TY  - JOUR
AU  - Bovo, Samuele
AU  - Ribani, Anisa
AU  - Munoz, Maria
AU  - Alves, Estefania
AU  - Araujo, Jose P.
AU  - Bozzi, Riccardo
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  - Gvozdanović, Katarina
AU  - Martins, Jose Manuel
AU  - Mercat, Marie J.
AU  - Nunez, Yolanda
AU  - Quintailla, Raquel
AU  - Radović, Čedomir
AU  - Razmaite, Violeta
AU  - Riquet, Juliette
AU  - Savić, Radomir
AU  - Schiavo, Giuseppina
AU  - Škrlep, Martin
AU  - Usai, Graziano
AU  - Utzeri, Valerio J.
AU  - Zimmer, Christoph
AU  - Ovilo, Cristina
AU  - Fontanesi, Luca
PY  - 2020
UR  - http://r.istocar.bg.ac.rs/handle/123456789/719
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 429. 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 (~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  - International Foundation for Animal Genetics
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
DO  - doi:10.1111/age.12954
ER  - 

@article{
author = "Bovo, Samuele and Ribani, Anisa and Munoz, Maria and Alves, Estefania and Araujo, Jose P. and Bozzi, Riccardo 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 Gvozdanović, Katarina and Martins, Jose Manuel and Mercat, Marie J. and Nunez, Yolanda and Quintailla, Raquel and Radović, Čedomir and Razmaite, Violeta and Riquet, Juliette and Savić, Radomir and Schiavo, Giuseppina and Škrlep, Martin and Usai, Graziano and Utzeri, Valerio J. and Zimmer, Christoph and Ovilo, Cristina and Fontanesi, Luca",
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 429. 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 (~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 = "International Foundation for Animal Genetics",
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",
doi = "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., Quintailla, R., Radović, Č., Razmaite, V., Riquet, J., Savić, R., Schiavo, G., Škrlep, M., Usai, G., Utzeri, V. J., Zimmer, C., Ovilo, C.,& Fontanesi, L.. (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
International Foundation for Animal Genetics..
https://doi.org/doi: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, Quintailla R, Radović Č, Razmaite V, Riquet J, Savić R, Schiavo G, Škrlep M, Usai G, Utzeri VJ, Zimmer C, Ovilo C, Fontanesi L. 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;.
doi:doi:10.1111/age.12954 .

Bovo, Samuele, Ribani, Anisa, Munoz, Maria, Alves, Estefania, Araujo, Jose P., Bozzi, Riccardo, Charneca, Rui, Di Palma, Federica, Etherington, Graham, Fernandez, Ana I., Garcia, Fabian, Garcia-Casco, Juan, Karolyi, Danijel, Gallo, Maurizio, Gvozdanović, Katarina, Martins, Jose Manuel, Mercat, Marie J., Nunez, Yolanda, Quintailla, Raquel, Radović, Čedomir, Razmaite, Violeta, Riquet, Juliette, Savić, Radomir, Schiavo, Giuseppina, Škrlep, Martin, Usai, Graziano, Utzeri, Valerio J., Zimmer, Christoph, Ovilo, Cristina, Fontanesi, Luca, "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),
https://doi.org/doi:10.1111/age.12954 . .