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 . .