TY  - JOUR
AU  - Schiavo, G.
AU  - Bovo, S.
AU  - Munoz, M.
AU  - Ribani, A.
AU  - Alves, E.
AU  - Araujo, J. P.
AU  - Bozzi, R.
AU  - Čandek-Potokar, M.
AU  - Charneca, R.
AU  - Fernandez, A. I.
AU  - Gallo, M.
AU  - Garcia, F.
AU  - Karolyi, D.
AU  - Kušec, G.
AU  - Martins, J. M.
AU  - Mercat, M.-J.
AU  - Nunez, Y.
AU  - Quintanilla, R.
AU  - Radović, C.
AU  - Razmaite, V.
AU  - Riquet, J.
AU  - Savić, R.
AU  - Usai, G.
AU  - Utzeri, V. J.
AU  - Zimmer, C.
AU  - Ovilo, C.
AU  - Fontanesi, L.
PY  - 2021
UR  - http://aspace.agrif.bg.ac.rs/handle/123456789/5804
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 commonROHs withinthe samepopulationdefineROHislandsand indicatehotspots of
selection. In this work, we investigated ROHs in a total of 1131 pigs from20 European local pig
breeds and in three cosmopolitan breeds, genotyped with the GGP PorcineHDGenomic 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
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
DO  - 10.1111/age.13045
ER  - 

@article{
author = "Schiavo, G. and Bovo, S. and Munoz, M. and Ribani, A. and Alves, E. and Araujo, J. P. and Bozzi, R. and Čandek-Potokar, M. and Charneca, R. and Fernandez, A. I. and Gallo, M. and Garcia, F. and Karolyi, D. and Kušec, G. and Martins, J. M. and Mercat, M.-J. and Nunez, Y. and Quintanilla, R. and Radović, C. and Razmaite, V. and Riquet, J. and Savić, R. and Usai, G. and Utzeri, V. J. and Zimmer, C. and Ovilo, C. and Fontanesi, L.",
year = "2021",
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 commonROHs withinthe samepopulationdefineROHislandsand indicatehotspots of
selection. In this work, we investigated ROHs in a total of 1131 pigs from20 European local pig
breeds and in three cosmopolitan breeds, genotyped with the GGP PorcineHDGenomic 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",
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",
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.-J., Nunez, Y., Quintanilla, R., Radović, C., Razmaite, V., Riquet, J., Savić, R., Usai, G., Utzeri, V. J., Zimmer, C., Ovilo, C.,& Fontanesi, L.. (2021). 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..
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 C, 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;.
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.-J., Nunez, Y., Quintanilla, R., Radović, C., Razmaite, V., Riquet, J., Savić, R., Usai, G., Utzeri, V. J., 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),
https://doi.org/10.1111/age.13045 . .

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 . .