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  - Zorc, Minja
AU  - Škorput, Dubravko
AU  - Gvozdanović, Kristina
AU  - Margeta, Polona
AU  - Karolyi, Danijel
AU  - Luković, Zoran
AU  - Salajpal, Krešimir
AU  - Savić, Radomir
AU  - Munoz, Maria
AU  - Bovo, Samuele
AU  - Đurkin Kušec, Ivona
AU  - Radović, Čedomir
AU  - Kušec, Goran
AU  - Čandek Potokar, Marjeta
AU  - Dovč, Peter
PY  - 2022
UR  - http://r.istocar.bg.ac.rs/handle/123456789/818
AB  - Background: The importance of local breeds as genetic reservoirs of valuable genetic variation is well established.
Pig breeding in Central and South-Eastern Europe has a long tradition that led to the formation of several local
pig breeds. In the present study, genetic diversity parameters were analysed in six autochthonous pig breeds from
Slovenia, Croatia and Serbia (Banija spotted, Black Slavonian, Turopolje pig, Swallow-bellied Mangalitsa, Moravka
and Krskopolje pig). Animals from each of these breeds were genotyped using microsatellites and single nucleotide
polymorphisms (SNPs). The results obtained with these two marker systems and those based on pedigree data were
compared. In addition, we estimated inbreeding levels based on the distribution of runs of homozygosity (ROH) and
identifed genomic regions under selection pressure using ROH islands and the integrated haplotype score (iHS).
Results: The lowest heterozygosity values calculated from microsatellite and SNP data were observed in the Turopolje pig. The observed heterozygosity was higher than the expected heterozygosity in the Black Slavonian, Moravka
and Turopolje pig. Both types of markers allowed us to distinguish clusters of individuals belonging to each breed.
The analysis of admixture between breeds revealed potential gene fow between the Mangalitsa and Moravka, and
between the Mangalitsa and Black Slavonian, but no introgression events were detected in the Banija spotted and
Turopolje pig. The distribution of ROH across the genome was not uniform. Analysis of the ROH islands identifed
genomic regions with an extremely high frequency of shared ROH within the Swallow-bellied Mangalitsa, which
harboured genes associated with cholesterol biosynthesis, fatty acid metabolism and daily weight gain. The iHS
approach to detect signatures of selection revealed candidate regions containing genes with potential roles in reproduction traits and disease resistance.
Conclusions: Based on the estimation of population parameters obtained from three data sets, we showed the
existence of relationships among the six pig breeds analysed here. Analysis of the distribution of ROH allowed us to
estimate the level of inbreeding and the extent of homozygous regions in these breeds. The iHS analysis revealed
genomic regions potentially associated with phenotypic traits and allowed the detection of genomic regions under
selection pressure.
PB  - BMC
T2  - Genetic Selection Evolution
T1  - Genetic diversity and population structure of six autochthonous pig breeds from Croatia, Serbia, and Slovenia
DO  - https://doi.org/10.1186/s12711-022-00718-6
ER  - 

@article{
author = "Zorc, Minja and Škorput, Dubravko and Gvozdanović, Kristina and Margeta, Polona and Karolyi, Danijel and Luković, Zoran and Salajpal, Krešimir and Savić, Radomir and Munoz, Maria and Bovo, Samuele and Đurkin Kušec, Ivona and Radović, Čedomir and Kušec, Goran and Čandek Potokar, Marjeta and Dovč, Peter",
year = "2022",
abstract = "Background: The importance of local breeds as genetic reservoirs of valuable genetic variation is well established.
Pig breeding in Central and South-Eastern Europe has a long tradition that led to the formation of several local
pig breeds. In the present study, genetic diversity parameters were analysed in six autochthonous pig breeds from
Slovenia, Croatia and Serbia (Banija spotted, Black Slavonian, Turopolje pig, Swallow-bellied Mangalitsa, Moravka
and Krskopolje pig). Animals from each of these breeds were genotyped using microsatellites and single nucleotide
polymorphisms (SNPs). The results obtained with these two marker systems and those based on pedigree data were
compared. In addition, we estimated inbreeding levels based on the distribution of runs of homozygosity (ROH) and
identifed genomic regions under selection pressure using ROH islands and the integrated haplotype score (iHS).
Results: The lowest heterozygosity values calculated from microsatellite and SNP data were observed in the Turopolje pig. The observed heterozygosity was higher than the expected heterozygosity in the Black Slavonian, Moravka
and Turopolje pig. Both types of markers allowed us to distinguish clusters of individuals belonging to each breed.
The analysis of admixture between breeds revealed potential gene fow between the Mangalitsa and Moravka, and
between the Mangalitsa and Black Slavonian, but no introgression events were detected in the Banija spotted and
Turopolje pig. The distribution of ROH across the genome was not uniform. Analysis of the ROH islands identifed
genomic regions with an extremely high frequency of shared ROH within the Swallow-bellied Mangalitsa, which
harboured genes associated with cholesterol biosynthesis, fatty acid metabolism and daily weight gain. The iHS
approach to detect signatures of selection revealed candidate regions containing genes with potential roles in reproduction traits and disease resistance.
Conclusions: Based on the estimation of population parameters obtained from three data sets, we showed the
existence of relationships among the six pig breeds analysed here. Analysis of the distribution of ROH allowed us to
estimate the level of inbreeding and the extent of homozygous regions in these breeds. The iHS analysis revealed
genomic regions potentially associated with phenotypic traits and allowed the detection of genomic regions under
selection pressure.",
publisher = "BMC",
journal = "Genetic Selection Evolution",
title = "Genetic diversity and population structure of six autochthonous pig breeds from Croatia, Serbia, and Slovenia",
doi = "https://doi.org/10.1186/s12711-022-00718-6"
}

Zorc, M., Škorput, D., Gvozdanović, K., Margeta, P., Karolyi, D., Luković, Z., Salajpal, K., Savić, R., Munoz, M., Bovo, S., Đurkin Kušec, I., Radović, Č., Kušec, G., Čandek Potokar, M.,& Dovč, P.. (2022). Genetic diversity and population structure of six autochthonous pig breeds from Croatia, Serbia, and Slovenia. in Genetic Selection Evolution
BMC..
https://doi.org/https://doi.org/10.1186/s12711-022-00718-6

Zorc M, Škorput D, Gvozdanović K, Margeta P, Karolyi D, Luković Z, Salajpal K, Savić R, Munoz M, Bovo S, Đurkin Kušec I, Radović Č, Kušec G, Čandek Potokar M, Dovč P. Genetic diversity and population structure of six autochthonous pig breeds from Croatia, Serbia, and Slovenia. in Genetic Selection Evolution. 2022;.
doi:https://doi.org/10.1186/s12711-022-00718-6 .

Zorc, Minja, Škorput, Dubravko, Gvozdanović, Kristina, Margeta, Polona, Karolyi, Danijel, Luković, Zoran, Salajpal, Krešimir, Savić, Radomir, Munoz, Maria, Bovo, Samuele, Đurkin Kušec, Ivona, Radović, Čedomir, Kušec, Goran, Čandek Potokar, Marjeta, Dovč, Peter, "Genetic diversity and population structure of six autochthonous pig breeds from Croatia, Serbia, and Slovenia" in Genetic Selection Evolution (2022),
https://doi.org/https://doi.org/10.1186/s12711-022-00718-6 . .

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  - 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 . .