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 M.
AU  - Mercat, Marie J.
AU  - Moscatelli, Giulia
AU  - Nunez, Yolanda
AU  - Quintanilla, 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://aspace.agrif.bg.ac.rs/handle/123456789/5252
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, Bisara, Majorcan Black, Basque, Gascon, Apulo-Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano, Sarda, Krskopolje pig, Black Slavonian, Turopolje, Moravka, Swallow-Bellied Mangalitsa, Schwabisch-Hallisches 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 (H-P) and fixation index (F-ST)] and group-based F(ST)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, London
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
IS  - 1
VL  - 52
DO  - 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 M. and Mercat, Marie J. and Moscatelli, Giulia and Nunez, Yolanda and Quintanilla, 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, Bisara, Majorcan Black, Basque, Gascon, Apulo-Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano, Sarda, Krskopolje pig, Black Slavonian, Turopolje, Moravka, Swallow-Bellied Mangalitsa, Schwabisch-Hallisches 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 (H-P) and fixation index (F-ST)] and group-based F(ST)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, London",
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",
number = "1",
volume = "52",
doi = "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., Nunez, Y., Quintanilla, 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, London., 52(1).
https://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, Nunez Y, Quintanilla 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(1).
doi: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 M., Mercat, Marie J., Moscatelli, Giulia, Nunez, Yolanda, Quintanilla, 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. 1 (2020),
https://doi.org/10.1186/s12711-020-00553-7 . .

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  - 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 . .