TY  - JOUR
AU  - Bovo, Samuele
AU  - Ribani, A.
AU  - Munoz, Maria
AU  - Alves, Estefania
AU  - Araujo, Jose P.
AU  - Bozzi, Riccardo
AU  - Charneca, R.
AU  - Di Palma, F.
AU  - Etherington, G.
AU  - Fernandez, Ana I
AU  - Garcia, Fabian
AU  - Garcia-Casco, Juan
AU  - Karolyi, Danijel
AU  - Gallo, Maurizio
AU  - Gvozdanović, K.
AU  - Martins, Jose M.
AU  - Mercat, Marie J.
AU  - Nunez, Yolanda
AU  - Quintanilla, Raquel
AU  - Razmaite, Violeta
AU  - Riquet, Juliette
AU  - Savić, Radomir
AU  - Schiavo, Giuseppina
AU  - Skrlep, Martin
AU  - Usai, Graziano
AU  - Utzeri, Valerio J.
AU  - Zimmer, Christoph
AU  - Ovilo, Cristina
AU  - Fontanesi, Luca
AU  - Radović, Čedomir
PY  - 2020
UR  - http://aspace.agrif.bg.ac.rs/handle/123456789/5349
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 42x. 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 (similar to 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  - Wiley, Hoboken
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
EP  - 556
IS  - 4
SP  - 541
VL  - 51
DO  - 10.1111/age.12954
ER  - 

@article{
author = "Bovo, Samuele and Ribani, A. and Munoz, Maria and Alves, Estefania and Araujo, Jose P. and Bozzi, Riccardo and Charneca, R. and Di Palma, F. and Etherington, G. and Fernandez, Ana I and Garcia, Fabian and Garcia-Casco, Juan and Karolyi, Danijel and Gallo, Maurizio and Gvozdanović, K. and Martins, Jose M. and Mercat, Marie J. and Nunez, Yolanda and Quintanilla, Raquel and Razmaite, Violeta and Riquet, Juliette and Savić, Radomir and Schiavo, Giuseppina and Skrlep, Martin and Usai, Graziano and Utzeri, Valerio J. and Zimmer, Christoph and Ovilo, Cristina and Fontanesi, Luca and Radović, Čedomir",
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 42x. 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 (similar to 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 = "Wiley, Hoboken",
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",
pages = "556-541",
number = "4",
volume = "51",
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., Quintanilla, R., Razmaite, V., Riquet, J., Savić, R., Schiavo, G., Skrlep, M., Usai, G., Utzeri, V. J., Zimmer, C., Ovilo, C., Fontanesi, L.,& Radović, Č.. (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
Wiley, Hoboken., 51(4), 541-556.
https://doi.org/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, Quintanilla R, Razmaite V, Riquet J, Savić R, Schiavo G, Skrlep M, Usai G, Utzeri VJ, Zimmer C, Ovilo C, Fontanesi L, Radović Č. 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;51(4):541-556.
doi:10.1111/age.12954 .

Bovo, Samuele, Ribani, A., Munoz, Maria, Alves, Estefania, Araujo, Jose P., Bozzi, Riccardo, Charneca, R., Di Palma, F., Etherington, G., Fernandez, Ana I, Garcia, Fabian, Garcia-Casco, Juan, Karolyi, Danijel, Gallo, Maurizio, Gvozdanović, K., Martins, Jose M., Mercat, Marie J., Nunez, Yolanda, Quintanilla, Raquel, Razmaite, Violeta, Riquet, Juliette, Savić, Radomir, Schiavo, Giuseppina, Skrlep, Martin, Usai, Graziano, Utzeri, Valerio J., Zimmer, Christoph, Ovilo, Cristina, Fontanesi, Luca, Radović, Čedomir, "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, 51, no. 4 (2020):541-556,
https://doi.org/10.1111/age.12954 . .

TY  - JOUR
AU  - Skrlep, Martin
AU  - Tomašević, Igor
AU  - Moerlein, Daniel
AU  - Novaković, Saša
AU  - Egea, Macarena
AU  - Garrido, Maria Dolores
AU  - Linares, Maria Belen
AU  - Penaranda, Irene
AU  - Aluwe, Marijke
AU  - Font-i-Furnols, Maria
PY  - 2020
UR  - http://aspace.agrif.bg.ac.rs/handle/123456789/5297
AB  - Simple Summary Introducing alternatives to surgical castration of pigs bring welfare and economical benefits, but also reveal several quality-related issues. Most important is the presence of boar taint, but also includes low quantity and quality of fat, meat texture and color deviations in addition to inferior water binding properties, most of them negatively influencing meat product characteristics. The present paper highlights the important differences between the conventionally used surgical castrates and the most likely introduced alternatives: entire males and immunocastrates. Based on the review of the available research, the possible reasons for quality alterations are elaborated according to the type of meat product and recommendations for improving product quality or preventing boar taint perception are given. Due to the strong public initiative in Europe and increased regulator focus to mitigate pain, surgical castration of pigs is being gradually abandoned, while the importance of other sex categories like entire males (EM) and immunocastrates (IC) increases. Although beneficial for animal welfare and economics, their use also brings forward several quality problems. Besides the occurrence of boar taint in EM, these include excessive carcass leanness, softer fat, meat color and pH deviations, inferior water holding capacity and increased meat toughness. In this paper, the raw material differences between the male sex categories and their influence on product quality are reviewed, and possible solutions are presented. Using EM for dried or thermally processed products may result in lower processing yields and inferior sensory quality, which may partially be prevented by applying specific processing adaptations. Immunocastration is a viable solution, especially when prolonging the vaccination to slaughter interval. Low to medium levels of boar taint can be effectively managed in most of the meat products, applying procedures like cooking, microbial inoculation or masking (by spices and especially smoking), while highly tainted material can be valorized only by combining various methods and/or with dilution of the tainted meat.
PB  - MDPI, BASEL
T2  - Animals
T1  - The Use of Pork from Entire Male and Immunocastrated Pigs for Meat Products-An Overview with Recommendations
IS  - 10
VL  - 10
DO  - 10.3390/ani10101754
ER  - 

@article{
author = "Skrlep, Martin and Tomašević, Igor and Moerlein, Daniel and Novaković, Saša and Egea, Macarena and Garrido, Maria Dolores and Linares, Maria Belen and Penaranda, Irene and Aluwe, Marijke and Font-i-Furnols, Maria",
year = "2020",
abstract = "Simple Summary Introducing alternatives to surgical castration of pigs bring welfare and economical benefits, but also reveal several quality-related issues. Most important is the presence of boar taint, but also includes low quantity and quality of fat, meat texture and color deviations in addition to inferior water binding properties, most of them negatively influencing meat product characteristics. The present paper highlights the important differences between the conventionally used surgical castrates and the most likely introduced alternatives: entire males and immunocastrates. Based on the review of the available research, the possible reasons for quality alterations are elaborated according to the type of meat product and recommendations for improving product quality or preventing boar taint perception are given. Due to the strong public initiative in Europe and increased regulator focus to mitigate pain, surgical castration of pigs is being gradually abandoned, while the importance of other sex categories like entire males (EM) and immunocastrates (IC) increases. Although beneficial for animal welfare and economics, their use also brings forward several quality problems. Besides the occurrence of boar taint in EM, these include excessive carcass leanness, softer fat, meat color and pH deviations, inferior water holding capacity and increased meat toughness. In this paper, the raw material differences between the male sex categories and their influence on product quality are reviewed, and possible solutions are presented. Using EM for dried or thermally processed products may result in lower processing yields and inferior sensory quality, which may partially be prevented by applying specific processing adaptations. Immunocastration is a viable solution, especially when prolonging the vaccination to slaughter interval. Low to medium levels of boar taint can be effectively managed in most of the meat products, applying procedures like cooking, microbial inoculation or masking (by spices and especially smoking), while highly tainted material can be valorized only by combining various methods and/or with dilution of the tainted meat.",
publisher = "MDPI, BASEL",
journal = "Animals",
title = "The Use of Pork from Entire Male and Immunocastrated Pigs for Meat Products-An Overview with Recommendations",
number = "10",
volume = "10",
doi = "10.3390/ani10101754"
}

Skrlep, M., Tomašević, I., Moerlein, D., Novaković, S., Egea, M., Garrido, M. D., Linares, M. B., Penaranda, I., Aluwe, M.,& Font-i-Furnols, M.. (2020). The Use of Pork from Entire Male and Immunocastrated Pigs for Meat Products-An Overview with Recommendations. in Animals
MDPI, BASEL., 10(10).
https://doi.org/10.3390/ani10101754

Skrlep M, Tomašević I, Moerlein D, Novaković S, Egea M, Garrido MD, Linares MB, Penaranda I, Aluwe M, Font-i-Furnols M. The Use of Pork from Entire Male and Immunocastrated Pigs for Meat Products-An Overview with Recommendations. in Animals. 2020;10(10).
doi:10.3390/ani10101754 .

Skrlep, Martin, Tomašević, Igor, Moerlein, Daniel, Novaković, Saša, Egea, Macarena, Garrido, Maria Dolores, Linares, Maria Belen, Penaranda, Irene, Aluwe, Marijke, Font-i-Furnols, Maria, "The Use of Pork from Entire Male and Immunocastrated Pigs for Meat Products-An Overview with Recommendations" in Animals, 10, no. 10 (2020),
https://doi.org/10.3390/ani10101754 . .

TY  - JOUR
AU  - Aluwe, Marijke
AU  - Heyrman, Evert
AU  - Almeida, Joao M.
AU  - Babol, Jakub
AU  - Battacone, Gianni
AU  - Citek, Jaroslav
AU  - Font-i-Furnols, Maria
AU  - Getya, Andriy
AU  - Karolyi, Danijel
AU  - Kostyra, Eliza
AU  - Kress, Kevin
AU  - Kusec, Goran
AU  - Moerlein, Daniel
AU  - Semenova, Anastasia
AU  - Skrlep, Martin
AU  - Stoyanchev, Todor
AU  - Tomašević, Igor
AU  - Tudoreanu, Liliana
AU  - Van Son, Maren
AU  - Zakowska-Biemans, Sylwia
AU  - Zamaratskaia, Galia
AU  - Van den Broeke, Alice
AU  - Egea, Macarena
PY  - 2020
UR  - http://aspace.agrif.bg.ac.rs/handle/123456789/5302
AB  - Simple Summary In many countries, surgical castration of piglets without pain relief or anaesthesia is still common practice. Castration is performed to minimise the incidence of boar taint, a bad taste (urine/fecal like), typically present in the meat of 5 to 10% of uncastrated male pigs. It also helps to avoid aggressive and sexual behaviour. For animal welfare reasons, alternatives are being considered, and in some countries, an alternative is already practiced. One option is to perform surgical castration with anaesthesia and relieve pain. A second option is to produce male pigs without castration, which requires detection of tainted carcasses in the slaughter house. A third option is to apply immunocastration: by a two-fold injection of a vaccine, the testes function is inhibited, which reduces boar-like behaviour and avoids boar taint. In this study, we evaluated the acceptability of each of these methods in 16 countries in Europe. Of the 4 presented options, the practice of surgical castration was least accepted (32%), whilst there was a high acceptance of castration with anaesthesia (85%), followed by immunocastration (71%) and production of boars (49%). The developed questionnaire and infographic can be used in future studies to further gain insights in consumer and stakeholder attitudes on this topic. Surgical castration of piglets without pain relief is still common practice in many countries. Possible alternatives for surgical castration are application of pain relief or anaesthesia or production of boars (entire males) and immunocastrates. Each of these alternatives faces advantages and disadvantages which may result in different citizen attitudes and consumers acceptability. Understanding which practice is acceptable to whom and why may further stimulate implementation. Consumer (n = 3251) and stakeholder (n = 1027) attitudes towards surgical castration without pain relief, surgical castration with anaesthesia, immunocastration, and production of boars were surveyed from April to June 2020 via an online questionnaire in 16 countries (>175 respondents per country). Surgical castration without pain relief was separated from each of the alternatives due to animal welfare and showed the lowest acceptability (32%). Within the alternatives, a further partitioning between the alternatives was based on perceived quality and food safety, with an acceptance of 85% for applying anaesthesia, 71% for immunocastration, and 49% for boar production. Differences depending on professional involvement and familiarity with agriculture could be observed, mainly for the acceptance of surgical castration without anaesthesia, immunocastration, and boars. Castration with anaesthesia was highly accepted by all types of respondents.
PB  - MDPI, BASEL
T2  - Animals
T1  - Exploratory Survey on European Consumer and Stakeholder Attitudes towards Alternatives for Surgical Castration of Piglets
IS  - 10
VL  - 10
DO  - 10.3390/ani10101758
ER  - 

@article{
author = "Aluwe, Marijke and Heyrman, Evert and Almeida, Joao M. and Babol, Jakub and Battacone, Gianni and Citek, Jaroslav and Font-i-Furnols, Maria and Getya, Andriy and Karolyi, Danijel and Kostyra, Eliza and Kress, Kevin and Kusec, Goran and Moerlein, Daniel and Semenova, Anastasia and Skrlep, Martin and Stoyanchev, Todor and Tomašević, Igor and Tudoreanu, Liliana and Van Son, Maren and Zakowska-Biemans, Sylwia and Zamaratskaia, Galia and Van den Broeke, Alice and Egea, Macarena",
year = "2020",
abstract = "Simple Summary In many countries, surgical castration of piglets without pain relief or anaesthesia is still common practice. Castration is performed to minimise the incidence of boar taint, a bad taste (urine/fecal like), typically present in the meat of 5 to 10% of uncastrated male pigs. It also helps to avoid aggressive and sexual behaviour. For animal welfare reasons, alternatives are being considered, and in some countries, an alternative is already practiced. One option is to perform surgical castration with anaesthesia and relieve pain. A second option is to produce male pigs without castration, which requires detection of tainted carcasses in the slaughter house. A third option is to apply immunocastration: by a two-fold injection of a vaccine, the testes function is inhibited, which reduces boar-like behaviour and avoids boar taint. In this study, we evaluated the acceptability of each of these methods in 16 countries in Europe. Of the 4 presented options, the practice of surgical castration was least accepted (32%), whilst there was a high acceptance of castration with anaesthesia (85%), followed by immunocastration (71%) and production of boars (49%). The developed questionnaire and infographic can be used in future studies to further gain insights in consumer and stakeholder attitudes on this topic. Surgical castration of piglets without pain relief is still common practice in many countries. Possible alternatives for surgical castration are application of pain relief or anaesthesia or production of boars (entire males) and immunocastrates. Each of these alternatives faces advantages and disadvantages which may result in different citizen attitudes and consumers acceptability. Understanding which practice is acceptable to whom and why may further stimulate implementation. Consumer (n = 3251) and stakeholder (n = 1027) attitudes towards surgical castration without pain relief, surgical castration with anaesthesia, immunocastration, and production of boars were surveyed from April to June 2020 via an online questionnaire in 16 countries (>175 respondents per country). Surgical castration without pain relief was separated from each of the alternatives due to animal welfare and showed the lowest acceptability (32%). Within the alternatives, a further partitioning between the alternatives was based on perceived quality and food safety, with an acceptance of 85% for applying anaesthesia, 71% for immunocastration, and 49% for boar production. Differences depending on professional involvement and familiarity with agriculture could be observed, mainly for the acceptance of surgical castration without anaesthesia, immunocastration, and boars. Castration with anaesthesia was highly accepted by all types of respondents.",
publisher = "MDPI, BASEL",
journal = "Animals",
title = "Exploratory Survey on European Consumer and Stakeholder Attitudes towards Alternatives for Surgical Castration of Piglets",
number = "10",
volume = "10",
doi = "10.3390/ani10101758"
}

Aluwe, M., Heyrman, E., Almeida, J. M., Babol, J., Battacone, G., Citek, J., Font-i-Furnols, M., Getya, A., Karolyi, D., Kostyra, E., Kress, K., Kusec, G., Moerlein, D., Semenova, A., Skrlep, M., Stoyanchev, T., Tomašević, I., Tudoreanu, L., Van Son, M., Zakowska-Biemans, S., Zamaratskaia, G., Van den Broeke, A.,& Egea, M.. (2020). Exploratory Survey on European Consumer and Stakeholder Attitudes towards Alternatives for Surgical Castration of Piglets. in Animals
MDPI, BASEL., 10(10).
https://doi.org/10.3390/ani10101758

Aluwe M, Heyrman E, Almeida JM, Babol J, Battacone G, Citek J, Font-i-Furnols M, Getya A, Karolyi D, Kostyra E, Kress K, Kusec G, Moerlein D, Semenova A, Skrlep M, Stoyanchev T, Tomašević I, Tudoreanu L, Van Son M, Zakowska-Biemans S, Zamaratskaia G, Van den Broeke A, Egea M. Exploratory Survey on European Consumer and Stakeholder Attitudes towards Alternatives for Surgical Castration of Piglets. in Animals. 2020;10(10).
doi:10.3390/ani10101758 .

Aluwe, Marijke, Heyrman, Evert, Almeida, Joao M., Babol, Jakub, Battacone, Gianni, Citek, Jaroslav, Font-i-Furnols, Maria, Getya, Andriy, Karolyi, Danijel, Kostyra, Eliza, Kress, Kevin, Kusec, Goran, Moerlein, Daniel, Semenova, Anastasia, Skrlep, Martin, Stoyanchev, Todor, Tomašević, Igor, Tudoreanu, Liliana, Van Son, Maren, Zakowska-Biemans, Sylwia, Zamaratskaia, Galia, Van den Broeke, Alice, Egea, Macarena, "Exploratory Survey on European Consumer and Stakeholder Attitudes towards Alternatives for Surgical Castration of Piglets" in Animals, 10, no. 10 (2020),
https://doi.org/10.3390/ani10101758 . .

TY  - JOUR
AU  - Ribani, A.
AU  - Utzeri, Valerio J.
AU  - Geraci, Claudia
AU  - Tinarelli, S.
AU  - Djan, M.
AU  - Velicković, N.
AU  - Doneva, R.
AU  - Dall'Olio, S.
AU  - Costa, L.Nanni
AU  - Schiavo, Giuseppina
AU  - Bovo, Samuele
AU  - Usai, Graziano
AU  - Gallo, Maurizio
AU  - Radović, Čedomir
AU  - Savić, Radomir
AU  - Karolyi, Danijel
AU  - Salajpal, K.
AU  - Gvozdanović, K.
AU  - Djurkin-Kusec, Ivona
AU  - Skrlep, Martin
AU  - Čandek-Potokar, Marjeta
AU  - Ovilo, Cristina
AU  - Fontanesi, Luca
PY  - 2019
UR  - http://aspace.agrif.bg.ac.rs/handle/123456789/5109
AB  - Autochthonous pig breeds are usually reared in extensive or semi-extensive production systems that might facilitate contact with wild boars and, thus, reciprocal genetic exchanges. In this study, we analysed variants in the melanocortin 1 receptor (MC1R) gene (which cause different coat colour phenotypes) and in the nuclear receptor subfamily 6 group A member 1 (NR6A1) gene (associated with increased vertebral number) in 712 pigs of 12 local pig breeds raised in Italy (Apulo-Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano and Sarda) and south-eastern European countries (Krskopolje from Slovenia, Black Slavonian and Turopolje from Croatia, Mangalitsa and Moravka from Serbia and East Balkan Swine from Bulgaria) and compared the data with the genetic variability at these loci investigated in 229 wild boars from populations spread in the same macro-geographic areas. None of the autochthonous pig breeds or wild boar populations were fixed for one allele at both loci. Domestic and wild-type alleles at these two genes were present in both domestic and wild populations. Findings of the distribution of MC1R alleles might be useful for tracing back the complex genetic history of autochthonous breeds. Altogether, these results indirectly demonstrate that bidirectional introgression of wild and domestic alleles is derived and affected by the human and naturally driven evolutionary forces that are shaping the Sus scrofa genome: autochthonous breeds are experiencing a sort of 'de-domestication' process, and wild resources are challenged by a 'domestication' drift. Both need to be further investigated and managed.
PB  - Wiley, Hoboken
T2  - Animal Genetics
T1  - Signatures of de-domestication in autochthonous pig breeds and of domestication in wild boar populations from MC1R and NR6A1 allele distribution
EP  - 171
IS  - 2
SP  - 166
VL  - 50
DO  - 10.1111/age.12771
ER  - 

@article{
author = "Ribani, A. and Utzeri, Valerio J. and Geraci, Claudia and Tinarelli, S. and Djan, M. and Velicković, N. and Doneva, R. and Dall'Olio, S. and Costa, L.Nanni and Schiavo, Giuseppina and Bovo, Samuele and Usai, Graziano and Gallo, Maurizio and Radović, Čedomir and Savić, Radomir and Karolyi, Danijel and Salajpal, K. and Gvozdanović, K. and Djurkin-Kusec, Ivona and Skrlep, Martin and Čandek-Potokar, Marjeta and Ovilo, Cristina and Fontanesi, Luca",
year = "2019",
abstract = "Autochthonous pig breeds are usually reared in extensive or semi-extensive production systems that might facilitate contact with wild boars and, thus, reciprocal genetic exchanges. In this study, we analysed variants in the melanocortin 1 receptor (MC1R) gene (which cause different coat colour phenotypes) and in the nuclear receptor subfamily 6 group A member 1 (NR6A1) gene (associated with increased vertebral number) in 712 pigs of 12 local pig breeds raised in Italy (Apulo-Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano and Sarda) and south-eastern European countries (Krskopolje from Slovenia, Black Slavonian and Turopolje from Croatia, Mangalitsa and Moravka from Serbia and East Balkan Swine from Bulgaria) and compared the data with the genetic variability at these loci investigated in 229 wild boars from populations spread in the same macro-geographic areas. None of the autochthonous pig breeds or wild boar populations were fixed for one allele at both loci. Domestic and wild-type alleles at these two genes were present in both domestic and wild populations. Findings of the distribution of MC1R alleles might be useful for tracing back the complex genetic history of autochthonous breeds. Altogether, these results indirectly demonstrate that bidirectional introgression of wild and domestic alleles is derived and affected by the human and naturally driven evolutionary forces that are shaping the Sus scrofa genome: autochthonous breeds are experiencing a sort of 'de-domestication' process, and wild resources are challenged by a 'domestication' drift. Both need to be further investigated and managed.",
publisher = "Wiley, Hoboken",
journal = "Animal Genetics",
title = "Signatures of de-domestication in autochthonous pig breeds and of domestication in wild boar populations from MC1R and NR6A1 allele distribution",
pages = "171-166",
number = "2",
volume = "50",
doi = "10.1111/age.12771"
}

Ribani, A., Utzeri, V. J., Geraci, C., Tinarelli, S., Djan, M., Velicković, N., Doneva, R., Dall'Olio, S., Costa, L.Nanni, Schiavo, G., Bovo, S., Usai, G., Gallo, M., Radović, Č., Savić, R., Karolyi, D., Salajpal, K., Gvozdanović, K., Djurkin-Kusec, I., Skrlep, M., Čandek-Potokar, M., Ovilo, C.,& Fontanesi, L.. (2019). Signatures of de-domestication in autochthonous pig breeds and of domestication in wild boar populations from MC1R and NR6A1 allele distribution. in Animal Genetics
Wiley, Hoboken., 50(2), 166-171.
https://doi.org/10.1111/age.12771

Ribani A, Utzeri VJ, Geraci C, Tinarelli S, Djan M, Velicković N, Doneva R, Dall'Olio S, Costa L, Schiavo G, Bovo S, Usai G, Gallo M, Radović Č, Savić R, Karolyi D, Salajpal K, Gvozdanović K, Djurkin-Kusec I, Skrlep M, Čandek-Potokar M, Ovilo C, Fontanesi L. Signatures of de-domestication in autochthonous pig breeds and of domestication in wild boar populations from MC1R and NR6A1 allele distribution. in Animal Genetics. 2019;50(2):166-171.
doi:10.1111/age.12771 .

Ribani, A., Utzeri, Valerio J., Geraci, Claudia, Tinarelli, S., Djan, M., Velicković, N., Doneva, R., Dall'Olio, S., Costa, L.Nanni, Schiavo, Giuseppina, Bovo, Samuele, Usai, Graziano, Gallo, Maurizio, Radović, Čedomir, Savić, Radomir, Karolyi, Danijel, Salajpal, K., Gvozdanović, K., Djurkin-Kusec, Ivona, Skrlep, Martin, Čandek-Potokar, Marjeta, Ovilo, Cristina, Fontanesi, Luca, "Signatures of de-domestication in autochthonous pig breeds and of domestication in wild boar populations from MC1R and NR6A1 allele distribution" in Animal Genetics, 50, no. 2 (2019):166-171,
https://doi.org/10.1111/age.12771 . .

TY  - JOUR
AU  - Munoz, Maria
AU  - Bozzi, Riccardo
AU  - Garcia-Casco, Juan
AU  - Nunez, Yolanda
AU  - Ribani, A.
AU  - Franci, O.
AU  - Garcia, Fabian
AU  - Skrlep, Martin
AU  - Schiavo, Giuseppina
AU  - Bovo, Samuele
AU  - Utzeri, Valerio J.
AU  - Charneca, R.
AU  - Martins, Jose M.
AU  - Quintanilla, Raquel
AU  - Tibau, J.
AU  - Margeta, Vladimir
AU  - Djurkin-Kusec, Ivona
AU  - Mercat, Marie J.
AU  - Riquet, Juliette
AU  - Estelle, Jordi
AU  - Zimmer, Christoph
AU  - Razmaite, Violeta
AU  - Araujo, Jose P.
AU  - Radović, Čedomir
AU  - Savić, Radomir
AU  - Karolyi, Danijel
AU  - Gallo, Maurizio
AU  - Čandek-Potokar, Marjeta
AU  - Fernandez, Ana I
AU  - Fontanesi, Luca
AU  - Ovilo, Cristina
PY  - 2019
UR  - http://aspace.agrif.bg.ac.rs/handle/123456789/4915
AB  - Genetic characterization of local breeds is essential to preserve their genomic variability, to advance conservation policies and to contribute to their promotion and sustainability. Genomic diversity of twenty European local pig breeds and a small sample of Spanish wild pigs was assessed using high density SNP chips. A total of 992 DNA samples were analyzed with the GeneSeek Genomic Profiler (GGP) 70 K HD porcine genotyping chip. Genotype data was employed to compute genetic diversity, population differentiation and structure, genetic distances, linkage disequilibrium and effective population size. Our results point out several breeds, such as Turopolje, Apulo Calabrese, Casertana, Mora Romagnola and Lithuanian indigenous wattle, having the lowest genetic diversity, supported by low heterozygosity and very small effective population size, demonstrating the need of enhanced conservation strategies. Principal components analysis showed the clustering of the individuals of the same breed, with few breeds being clearly isolated from the rest. Several breeds were partially overlapped, suggesting genetic closeness, which was particularly marked in the case of Iberian and Alentejana breeds. Spanish wild boar was also narrowly related to other western populations, in agreement with recurrent admixture between wild and domestic animals. We also searched across the genome for loci under diversifying selection based on F-S(T) outlier tests. Candidate genes that may underlie differences in adaptation to specific environments and productive systems and phenotypic traits were detected in potentially selected genomic regions.
PB  - Nature Publishing Group, London
T2  - Scientific Reports
T1  - Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip
VL  - 9
DO  - 10.1038/s41598-019-49830-6
ER  - 

@article{
author = "Munoz, Maria and Bozzi, Riccardo and Garcia-Casco, Juan and Nunez, Yolanda and Ribani, A. and Franci, O. and Garcia, Fabian and Skrlep, Martin and Schiavo, Giuseppina and Bovo, Samuele and Utzeri, Valerio J. and Charneca, R. and Martins, Jose M. and Quintanilla, Raquel and Tibau, J. and Margeta, Vladimir and Djurkin-Kusec, Ivona and Mercat, Marie J. and Riquet, Juliette and Estelle, Jordi and Zimmer, Christoph and Razmaite, Violeta and Araujo, Jose P. and Radović, Čedomir and Savić, Radomir and Karolyi, Danijel and Gallo, Maurizio and Čandek-Potokar, Marjeta and Fernandez, Ana I and Fontanesi, Luca and Ovilo, Cristina",
year = "2019",
abstract = "Genetic characterization of local breeds is essential to preserve their genomic variability, to advance conservation policies and to contribute to their promotion and sustainability. Genomic diversity of twenty European local pig breeds and a small sample of Spanish wild pigs was assessed using high density SNP chips. A total of 992 DNA samples were analyzed with the GeneSeek Genomic Profiler (GGP) 70 K HD porcine genotyping chip. Genotype data was employed to compute genetic diversity, population differentiation and structure, genetic distances, linkage disequilibrium and effective population size. Our results point out several breeds, such as Turopolje, Apulo Calabrese, Casertana, Mora Romagnola and Lithuanian indigenous wattle, having the lowest genetic diversity, supported by low heterozygosity and very small effective population size, demonstrating the need of enhanced conservation strategies. Principal components analysis showed the clustering of the individuals of the same breed, with few breeds being clearly isolated from the rest. Several breeds were partially overlapped, suggesting genetic closeness, which was particularly marked in the case of Iberian and Alentejana breeds. Spanish wild boar was also narrowly related to other western populations, in agreement with recurrent admixture between wild and domestic animals. We also searched across the genome for loci under diversifying selection based on F-S(T) outlier tests. Candidate genes that may underlie differences in adaptation to specific environments and productive systems and phenotypic traits were detected in potentially selected genomic regions.",
publisher = "Nature Publishing Group, London",
journal = "Scientific Reports",
title = "Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip",
volume = "9",
doi = "10.1038/s41598-019-49830-6"
}

Munoz, M., Bozzi, R., Garcia-Casco, J., Nunez, Y., Ribani, A., Franci, O., Garcia, F., Skrlep, M., Schiavo, G., Bovo, S., Utzeri, V. J., Charneca, R., Martins, J. M., Quintanilla, R., Tibau, J., Margeta, V., Djurkin-Kusec, I., Mercat, M. J., Riquet, J., Estelle, J., Zimmer, C., Razmaite, V., Araujo, J. P., Radović, Č., Savić, R., Karolyi, D., Gallo, M., Čandek-Potokar, M., Fernandez, A. I., Fontanesi, L.,& Ovilo, C.. (2019). Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip. in Scientific Reports
Nature Publishing Group, London., 9.
https://doi.org/10.1038/s41598-019-49830-6

Munoz M, Bozzi R, Garcia-Casco J, Nunez Y, Ribani A, Franci O, Garcia F, Skrlep M, Schiavo G, Bovo S, Utzeri VJ, Charneca R, Martins JM, Quintanilla R, Tibau J, Margeta V, Djurkin-Kusec I, Mercat MJ, Riquet J, Estelle J, Zimmer C, Razmaite V, Araujo JP, Radović Č, Savić R, Karolyi D, Gallo M, Čandek-Potokar M, Fernandez AI, Fontanesi L, Ovilo C. Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip. in Scientific Reports. 2019;9.
doi:10.1038/s41598-019-49830-6 .

Munoz, Maria, Bozzi, Riccardo, Garcia-Casco, Juan, Nunez, Yolanda, Ribani, A., Franci, O., Garcia, Fabian, Skrlep, Martin, Schiavo, Giuseppina, Bovo, Samuele, Utzeri, Valerio J., Charneca, R., Martins, Jose M., Quintanilla, Raquel, Tibau, J., Margeta, Vladimir, Djurkin-Kusec, Ivona, Mercat, Marie J., Riquet, Juliette, Estelle, Jordi, Zimmer, Christoph, Razmaite, Violeta, Araujo, Jose P., Radović, Čedomir, Savić, Radomir, Karolyi, Danijel, Gallo, Maurizio, Čandek-Potokar, Marjeta, Fernandez, Ana I, Fontanesi, Luca, Ovilo, Cristina, "Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip" in Scientific Reports, 9 (2019),
https://doi.org/10.1038/s41598-019-49830-6 . .

TY  - JOUR
AU  - Munoz, Maria
AU  - Bozzi, Riccardo
AU  - Garcia, Fabian
AU  - Nunez, Yolanda
AU  - Geraci, Claudia
AU  - Crovetti, Alessandro
AU  - Garcia-Casco, Juan
AU  - Alves, Estefania
AU  - Skrlep, Martin
AU  - Charneca, Rui
AU  - Martins, Jose M.
AU  - Quintanilla, Raquel
AU  - Tibau, Joan
AU  - Kusec, Goran
AU  - Djurkin-Kusec, Ivona
AU  - Mercat, Marie J.
AU  - Riquet, Juliette
AU  - Estelle, Jordi
AU  - Zimmer, Christoph
AU  - Razmaite, Violeta
AU  - Araujo, Jose P.
AU  - Radović, Čedomir
AU  - Savić, Radomir
AU  - Karolyi, Danijel
AU  - Gallo, Maurizio
AU  - Čandek-Potokar, Marjeta
AU  - Fontanesi, Luca
AU  - Fernandez, Ana I
AU  - Ovilo, Cristina
PY  - 2018
UR  - http://aspace.agrif.bg.ac.rs/handle/123456789/4698
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, ApuloCalabrese, Basque, Bisara, Majorcan Black, Black Slavonian (Crna slavonska), Casertana, Cinta Senese, Gascon, Iberian, Kr6kopolje (Kr6kopoljski), Lithuanian indigenous wattle, Lithuanian White Old Type, Mora Romagnola, Moravka, Nero Siciliano, Sarda, Schwabisch-Hallisches 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 Science, San Francisco
T2  - Plos One
T1  - Diversity across major and candidate genes in European local pig breeds
IS  - 11
VL  - 13
DO  - 10.1371/journal.pone.0207475
ER  - 

@article{
author = "Munoz, Maria and Bozzi, Riccardo and Garcia, Fabian and Nunez, Yolanda and Geraci, Claudia and Crovetti, Alessandro and Garcia-Casco, Juan and Alves, Estefania and Skrlep, Martin and Charneca, Rui and Martins, Jose M. and Quintanilla, Raquel and Tibau, Joan and Kusec, Goran and Djurkin-Kusec, Ivona and Mercat, Marie J. and Riquet, Juliette and Estelle, Jordi and Zimmer, Christoph and Razmaite, Violeta and Araujo, Jose P. and Radović, Čedomir and Savić, Radomir and Karolyi, Danijel and Gallo, Maurizio and Čandek-Potokar, Marjeta and Fontanesi, Luca and Fernandez, Ana I and Ovilo, Cristina",
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, ApuloCalabrese, Basque, Bisara, Majorcan Black, Black Slavonian (Crna slavonska), Casertana, Cinta Senese, Gascon, Iberian, Kr6kopolje (Kr6kopoljski), Lithuanian indigenous wattle, Lithuanian White Old Type, Mora Romagnola, Moravka, Nero Siciliano, Sarda, Schwabisch-Hallisches 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 Science, San Francisco",
journal = "Plos One",
title = "Diversity across major and candidate genes in European local pig breeds",
number = "11",
volume = "13",
doi = "10.1371/journal.pone.0207475"
}

Munoz, M., Bozzi, R., Garcia, F., Nunez, Y., Geraci, C., Crovetti, A., Garcia-Casco, J., Alves, E., Skrlep, M., Charneca, R., Martins, J. M., Quintanilla, R., Tibau, J., Kusec, G., Djurkin-Kusec, I., Mercat, M. J., Riquet, J., Estelle, J., Zimmer, C., Razmaite, V., Araujo, J. P., Radović, Č., Savić, R., Karolyi, D., Gallo, M., Čandek-Potokar, M., Fontanesi, L., Fernandez, A. I.,& Ovilo, C.. (2018). Diversity across major and candidate genes in European local pig breeds. in Plos One
Public Library Science, San Francisco., 13(11).
https://doi.org/10.1371/journal.pone.0207475

Munoz M, Bozzi R, Garcia F, Nunez Y, Geraci C, Crovetti A, Garcia-Casco J, Alves E, Skrlep M, Charneca R, Martins JM, Quintanilla R, Tibau J, Kusec G, Djurkin-Kusec I, Mercat MJ, Riquet J, Estelle J, Zimmer C, Razmaite V, Araujo JP, Radović Č, Savić R, Karolyi D, Gallo M, Čandek-Potokar M, Fontanesi L, Fernandez AI, Ovilo C. Diversity across major and candidate genes in European local pig breeds. in Plos One. 2018;13(11).
doi:10.1371/journal.pone.0207475 .

Munoz, Maria, Bozzi, Riccardo, Garcia, Fabian, Nunez, Yolanda, Geraci, Claudia, Crovetti, Alessandro, Garcia-Casco, Juan, Alves, Estefania, Skrlep, Martin, Charneca, Rui, Martins, Jose M., Quintanilla, Raquel, Tibau, Joan, Kusec, Goran, Djurkin-Kusec, Ivona, Mercat, Marie J., Riquet, Juliette, Estelle, Jordi, Zimmer, Christoph, Razmaite, Violeta, Araujo, Jose P., Radović, Čedomir, Savić, Radomir, Karolyi, Danijel, Gallo, Maurizio, Čandek-Potokar, Marjeta, Fontanesi, Luca, Fernandez, Ana I, Ovilo, Cristina, "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 . .