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
Аутори
Bovo, SamueleRibani, 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
Чланак у часопису (Објављена верзија)
Метаподаци
Приказ свих података о документуАпстракт
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 multi...ple 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
Кључне речи:
copy number variant / ELOVL6 / genetic resource / KIT / MSRB3 / next-generation sequencing / Sus scrofa / ZNF622Извор:
Animal Genetics, 2020Издавач:
- International Foundation for Animal Genetics
Финансирање / пројекти:
- Diversity of local pig breeds and production systems for high quality traditional products and sustainable pork chains (EU-H2020-634476)
Институција/група
RIStocarTY - 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 . .