Riccardo and García, F. and Nuñez, Yolanda and Geraci, Claudia and Crovetti, Alessandro and Garcia Casco, Juan Maria and Alves, Estefânia and Škrlep, Martin and Charneca, Rui and Quintanilla, Raquel and Kušec, Goran and Riquet, Juliette and Mercat, Marie-José and Zimmer, Christoph and Razmaitė, Violeta and Araujo, José Pedro and Radović, Čedomir and Savić, Radomir and Čandek-Potokar, Marjeta and Fontanesi, Luca and Fernández, Ana and Muñoz, Maria",
year = "2017",
abstract = "In the frame of the European TREASURE* project, the genetic characterization of 20 local pig breeds is being performed with genetic and genomic tools. The objectives are the study of genetic diversity in these populations and the identification of useful markers for authentication, traceability, conservation and breeding programs. In first place, a candidate gene approach has been applied and the most relevant genes and mutations associated with pig productive, meat quality, reproductive and disease resistance traits have  been prioritized and analyzed. Two OpenArray® chips of 32 and 16 SNPs were designed and genotyped in 48 animals from each one of 20 breeds included in the project (Alentejana, Apulo Calabrese, Basque, Bísaro, Black Majorcan, Black Sicilian, Black Slavonian, Casertana, Cinta Senese, Gascon, Iberian, Krskopolje, Lithuanian indigenous wattle, Mangalitsa, Mora Romagnola, Moravka, Old Lithuanian White, Sarda, Schwäbisch Hällisches, Turopolje). Forty SNPs located in 34 genes were successfully genotyped (MC1R, TYRP1, NR6A, PCK1, RYR1, IGF2, MC4R, PHKG1, SCD, GBP5, TAS2R39, TAS2R4, MUC4, ESR1, CYP2E1, LEP, CAST, MTTP, CYB5A, FTO, PPARGC1A, CAPN1, PPARD, CTSL, LEPR, PRKAG3, ACACA, KIT, ACSL4, ADIPOQ, FASN, AHR, FUT1, MSTN). Results provide relevant information regarding genetic diversity and segregation of SNPs responsible for specific production and quality traits. Coat color and morphological trait-genes, showing low level of segregation, and fixed SNPs may be useful for traceability. On the other hand, we detected SNPs which may be useful for breeding programs. For instance, we observed predominance of unfavorable alleles for disease resistance and boar taint genes in most breeds, and segregation of many genes involved in meat quality, fatness and growth. These results joint with ongoing genomic assays, will provide essential information regarding genetic diversity, structure, selective signatures and biological processes responsible for specific production and quality traits.",
publisher = "Badajoz : CICYTEX",
journal = "Book of Abstracts of the 4th Fatty Pig Science and Utilization International Conference",
title = "Diversity across Major and Candidate Genes in European Local Pig Breeds",
pages = "51-52",
doi = "10.5281/zenodo.1135160"
}

Óvilo, C., Bozzi, R., García, F., Nuñez, Y., Geraci, C., Crovetti, A., Garcia Casco, J. M., Alves, E., Škrlep, M., Charneca, R., Quintanilla, R., Kušec, G., Riquet, J., Mercat, M., Zimmer, C., Razmaitė, V., Araujo, J. P., Radović, Č., Savić, R., Čandek-Potokar, M., Fontanesi, L., Fernández, A.,& Muñoz, M.. (2017). Diversity across Major and Candidate Genes in European Local Pig Breeds. in Book of Abstracts of the 4th Fatty Pig Science and Utilization International Conference
Badajoz : CICYTEX., 51-52.
https://doi.org/10.5281/zenodo.1135160

Óvilo C, Bozzi R, García F, Nuñez Y, Geraci C, Crovetti A, Garcia Casco JM, Alves E, Škrlep M, Charneca R, Quintanilla R, Kušec G, Riquet J, Mercat M, Zimmer C, Razmaitė V, Araujo JP, Radović Č, Savić R, Čandek-Potokar M, Fontanesi L, Fernández A, Muñoz M. Diversity across Major and Candidate Genes in European Local Pig Breeds. in Book of Abstracts of the 4th Fatty Pig Science and Utilization International Conference. 2017;:51-52.
doi:10.5281/zenodo.1135160 .

Óvilo, Cristina, Bozzi, Riccardo, García, F., Nuñez, Yolanda, Geraci, Claudia, Crovetti, Alessandro, Garcia Casco, Juan Maria, Alves, Estefânia, Škrlep, Martin, Charneca, Rui, Quintanilla, Raquel, Kušec, Goran, Riquet, Juliette, Mercat, Marie-José, Zimmer, Christoph, Razmaitė, Violeta, Araujo, José Pedro, Radović, Čedomir, Savić, Radomir, Čandek-Potokar, Marjeta, Fontanesi, Luca, Fernández, Ana, Muñoz, Maria, "Diversity across Major and Candidate Genes in European Local Pig Breeds" in Book of Abstracts of the 4th Fatty Pig Science and Utilization International Conference (2017):51-52,
https://doi.org/10.5281/zenodo.1135160 . .