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  - 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  - Čandek-Potokar, Marjeta
AU  - Nieto, R.
AU  - Pugliese, C.
AU  - Araujo, Jose P.
AU  - Charneca, R.
AU  - Garcia-Casco, Juan
AU  - González Sánchez, E.
AU  - Hernandez-Garcia, F.I.
AU  - Izquierdo, M.
AU  - Karolyi, Danijel
AU  - Kusec, Goran
AU  - Lebret, B.
AU  - Mercat, Marie J.
AU  - Petig, M.
AU  - Radović, Čedomir
AU  - Savić, R.
PY  - 2017
UR  - http://aspace.agrif.bg.ac.rs/handle/123456789/4512
AB  - TREASURE is a research and innovation project of European Union’s Horizon 2020 programme which is devoted to traditional genetic resources in pig production with aim to improve their potentials for enhanced use. Studying and improving management of local pig breeds in their production systems is one of the challenges in which we address their performances and nutrition with special attention on locally available feeding resources and innovative practices aiming to improved welfare. For that purpose 15 experiments on 12 breeds were designed in the project, which are hereafter shortly presented. Their concepts and main objectives with some highlights on already available results are described.
PB  - University of Zagreb
T2  - Agriculturae Conspectus Scientificus
T1  - Local pig breeds: Nutritional requirements, innovative practices and local feeding resources as challenges in project TREASURE
EP  - 131
IS  - 2 Special Issue 1
SP  - 127
VL  - 82
UR  - https://hdl.handle.net/21.15107/rcub_agrospace_4512
ER  - 

@article{
author = "Čandek-Potokar, Marjeta and Nieto, R. and Pugliese, C. and Araujo, Jose P. and Charneca, R. and Garcia-Casco, Juan and González Sánchez, E. and Hernandez-Garcia, F.I. and Izquierdo, M. and Karolyi, Danijel and Kusec, Goran and Lebret, B. and Mercat, Marie J. and Petig, M. and Radović, Čedomir and Savić, R.",
year = "2017",
abstract = "TREASURE is a research and innovation project of European Union’s Horizon 2020 programme which is devoted to traditional genetic resources in pig production with aim to improve their potentials for enhanced use. Studying and improving management of local pig breeds in their production systems is one of the challenges in which we address their performances and nutrition with special attention on locally available feeding resources and innovative practices aiming to improved welfare. For that purpose 15 experiments on 12 breeds were designed in the project, which are hereafter shortly presented. Their concepts and main objectives with some highlights on already available results are described.",
publisher = "University of Zagreb",
journal = "Agriculturae Conspectus Scientificus",
title = "Local pig breeds: Nutritional requirements, innovative practices and local feeding resources as challenges in project TREASURE",
pages = "131-127",
number = "2 Special Issue 1",
volume = "82",
url = "https://hdl.handle.net/21.15107/rcub_agrospace_4512"
}

Čandek-Potokar, M., Nieto, R., Pugliese, C., Araujo, J. P., Charneca, R., Garcia-Casco, J., González Sánchez, E., Hernandez-Garcia, F.I., Izquierdo, M., Karolyi, D., Kusec, G., Lebret, B., Mercat, M. J., Petig, M., Radović, Č.,& Savić, R.. (2017). Local pig breeds: Nutritional requirements, innovative practices and local feeding resources as challenges in project TREASURE. in Agriculturae Conspectus Scientificus
University of Zagreb., 82(2 Special Issue 1), 127-131.
https://hdl.handle.net/21.15107/rcub_agrospace_4512

Čandek-Potokar M, Nieto R, Pugliese C, Araujo JP, Charneca R, Garcia-Casco J, González Sánchez E, Hernandez-Garcia F, Izquierdo M, Karolyi D, Kusec G, Lebret B, Mercat MJ, Petig M, Radović Č, Savić R. Local pig breeds: Nutritional requirements, innovative practices and local feeding resources as challenges in project TREASURE. in Agriculturae Conspectus Scientificus. 2017;82(2 Special Issue 1):127-131.
https://hdl.handle.net/21.15107/rcub_agrospace_4512 .

Čandek-Potokar, Marjeta, Nieto, R., Pugliese, C., Araujo, Jose P., Charneca, R., Garcia-Casco, Juan, González Sánchez, E., Hernandez-Garcia, F.I., Izquierdo, M., Karolyi, Danijel, Kusec, Goran, Lebret, B., Mercat, Marie J., Petig, M., Radović, Čedomir, Savić, R., "Local pig breeds: Nutritional requirements, innovative practices and local feeding resources as challenges in project TREASURE" in Agriculturae Conspectus Scientificus, 82, no. 2 Special Issue 1 (2017):127-131,
https://hdl.handle.net/21.15107/rcub_agrospace_4512 .