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
2020
Аутори
Bovo, SamueleRibani, 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
Чланак у часопису (Објављена верзија)
Метаподаци
Приказ свих података о документуАпстракт
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.
Извор:
Genetics Selection Evolution, 2020, 52, 1Издавач:
- Bmc, London
Финансирање / пројекти:
- Europe-FAANG COST ActionEuropean Cooperation in Science and Technology (COST)
- University of Bologna [RFO 2016-2019]
- Diversity of local pig breeds and production systems for high quality traditional products and sustainable pork chains (EU-H2020-634476)
DOI: 10.1186/s12711-020-00553-7
ISSN: 0999-193X
PubMed: 32591011
WoS: 000545946400001
Scopus: 2-s2.0-85087320667
Институција/група
Poljoprivredni fakultetTY - 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 . .