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1. Admixture and breed traceability in European indigenous pig breeds and wild boar using genome-wide SNP data

Author

Dadousis, Christos, Muñoz, Maria, Óvilo, Cristina, Fabbri, Maria Chiara, Araújo, José Pedro, Bovo, Samuele, Potokar, Marjeta Čandek, Charneca, Rui, Crovetti, Alessandro, Gallo, Maurizio, García-Casco, Juan María, Karolyi, Danijel, Kušec, Goran, Martins, José Manuel, Mercat, Marie-José, Pugliese, Carolina, Quintanilla, Raquel, Radović, Čedomir, Razmaite, Violeta, Ribani, Anisa, Riquet, Juliet, Savić, Radomir, Schiavo, Giuseppina, Škrlep, Martin, Tinarelli, Silvia, Usai, Graziano, Zimmer, Christoph, Fontanesi, Luca, and Bozzi, Riccardo

Published
2022
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2. Describing variability in pig genes involved in coronavirus infections for a One Health perspective in conservation of animal genetic resources

Author

Bovo, Samuele, Schiavo, Giuseppina, Ribani, Anisa, Utzeri, Valerio J., Taurisano, Valeria, Ballan, Mohamad, Muñoz, Maria, Alves, Estefania, Araujo, Jose P., Bozzi, Riccardo, Charneca, Rui, Di Palma, Federica, Djurkin Kušec, Ivona, Etherington, Graham, Fernandez, Ana I., García, Fabián, García-Casco, Juan, Karolyi, Danijel, Gallo, Maurizio, Martins, José Manuel, Mercat, Marie-José, Núñez, Yolanda, Quintanilla, Raquel, Radović, Čedomir, Razmaite, Violeta, Riquet, Juliette, Savić, Radomir, Škrlep, Martin, Usai, Graziano, Zimmer, Christoph, Ovilo, Cristina, and Fontanesi, Luca

Published
2021
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3. 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

Author

Bovo, Samuele, Ribani, Anisa, Muñoz, Maria, Alves, Estefania, Araujo, Jose P., Bozzi, Riccardo, Čandek-Potokar, Marjeta, Charneca, Rui, Di Palma, Federica, Etherington, Graham, Fernandez, Ana I., García, Fabián, García-Casco, Juan, Karolyi, Danijel, Gallo, Maurizio, Margeta, Vladimir, Martins, José Manuel, Mercat, Marie J., Moscatelli, Giulia, Núñez, Yolanda, Quintanilla, Raquel, Radović, Čedomir, Razmaite, Violeta, Riquet, Juliette, Savić, Radomir, Schiavo, Giuseppina, Usai, Graziano, Utzeri, Valerio J., Zimmer, Christoph, Ovilo, Cristina, and Fontanesi, Luca

Published
2020
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4. Admixture and breed traceability in European indigenous pig breeds and wild boar using genome-wide SNP data

Author

European Commission, Slovenian Research Agency, Dadousis, Christos [0000-0002-7689-6443], Óvilo, Cristina [0000-0002-5738-8435], Fabbri, Maria Chiara [0000-0002-3224-745X], Araújo, José Pedro [0000-0002-1232-3160], Bovo, Samuele [0000-0002-5712-8211], Potokar, Marjeta Čandek [0000-0003-0231-126X], Charneca, Rui [0000-0002-3597-6746], Crovetti, Alessandro [0000-0002-4052-0794], García-Casco, Juan María [0000-0003-0851-608X], Karolyi, Danijel [0000-0003-0409-9071], Kušec, Goran [0000-0002-2900-4019], Mercat, Marie-José [0000-0002-3087-082X], Pugliese, Carolina [000-0002-3735-8714], Tinarelli, Silvia [0000-0001-8875-5456], Usai, Graziano [0000-0002-6002-2223], Fontanesi, Luca [00000000-0001-7050-3760-0001-7050-3760], Riccardo Bozzi [0000-0001-8854-0834], Riquet, Juliette [0000-0001-7787-031X], Dadousis, Christos, Muñoz, María, Óvilo Martín, Cristina, Fabbri, Maria Chiara, Araújo, José Pedro, Bovo, Samuele, Potokar, Marjeta Čandek, Charneca, Rui, Crovetti, Alessandro, Gallo, Maurizio, García Casco, Juan María, Karolyi, Danijel, Kušec, Goran, Martins, José Manuel, Mercat, Marie-José, Pugliese, Carolina, Quintanilla, Raquel, Radović, Čedomir, Razmaite, Violeta, Ribani, Anisa, Riquet, Juliette, Savić, Radomir, Schiavo, Giuseppina, Škrlep, Martin, Tinarelli, Silvia, Usai, Graziano, Zimmer, Christoph, Fontanesi, Luca, Bozzi, Riccardo, European Commission, Slovenian Research Agency, Dadousis, Christos [0000-0002-7689-6443], Óvilo, Cristina [0000-0002-5738-8435], Fabbri, Maria Chiara [0000-0002-3224-745X], Araújo, José Pedro [0000-0002-1232-3160], Bovo, Samuele [0000-0002-5712-8211], Potokar, Marjeta Čandek [0000-0003-0231-126X], Charneca, Rui [0000-0002-3597-6746], Crovetti, Alessandro [0000-0002-4052-0794], García-Casco, Juan María [0000-0003-0851-608X], Karolyi, Danijel [0000-0003-0409-9071], Kušec, Goran [0000-0002-2900-4019], Mercat, Marie-José [0000-0002-3087-082X], Pugliese, Carolina [000-0002-3735-8714], Tinarelli, Silvia [0000-0001-8875-5456], Usai, Graziano [0000-0002-6002-2223], Fontanesi, Luca [00000000-0001-7050-3760-0001-7050-3760], Riccardo Bozzi [0000-0001-8854-0834], Riquet, Juliette [0000-0001-7787-031X], Dadousis, Christos, Muñoz, María, Óvilo Martín, Cristina, Fabbri, Maria Chiara, Araújo, José Pedro, Bovo, Samuele, Potokar, Marjeta Čandek, Charneca, Rui, Crovetti, Alessandro, Gallo, Maurizio, García Casco, Juan María, Karolyi, Danijel, Kušec, Goran, Martins, José Manuel, Mercat, Marie-José, Pugliese, Carolina, Quintanilla, Raquel, Radović, Čedomir, Razmaite, Violeta, Ribani, Anisa, Riquet, Juliette, Savić, Radomir, Schiavo, Giuseppina, Škrlep, Martin, Tinarelli, Silvia, Usai, Graziano, Zimmer, Christoph, Fontanesi, Luca, and Bozzi, Riccardo

Abstract

Preserving diversity of indigenous pig (Sus scrofa) breeds is a key factor to (i) sustain the pork chain (both at local and global scales) including the production of high-quality branded products, (ii) enrich the animal biobanking and (iii) progress conservation policies. Single nucleotide polymorphism (SNP) chips offer the opportunity for whole-genome comparisons among individuals and breeds. Animals from twenty European local pigs breeds, reared in nine countries (Croatia: Black Slavonian, Turopolje; France: Basque, Gascon; Germany: Schwabisch-Hällisches Schwein; Italy: Apulo Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano, Sarda; Lithuania: Indigenous Wattle, White Old Type; Portugal: Alentejana, Bísara; Serbia: Moravka, Swallow-Bellied Mangalitsa; Slovenia: Krškopolje pig; Spain: Iberian, Majorcan Black), and three commercial breeds (Duroc, Landrace and Large White) were sampled and genotyped with the GeneSeek Genomic Profiler (GGP) 70 K HD porcine genotyping chip. A dataset of 51 Wild Boars from nine countries was also added, summing up to 1186 pigs (~ 49 pigs/breed). The aim was to: (i) investigate individual admixture ancestries and (ii) assess breed traceability via discriminant analysis on principal components (DAPC). Albeit the mosaic of shared ancestries found for Nero Siciliano, Sarda and Moravka, admixture analysis indicated independent evolvement for the rest of the breeds. High prediction accuracy of DAPC mark SNP data as a reliable solution for the traceability of breed-specific pig products.

Published
2022

5. Runs of homozygosity provide a genome landscape picture of inbreeding and genetic history of European autochthonous and commercial pig breeds

Author

Università di Bologna, European Commission, Schiavo, Giampietro [0000-0002-3497-1337], Bovo, S. [0000-0002-5712-8211], Ribani, Anisa [0000-0001-6778-1938], Araújo, J.P. [0000-0002-1232-3160], Bozzi, R. [0000-0001-8854-0834], Čandek-Potokar, M. [0000-0003-0231-126X], Charneca, Rui [0000-0002-3597-6746], Fernández, Ana Isabel [0000-0002-1509-5191], Kušec, Goran [0000-0002-2900-4019], Campos Martín, José Miguel [0000-0002-7913-9851], Mercat, Marie-José [0000-0002-3087-082X], Núñez, Yolanda [0000-0001-5988-7628], Quintanilla, Raquel [0000-0003-3274-3434], Radović, Čedomir [0000-0002-1800-2448], Razmaite, V. [0000-0001-9006-5761], Riquet, Juliette [0000-0001-7787-031X], Savić, Radomir [0000-0003-2131-5303], Usai, Graziano [0000-0002-6002-2223], Utzeri, Valerio J. [0000-0001-5320-4216], Fontanesi, Luca [0000-0001-7050-3760], Karolyi, Danijel [0000-0003-0409-9071], Schiavo, Giampietro, Bovo, Samuele, Muñoz, María, Ribani, Anisa, Alves, Estefania, Araújo, José Pedro, Bozzi, Riccardo, Čandek-Potokar, M., Charneca, Rui, Fernández, Ana Isabel, Gallo, Maurizio, García, Fabián, Karolyi, Danijel, Kušec, Goran, Martins, José Manuel, Mercat, Marie-José, Núñez, Yolanda, Quintanilla, Raquel, Radović, Čedomir, Razmaite, Violeta, Riquet, Juliette, Savić, Radomir, Usai, Graziano, Utzeri, Valerio J., Zimmer, Christoph, Óvilo Martín, Cristina, Fontanesi, Luca, Università di Bologna, European Commission, Schiavo, Giampietro [0000-0002-3497-1337], Bovo, S. [0000-0002-5712-8211], Ribani, Anisa [0000-0001-6778-1938], Araújo, J.P. [0000-0002-1232-3160], Bozzi, R. [0000-0001-8854-0834], Čandek-Potokar, M. [0000-0003-0231-126X], Charneca, Rui [0000-0002-3597-6746], Fernández, Ana Isabel [0000-0002-1509-5191], Kušec, Goran [0000-0002-2900-4019], Campos Martín, José Miguel [0000-0002-7913-9851], Mercat, Marie-José [0000-0002-3087-082X], Núñez, Yolanda [0000-0001-5988-7628], Quintanilla, Raquel [0000-0003-3274-3434], Radović, Čedomir [0000-0002-1800-2448], Razmaite, V. [0000-0001-9006-5761], Riquet, Juliette [0000-0001-7787-031X], Savić, Radomir [0000-0003-2131-5303], Usai, Graziano [0000-0002-6002-2223], Utzeri, Valerio J. [0000-0001-5320-4216], Fontanesi, Luca [0000-0001-7050-3760], Karolyi, Danijel [0000-0003-0409-9071], Schiavo, Giampietro, Bovo, Samuele, Muñoz, María, Ribani, Anisa, Alves, Estefania, Araújo, José Pedro, Bozzi, Riccardo, Čandek-Potokar, M., Charneca, Rui, Fernández, Ana Isabel, Gallo, Maurizio, García, Fabián, Karolyi, Danijel, Kušec, Goran, Martins, José Manuel, Mercat, Marie-José, Núñez, Yolanda, Quintanilla, Raquel, Radović, Čedomir, Razmaite, Violeta, Riquet, Juliette, Savić, Radomir, Usai, Graziano, Utzeri, Valerio J., Zimmer, Christoph, Óvilo Martín, Cristina, and Fontanesi, Luca

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 common ROHs within the same population define ROH islands and indicate hotspots of selection. In this work, we investigated ROHs in a total of 1131 pigs from 20 European local pig breeds and in three cosmopolitan breeds, genotyped with the GGP Porcine HD Genomic 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 over-representation 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 Lithuanian White 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 the investigated pig breeds and provided information to manage these pig genetic resources.

Published
2021

6. Describing variability in pig genes involved in coronavirus infections for a One Health perspective in conservation of animal genetic resources

Author

Università di Bologna, European Commission, Bovo, Samuele [0000-0002-5712-8211], Schiavo, Giuseppina [0000-0002-3497-1337], Ribani, Anisa [0000-0001-6778-1938], Utzeri, Valerio J. [0000-0001-5320-4216], Taurisano, Valeria [0000-0001-5349-1606], Araujo, Jose P [0000-0002-1232-3160], Bozzi, Riccardo [0000-0001-8854-0834], Charneca, Rui [0000-0002-3597-6746], Di Palma, Federica [0000-0002-4394-0102], Djurkin Kušec, Ivona [0000-0002-1363-8447], Etherington, Graham [0000-0002-5003-1425], Fernández, Ana Isabel [0000-0002-1509-5191], Suárez García, Fabián [0000-0002-1970-293X], García-Casco, Juan [0000-0003-0851-608X], Karolyi, D 0000-003-0409-9071], Martins, José Manuel [0000-0003-3616-8406], Mercat, Marie-José [0000-0002-3087-082X], Núñez, Yolanda [0000-0001-5988-7628], Radović, Čedomir [0000-0002-1800-2448], Razmaite, Violeta [0000-0001-9006-5761], Riquet, Juliette [0000-0001-7787-031X], Savić, Radomir [0000-0003-2131-5303], Škrlep, Martin [0000-0002-8252-8022], Usai, Graziano [0000-0002-6002-2223], Ovilo, Cristina [0000-0002-5738-8435], Bovo, Samuele, Schiavo, Giuseppina, Ribani, Anisa, Utzeri, Valerio J., Taurisano, Valeria, Ballan, Mohamad, Muñoz, María, Alves, Estefania, Araújo, José Pedro, Bozzi, Riccardo, Charneca, Rui, Di Palma, Federica, Djurkin Kušec, Ivona, Etherington, Graham, Fernández, Ana Isabel, Suárez García, Fabián, García Casco, Juan María, Karolyi, Danijel, Gallo, Maurizio, Martins, José Manuel, Mercat, Marie-José, Núñez, Yolanda, Quintanilla, Raquel, Radović, Čedomir, Razmaite, Violeta, Riquet, Juliette, Savić, Radomir, Škrlep, Martin, Usai, Graziano, Zimmer, Christoph, Óvilo Martín, Cristina, Fontanesi, Luca, Università di Bologna, European Commission, Bovo, Samuele [0000-0002-5712-8211], Schiavo, Giuseppina [0000-0002-3497-1337], Ribani, Anisa [0000-0001-6778-1938], Utzeri, Valerio J. [0000-0001-5320-4216], Taurisano, Valeria [0000-0001-5349-1606], Araujo, Jose P [0000-0002-1232-3160], Bozzi, Riccardo [0000-0001-8854-0834], Charneca, Rui [0000-0002-3597-6746], Di Palma, Federica [0000-0002-4394-0102], Djurkin Kušec, Ivona [0000-0002-1363-8447], Etherington, Graham [0000-0002-5003-1425], Fernández, Ana Isabel [0000-0002-1509-5191], Suárez García, Fabián [0000-0002-1970-293X], García-Casco, Juan [0000-0003-0851-608X], Karolyi, D 0000-003-0409-9071], Martins, José Manuel [0000-0003-3616-8406], Mercat, Marie-José [0000-0002-3087-082X], Núñez, Yolanda [0000-0001-5988-7628], Radović, Čedomir [0000-0002-1800-2448], Razmaite, Violeta [0000-0001-9006-5761], Riquet, Juliette [0000-0001-7787-031X], Savić, Radomir [0000-0003-2131-5303], Škrlep, Martin [0000-0002-8252-8022], Usai, Graziano [0000-0002-6002-2223], Ovilo, Cristina [0000-0002-5738-8435], Bovo, Samuele, Schiavo, Giuseppina, Ribani, Anisa, Utzeri, Valerio J., Taurisano, Valeria, Ballan, Mohamad, Muñoz, María, Alves, Estefania, Araújo, José Pedro, Bozzi, Riccardo, Charneca, Rui, Di Palma, Federica, Djurkin Kušec, Ivona, Etherington, Graham, Fernández, Ana Isabel, Suárez García, Fabián, García Casco, Juan María, Karolyi, Danijel, Gallo, Maurizio, Martins, José Manuel, Mercat, Marie-José, Núñez, Yolanda, Quintanilla, Raquel, Radović, Čedomir, Razmaite, Violeta, Riquet, Juliette, Savić, Radomir, Škrlep, Martin, Usai, Graziano, Zimmer, Christoph, Óvilo Martín, Cristina, and Fontanesi, Luca

Abstract

Coronaviruses silently circulate in human and animal populations, causing mild to severe diseases. Therefore, livestock are important components of a "One Health" perspective aimed to control these viral infections. However, at present there is no example that considers pig genetic resources in this context. In this study, we investigated the variability of four genes (ACE2, ANPEP and DPP4 encoding for host receptors of the viral spike proteins and TMPRSS2 encoding for a host proteinase) in 23 European (19 autochthonous and three commercial breeds and one wild boar population) and two Asian Sus scrofa populations. A total of 2229 variants were identified in the four candidate genes: 26% of them were not previously described; 29 variants affected the protein sequence and might potentially interact with the infection mechanisms. The results coming from this work are a first step towards a "One Health" perspective that should consider conservation programs of pig genetic resources with twofold objectives: (i) genetic resources could be reservoirs of host gene variability useful to design selection programs to increase resistance to coronaviruses; (ii) the described variability in genes involved in coronavirus infections across many different pig populations might be part of a risk assessment including pig genetic resources.

Published
2021

7. 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

Author

European Commission, Università di Bologna, Bovo, Samuele [0000-0002-5712-8211], Ribani, Anisa [0000-0001-6778-1938], Araújo, José Pedro [0000-0002-1232-3160], Bozzi, Riccardo [0000-0001-8854-0834], Čandek-Potokar, M. [0000-0003-0231-126X], Charneca, Rui [0000-0002-3597-6746], Di Palma, Federica [0000-0002-4394-0102], Etherington, Graham [0000-0002-5003-1425], Suárez García, Fabián [0000-0002-1970-293X], García Casco, Juan María [0000-0003-0851-608X], Karolyi, Danijel [0000-0003-0409-9071], Gallo, Maurizio [0000-0002-9801-2856], Martins, José Manuel [0000-0003-3616-8406], Mercat, Marie-José [0000-0002-3087-082X], Moscatelli, Giulia [0000-0002-6284-2911], Núñez, Yolanda [0000-0001-5988-7628], Quintanilla, Raquel [0000-0003-3274-3434], Radović, Čedomir [0000-0002-1800-2448], Razmaite, Violeta [0000-0001-9006-5761], Riquet, Juliette [0000-0001-7787-031X], Savić, Radomir [0000-0003-2131-5303], Schiavo, Giuseppina [0000-0002-3497-1337], Usai, Graziano [0000-0002-6002-2223], Utzeri, Valerio J. [0000-0001-5320-4216], Óvilo Martín, Cristina [0000-0002-5738-8435], Fontanesi, Luca [0000-0001-7050-3760], Bovo, Samuele, Ribani, Anisa, Muñoz, María, Alves, Estefania, Araújo, José Pedro, Bozzi, Riccardo, Čandek-Potokar, M., Charneca, Rui, Di Palma, Federica, Etherington, Graham, Fernández, Ana Isabel, Suárez García, Fabián, García Casco, Juan María, Karolyi, Danijel, Gallo, Maurizio, Margeta, Vladimir, Martins, José Manuel, Mercat, Marie-José, Moscatelli, Giulia, Núñez, Yolanda, Quintanilla, Raquel, Radović, Čedomir, Razmaite, Violeta, Riquet, Juliette, Savić, Radomir, Schiavo, Giuseppina, Usai, Graziano, Utzeri, Valerio J., Zimmer, Christoph, Óvilo Martín, Cristina, Fontanesi, Luca, European Commission, Università di Bologna, Bovo, Samuele [0000-0002-5712-8211], Ribani, Anisa [0000-0001-6778-1938], Araújo, José Pedro [0000-0002-1232-3160], Bozzi, Riccardo [0000-0001-8854-0834], Čandek-Potokar, M. [0000-0003-0231-126X], Charneca, Rui [0000-0002-3597-6746], Di Palma, Federica [0000-0002-4394-0102], Etherington, Graham [0000-0002-5003-1425], Suárez García, Fabián [0000-0002-1970-293X], García Casco, Juan María [0000-0003-0851-608X], Karolyi, Danijel [0000-0003-0409-9071], Gallo, Maurizio [0000-0002-9801-2856], Martins, José Manuel [0000-0003-3616-8406], Mercat, Marie-José [0000-0002-3087-082X], Moscatelli, Giulia [0000-0002-6284-2911], Núñez, Yolanda [0000-0001-5988-7628], Quintanilla, Raquel [0000-0003-3274-3434], Radović, Čedomir [0000-0002-1800-2448], Razmaite, Violeta [0000-0001-9006-5761], Riquet, Juliette [0000-0001-7787-031X], Savić, Radomir [0000-0003-2131-5303], Schiavo, Giuseppina [0000-0002-3497-1337], Usai, Graziano [0000-0002-6002-2223], Utzeri, Valerio J. [0000-0001-5320-4216], Óvilo Martín, Cristina [0000-0002-5738-8435], Fontanesi, Luca [0000-0001-7050-3760], Bovo, Samuele, Ribani, Anisa, Muñoz, María, Alves, Estefania, Araújo, José Pedro, Bozzi, Riccardo, Čandek-Potokar, M., Charneca, Rui, Di Palma, Federica, Etherington, Graham, Fernández, Ana Isabel, Suárez García, Fabián, García Casco, Juan María, Karolyi, Danijel, Gallo, Maurizio, Margeta, Vladimir, Martins, José Manuel, Mercat, Marie-José, Moscatelli, Giulia, Núñez, Yolanda, Quintanilla, Raquel, Radović, Čedomir, Razmaite, Violeta, Riquet, Juliette, Savić, Radomir, Schiavo, Giuseppina, Usai, Graziano, Utzeri, Valerio J., Zimmer, Christoph, Óvilo Martín, Cristina, and Fontanesi, Luca

Abstract

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, Bísara, Majorcan Black, Basque, Gascon, Apulo-Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano, Sarda, Krškopolje pig, Black Slavonian, Turopolje, Moravka, Swallow-Bellied Mangalitsa, Schwäbisch-Hällisches 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 (HP) and fixation index (FST)] and group-based FST approaches, which compare groups of breeds defined according to external traits and use/specialization/type.

Published
2020

8. 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

Author

Università di Bologna, Slovenian Research Agency, European Commission, Bovo, Samuele [0000-0002-5712-8211], Ribani, Anisa [0000-0001-6778-1938], Muñoz, Marina [0000-0002-4216-6928], Araújo, José Pedro [0000-0002-1232-3160], Bozzi, Riccardo [0000-0001-8854-0834], Charneca, Rui [0000-0002-3597-6746], Di Palma, Federica [0000-0002-4394-0102], Etherington, Graham [0000-0002-5003-1425], Fernández, Ana Isabel [0000-0002-1509-5191], García Casco, Juan María [0000-0003-0851-608X], Karolyi, Danijel [0000-0003-0409-9071], Gvozdanović, Kristina [0000-0002-1989-2630], Martins, José Manuel [0000-0003-3616-8406], Mercat, Marie-José [0000-0002-3087-082X], Núñez, Yolanda [0000-0001-5988-7628], Quintanilla, Raquel [0000-0003-3274-3434], Radović, Čedomir [0000-0002-1800-2448], Razmaite, Violeta [0000-0001-9006-5761], Riquet, Juliette [0000-0001-7787-031X], Savić, Radomir [0000-0003-2131-5303], Schiavo, Giuseppina [0000-0002-3497-1337], Škrlep, Martin [0000-0002-8252-8022], Usai, Graziano [0000-0002-6002-2223], Utzeri, Valerio J. [0000-0001-5320-4216], Óvilo Martín, Cristina [0000-0002-5738-8435], Fontanesi, Luca [0000-0001-7050-3760], Bovo, Samuele, Ribani, Anisa, Muñoz, Marina, Alves, Estefania, Araújo, José Pedro, Bozzi, Riccardo, Charneca, Rui, Di Palma, Federica, Etherington, Graham, Fernández, Ana Isabel, García, Fabián, García Casco, Juan María, Karolyi, Danijel, Gallo, Maurizio, Gvozdanović, Kristina, Martins, José Manuel, Mercat, Marie-José, Núñez, Yolanda, Quintanilla, Raquel, Radović, Čedomir, Razmaite, Violeta, Riquet, Juliette, Savić, Radomir, Schiavo, Giuseppina, Škrlep, Martin, Usai, Graziano, Utzeri, Valerio J., Zimmer, Christoph, Óvilo Martín, Cristina, Fontanesi, Luca, Università di Bologna, Slovenian Research Agency, European Commission, Bovo, Samuele [0000-0002-5712-8211], Ribani, Anisa [0000-0001-6778-1938], Muñoz, Marina [0000-0002-4216-6928], Araújo, José Pedro [0000-0002-1232-3160], Bozzi, Riccardo [0000-0001-8854-0834], Charneca, Rui [0000-0002-3597-6746], Di Palma, Federica [0000-0002-4394-0102], Etherington, Graham [0000-0002-5003-1425], Fernández, Ana Isabel [0000-0002-1509-5191], García Casco, Juan María [0000-0003-0851-608X], Karolyi, Danijel [0000-0003-0409-9071], Gvozdanović, Kristina [0000-0002-1989-2630], Martins, José Manuel [0000-0003-3616-8406], Mercat, Marie-José [0000-0002-3087-082X], Núñez, Yolanda [0000-0001-5988-7628], Quintanilla, Raquel [0000-0003-3274-3434], Radović, Čedomir [0000-0002-1800-2448], Razmaite, Violeta [0000-0001-9006-5761], Riquet, Juliette [0000-0001-7787-031X], Savić, Radomir [0000-0003-2131-5303], Schiavo, Giuseppina [0000-0002-3497-1337], Škrlep, Martin [0000-0002-8252-8022], Usai, Graziano [0000-0002-6002-2223], Utzeri, Valerio J. [0000-0001-5320-4216], Óvilo Martín, Cristina [0000-0002-5738-8435], Fontanesi, Luca [0000-0001-7050-3760], Bovo, Samuele, Ribani, Anisa, Muñoz, Marina, Alves, Estefania, Araújo, José Pedro, Bozzi, Riccardo, Charneca, Rui, Di Palma, Federica, Etherington, Graham, Fernández, Ana Isabel, García, Fabián, García Casco, Juan María, Karolyi, Danijel, Gallo, Maurizio, Gvozdanović, Kristina, Martins, José Manuel, Mercat, Marie-José, Núñez, Yolanda, Quintanilla, Raquel, Radović, Čedomir, Razmaite, Violeta, Riquet, Juliette, Savić, Radomir, Schiavo, Giuseppina, Škrlep, Martin, Usai, Graziano, Utzeri, Valerio J., Zimmer, Christoph, Óvilo Martín, Cristina, and Fontanesi, Luca

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 42×. 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.

Published
2020

9. Runs of homozygosity provide a genome landscape picture of inbreeding and genetic history of European autochthonous and commercial pig breeds

Author

Schiavo, Giussepina, Bovo, Samuele, Munoz, Maria, Ribani, Anisa, Alves, Estefania, Araujo, Jose P., Bozzi, Riccardo, Čandek-Potokar, Marjeta, Charneca, Rui, Fernandez, Ana I., Gallo, Maurizio, Garcia, Fabian, Karolyi, Danijel, Kušec, Goran, Martins, Jose Manuel, Mercat, Marie-Jose, Nunez, Yolanda, Quintanilla, Raquel, Radović, Čedomir, Razmaite, Violeta, Riquet, Juliette, Savić, Radomir, Usai, Graziano, Utzeri, Valerio J., Zimmer, Christoph, Ovilo, Cristina, Fontanesi, Luca, Schiavo, Giussepina, Bovo, Samuele, Munoz, Maria, Ribani, Anisa, Alves, Estefania, Araujo, Jose P., Bozzi, Riccardo, Čandek-Potokar, Marjeta, Charneca, Rui, Fernandez, Ana I., Gallo, Maurizio, Garcia, Fabian, Karolyi, Danijel, Kušec, Goran, Martins, Jose Manuel, Mercat, Marie-Jose, Nunez, Yolanda, Quintanilla, Raquel, Radović, Čedomir, Razmaite, Violeta, Riquet, Juliette, Savić, Radomir, Usai, Graziano, Utzeri, Valerio J., Zimmer, Christoph, Ovilo, Cristina, and Fontanesi, Luca

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 common ROHs within the same population define ROH islands and indicate hotspots of selection. In this work, we investigated ROHs in a total of 1131 pigs from 20 European local pig breeds and in three cosmopolitan breeds, genotyped with the GGP Porcine HD Genomic 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 the investigated pig breeds and provided information to manage these pig genetic resources.

Published
2021

10. 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

Author

Bovo, Samuele, Ribani, Anisa, Muñoz, Maria, Alves, Estefania, Araujo, Jose P., Bozzi, Riccardo, Charneca, Rui, Di Palma, Federica, Etherington, Graham, Fernandez, Ana I., García, Fabián, García-Casco, Juan, Karolyi, Danijel, Gallo, Maurizio, Gvozdanović, Kristina, Martins, José Manuel, Mercat, Marie-José, Núñez, Yolanda, Quintanilla, Raquel, Radović, Čedomir, Razmaite, Violeta, Riquet, Juliette, Savić, Radomir, Schiavo, Giuseppina, Škrlep, Martin, Usai, Graziano, Utzeri, Valerio Joe, Zimmer, Christoph, Ovilo, Cristina, and Fontanesi, Luca

Subjects
Next generation sequencing, CNV, MSRB3, Sus scrofa, ELOVL6, Genetic resource, KIT, ZNF622
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 42×. This approach maximized CNV discovery as well as the related copy number states characterizing, 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 was considered as private. A few CNVRs were analysed in more details, 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 ELOV6 and ZNF622 genes were private features observed in the Lithuanian Indigenous Wattle and in the Turopolje pig breeds, respectively. Overall, genome variability here unravelled 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.

Published
2020

11. Selezione per la resistenza genetica alla Maedi Visna negli ovini: opportunità e problematiche

Author

Ligios, Ciriaco, Giantonella Puggioni, Ponti, Nicoletta, Pintus, Davide, Coraduzza, Elisabetta, Scivoli, Rosario, Pittau, Marco, Chessa, Bernardo, Carta, Antonello, Sechi, Tiziana, Carta, Patrizia, Usai, Graziano, Casu, Sara, Sotero Salaris, and Miari, Sabrina

Abstract

LaMaedi Visna(MV) è unapatologia ovina cronicacon manifestazioni cliniche molto variabili, causata da un virus appartenente al genereLentivirusche comprende anche il virus dell’Artrite Encefalite Caprina (CAEV). I virus responsabili di MV e CAEV appartengono al gruppoSmall Ruminants Lentivirus(SRLV). In passato, si ritenevano somiglianti e specifici dell’ospite mentre in realtà si tratta di virus adattati all’ospite. In effetti, vengono identificati ceppi MV-like nelle capre e ceppi CAEV-like nelle pecore. Gliorgani bersaglionell’ovino sono ilpolmone, la cui infezione provoca la forma clinica indicata comeMaedi, e moltopiù raramente il sistema nervoso centrale,determinando la forma clinica indicata comeVisna. Inoltre, il virus della MV si localizza molto frequentemente anche nellamammella, dove viene escreto con il colostro ed il latte e determina forme dimastite cronicaquasi sempre non apprezzabili clinicamente. L’andamento della malattia è generalmente lento, progressivo, persistente e spesso paucisintomatico mentre i casi clinici conclamati sono rari. Una volta che il virus penetra nell’allevamento, si diffonde soprattutto attraverso l’assunzione di colostro e di latte, che costituisce lavia principale di contagio, mentre è relativamente meno importante la trasmissione attraverso il contatto diretto tra animali. Alcune patologie concomitanti come l’Adenomatosi Polmonare, che spesso è accompagnata dall’emissione di muco dal naso con conseguente contaminazione dell’ambiente, possono accelerarne la trasmissione orizzontale. Una valutazione precisa dei danni economici diretti negli allevamenti ovini è dunque difficile. Relativamente agli effetti sulle produzioni lattee e sugli accrescimenti degli agnelli, in letteratura si riportano risultati contraddittori probabilmente legati alla variabilità dei disegni sperimentali. L’altissima prevalenza del virus di MV negli allevamenti ovini della Sardegna e la sua elevata variabilità genetica, lo rendono in ogni caso unagente infettivo potenzialmente pericolosoche merita l’attenzione di operatori sanitari, zootecnici e allevatori. Attualmentenon esistono in Sardegna piani di controllo. Eventuali piani di eradicazione si fonderebbero sulla separazione degli agnelli dalle madri alla nascita con successivo allattamento artificiale. Un piano così concepito, anche se limitato alla sola quota di rimonta, è laborioso e costoso in quanto prevedrebbe la presenza praticamente continua di operatori nel periodo dei parti. In Sardegna, i tentativi di eradicazione della CAEV nelle capre con protocolli di questo tipo non hanno avuto molte adesioni, anche quando è stato previsto un incentivo pubblico per la loro realizzazione. L’ultimo studio epidemiologicamente rilevante in Sardegna è stato realizzato nel 2007 su 306 allevamenti con 18.513 capi testati (Puggioni et al., 2007). Circa il 90% degli allevamenti ovini presentavano almeno un capo sieropositivo con una prevalenza media (percentuale di capi positivi per gregge) del 33%. Non esistono dati più recenti rilevati sistematicamente, ma è presumibile che in assenza di piani di controllo e di divieti nella circolazione di capi positivi la situazione si sia ulteriormente deteriorata negli ultimi anni. Alla luce di queste considerazioni, il Ministero della Salute e il Centro Regionale di Programmazione hanno finanziato aIZS,AGRISeDipartimento Medicina Veterinaria di UNISSricerche mirate a verificare la possibilità di attuarestrategie di riduzione della prevalenza della patologiafondate sullaselezione di ovini geneticamente resistenti. Di seguito verranno illustrati i principali risultati di queste ricerche.

Published
2020
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12. Signatures of de-domestication in autochthonous pig breeds and of domestication in wild boar populations from MC1R and NR6A1 allele distribution

Author

Ribani, A., 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, Ribani, A., 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, and Fontanesi, Luca

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.

Published
2019

13. Survey of demographic and phenotypic data of local pig breeds of TREASURE project

Author

Karolyi, Danijel [0000-0003-0409-9071], Quintanilla, Raquel [0000-0003-3274-3434], Radović, Čedomir [0000-0002-1800-2448], Bozzi, Riccardo, Škrlep, Martin, Lenoir, Herveline, Lebret, B., García Gasco, J. M., Petig, M., Charneca, Rui, Paixim, H., Karolyi, Danijel, Radović, Čedomir, Gallo, Maurizio, Geraci, C., Usai, Graziano, Quintanilla, Raquel, Araújo, José Pedro, Razmaite, Violeta, Gvozdanović, Kristina, Karolyi, Danijel [0000-0003-0409-9071], Quintanilla, Raquel [0000-0003-3274-3434], Radović, Čedomir [0000-0002-1800-2448], Bozzi, Riccardo, Škrlep, Martin, Lenoir, Herveline, Lebret, B., García Gasco, J. M., Petig, M., Charneca, Rui, Paixim, H., Karolyi, Danijel, Radović, Čedomir, Gallo, Maurizio, Geraci, C., Usai, Graziano, Quintanilla, Raquel, Araújo, José Pedro, Razmaite, Violeta, and Gvozdanović, Kristina

Abstract

The paper reports the results of a survey on the demographic and phenotypic characterization of 20 European local pig breeds involved in the H2020 TREASURE project including information on: demographic parameters, main morphological features, reproductive information, additional information collected at herd-level (i.e. temperament, holding, mating practices), origins and development of the breeds. Almost all the breeds (18 out of 20) possess a herd book even if the starting year is highly variable (from 1980 to 2006). Number of breeding females ranged from 24 (Moravka) to over 200,000 heads (Ibérico). Male/female ratio varied greatly with the highest values for the Italian breeds probably due to the different policy of animal recording. Almost all the breeds undergo a conservation program whereas really few are interested by other conservation techniques and for less than five breeds data related to effective number and inbreeding coefficient are easily available. Average values for teat number, litter size and weaned piglets are 12, 8 and 6 respectively with a great potential for their improvement. The depicted scenario is highly diversified and the data collected represent the starting point for the achievement of a collective trademark under the umbrella of the TREASURE project.

Published
2018

14. Survey of Demographic and Phenotypic Data of Local Pig Breeds of Treasure Project

Author

Bozzi, Riccardo, Škrlep, Martin, Lenoir, Herveline, Lebret, Benedicte, Garcia Casco, Juan Maria, Petig, Matthias, Charneca, Rui, Paixim, Hugo, Karolyi, Danijel, Gallo, Maurizio, Geraci, Claudia, Usai, Graziano, Quintanilla, Raquel, Araujo, José Pedro, Razmaite, Violeta, Gvozdanović, Kristina, Radović, Čedomir, Bozzi, Riccardo, Škrlep, Martin, Lenoir, Herveline, Lebret, Benedicte, Garcia Casco, Juan Maria, Petig, Matthias, Charneca, Rui, Paixim, Hugo, Karolyi, Danijel, Gallo, Maurizio, Geraci, Claudia, Usai, Graziano, Quintanilla, Raquel, Araujo, José Pedro, Razmaite, Violeta, Gvozdanović, Kristina, and Radović, Čedomir

Abstract

Local genetic resources represent an important reservoir of biodiversity in the animal sector. Sustainable use of these resources can be an important source of income for farmers taking advantage of the peculiar characteristics of their products.

Published
2017

16. Additional file 1 of 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

Author

Bovo, Samuele, Ribani, Anisa, Muñoz, Maria, Alves, Estefania, Araujo, Jose P., Bozzi, Riccardo, Čandek-Potokar, Marjeta, Charneca, Rui, Palma, Federica Di, Etherington, Graham, Fernandez, Ana I., Fabián García, García-Casco, Juan, Karolyi, Danijel, Gallo, Maurizio, Margeta, Vladimir, Martins, José Manuel, Mercat, Marie J., Moscatelli, Giulia, Núñez, Yolanda, Quintanilla, Raquel, Čedomir Radović, Razmaite, Violeta, Riquet, Juliette, Savić, Radomir, Schiavo, Giuseppina, Usai, Graziano, Utzeri, Valerio J., Zimmer, Christoph, Ovilo, Cristina, and Fontanesi, Luca

Subjects
2. Zero hunger
Abstract

Additional file 1: Table S1. Details on the animals analysed and breeds investigated, including geographical distribution and phenotypic description. Table S2. Summary of whole-genome sequencing statistics. Table S3. Statistics on SNPs detected in this study. Table S4. Statistics on annotated SNPs. Annotation was performed with the Variant Effect Predictor (VEP) tool. Table S5. Statistics on the window selection analysis. Table S6. Groups of breeds/populations compared in the current study. Table S7. Statistics of the genome-wide window-based heterozygosity (HP) values and fixation index (FST) values. Table S8. Statistics of the genome-wide FST values between groups of pig breeds/populations based on 100-kb windows. Table S9. Pearson’s correlation coefficient (r) based on the frequency of the alternative allele. Table S10. Single SNP FST distances between pairs of pig populations. Table S11. Within-breed average pooled heterozygosity (HP) and fixation index (FST) values. Table S12. HP analysis. The genome windows at the extreme lower end of the distributions (99.95th percentile) are presented. Table S13. Single-breed FST analysis. The genome windows at the extreme lower end of the distributions (99.95th percentile) are presented. Table S14. Comparative FST analysis of breed groups. The genome windows at the extreme lower end of the distributions (99.95th percentile) are presented. Table S15. Putative deleterious variants that showed a marked allele frequency difference between pig breeds and wild boars (> v80% in one group

17. Additional file 2 of 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

Author

Bovo, Samuele, Ribani, Anisa, Muñoz, Maria, Alves, Estefania, Araujo, Jose P., Bozzi, Riccardo, Čandek-Potokar, Marjeta, Charneca, Rui, Palma, Federica Di, Etherington, Graham, Fernandez, Ana I., Fabián García, García-Casco, Juan, Karolyi, Danijel, Gallo, Maurizio, Margeta, Vladimir, Martins, José Manuel, Mercat, Marie J., Moscatelli, Giulia, Núñez, Yolanda, Quintanilla, Raquel, Čedomir Radović, Razmaite, Violeta, Riquet, Juliette, Savić, Radomir, Schiavo, Giuseppina, Usai, Graziano, Utzeri, Valerio J., Zimmer, Christoph, Ovilo, Cristina, and Fontanesi, Luca

Subjects
2. Zero hunger
Abstract

Additional file 2: Figure S1. Evaluation of the D-statistics for the Kolmogorov–Smirnov test. Figure S2. Selection of the window size. (a) The number of windows with less than 10 SNPs over windows of variable size (in the range from 50 to 300-kb) is presented. Red dots represent windows larger than 100 kb, for which the number of windows with less than 10 SNPs started to asymptotically decrease. (b to d) Distribution of the number of SNPs contained in the 50-, 100- and 150-kb windows, respectively. Figure S3. FST based Neighbour-Joining tree. Next to the branches, the bootstrap test values expressed as percentage over 10,000 replicates are indicated in red. Figure S4. Mantel test between FST distance and the geographical distances (based on longitudinal and latitudinal coordinates) among autochthonous pig populations. Figure S5. Manhattan plots of the genome-wide HP analyses. Each dot represents a 100-kb genome window. Figure S6. Manhattan plots of the genome-wide FST analyses. Each dot represents a 100-kb genome window. Figure S7. Manhattan plots of the genome-wide FST analysis of breed groups Each dot represents a 100-kb genome window. Figure S8. Allele frequencies of SNPs in putative regions of signatures of selection detected in the FST analysis of middle vs large-sized pig breeds. Major signals were detected on: (a) SSC15 that carries the CASP10 gene, (b) SSC1 that carries the ARID1B gene, (c) SSC1 that carries the MAP3K5 gene (and the nearby PEX7) and (d) SSC2 that carries the PIK3C2A gene.

18. Additional file 1 of 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

Author

Bovo, Samuele, Ribani, Anisa, Muñoz, Maria, Alves, Estefania, Araujo, Jose P., Bozzi, Riccardo, Čandek-Potokar, Marjeta, Charneca, Rui, Palma, Federica Di, Etherington, Graham, Fernandez, Ana I., Fabián García, García-Casco, Juan, Karolyi, Danijel, Gallo, Maurizio, Margeta, Vladimir, Martins, José Manuel, Mercat, Marie J., Moscatelli, Giulia, Núñez, Yolanda, Quintanilla, Raquel, Čedomir Radović, Razmaite, Violeta, Riquet, Juliette, Savić, Radomir, Schiavo, Giuseppina, Usai, Graziano, Utzeri, Valerio J., Zimmer, Christoph, Ovilo, Cristina, and Fontanesi, Luca

Subjects
2. Zero hunger
Abstract

Additional file 1: Table S1. Details on the animals analysed and breeds investigated, including geographical distribution and phenotypic description. Table S2. Summary of whole-genome sequencing statistics. Table S3. Statistics on SNPs detected in this study. Table S4. Statistics on annotated SNPs. Annotation was performed with the Variant Effect Predictor (VEP) tool. Table S5. Statistics on the window selection analysis. Table S6. Groups of breeds/populations compared in the current study. Table S7. Statistics of the genome-wide window-based heterozygosity (HP) values and fixation index (FST) values. Table S8. Statistics of the genome-wide FST values between groups of pig breeds/populations based on 100-kb windows. Table S9. Pearson’s correlation coefficient (r) based on the frequency of the alternative allele. Table S10. Single SNP FST distances between pairs of pig populations. Table S11. Within-breed average pooled heterozygosity (HP) and fixation index (FST) values. Table S12. HP analysis. The genome windows at the extreme lower end of the distributions (99.95th percentile) are presented. Table S13. Single-breed FST analysis. The genome windows at the extreme lower end of the distributions (99.95th percentile) are presented. Table S14. Comparative FST analysis of breed groups. The genome windows at the extreme lower end of the distributions (99.95th percentile) are presented. Table S15. Putative deleterious variants that showed a marked allele frequency difference between pig breeds and wild boars (> v80% in one group

19. Additional file 2 of 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

Author

Bovo, Samuele, Ribani, Anisa, Muñoz, Maria, Alves, Estefania, Araujo, Jose P., Bozzi, Riccardo, Čandek-Potokar, Marjeta, Charneca, Rui, Palma, Federica Di, Etherington, Graham, Fernandez, Ana I., Fabián García, García-Casco, Juan, Karolyi, Danijel, Gallo, Maurizio, Margeta, Vladimir, Martins, José Manuel, Mercat, Marie J., Moscatelli, Giulia, Núñez, Yolanda, Quintanilla, Raquel, Čedomir Radović, Razmaite, Violeta, Riquet, Juliette, Savić, Radomir, Schiavo, Giuseppina, Usai, Graziano, Utzeri, Valerio J., Zimmer, Christoph, Ovilo, Cristina, and Fontanesi, Luca

Subjects
2. Zero hunger
Abstract

Additional file 2: Figure S1. Evaluation of the D-statistics for the Kolmogorov–Smirnov test. Figure S2. Selection of the window size. (a) The number of windows with less than 10 SNPs over windows of variable size (in the range from 50 to 300-kb) is presented. Red dots represent windows larger than 100 kb, for which the number of windows with less than 10 SNPs started to asymptotically decrease. (b to d) Distribution of the number of SNPs contained in the 50-, 100- and 150-kb windows, respectively. Figure S3. FST based Neighbour-Joining tree. Next to the branches, the bootstrap test values expressed as percentage over 10,000 replicates are indicated in red. Figure S4. Mantel test between FST distance and the geographical distances (based on longitudinal and latitudinal coordinates) among autochthonous pig populations. Figure S5. Manhattan plots of the genome-wide HP analyses. Each dot represents a 100-kb genome window. Figure S6. Manhattan plots of the genome-wide FST analyses. Each dot represents a 100-kb genome window. Figure S7. Manhattan plots of the genome-wide FST analysis of breed groups Each dot represents a 100-kb genome window. Figure S8. Allele frequencies of SNPs in putative regions of signatures of selection detected in the FST analysis of middle vs large-sized pig breeds. Major signals were detected on: (a) SSC15 that carries the CASP10 gene, (b) SSC1 that carries the ARID1B gene, (c) SSC1 that carries the MAP3K5 gene (and the nearby PEX7) and (d) SSC2 that carries the PIK3C2A gene.

20. Admixture and breed traceability in European indigenous pig breeds and wild boar using genome-wide SNP data

Author

Christos Dadousis, Maria Muñoz, Cristina Óvilo, Maria Chiara Fabbri, José Pedro Araújo, Samuele Bovo, Marjeta Čandek Potokar, Rui Charneca, Alessandro Crovetti, Maurizio Gallo, Juan María García-Casco, Danijel Karolyi, Goran Kušec, José Manuel Martins, Marie-José Mercat, Carolina Pugliese, Raquel Quintanilla, Čedomir Radović, Violeta Razmaite, Anisa Ribani, Juliet Riquet, Radomir Savić, Giuseppina Schiavo, Martin Škrlep, Silvia Tinarelli, Graziano Usai, Christoph Zimmer, Luca Fontanesi, Riccardo Bozzi, European Commission, Slovenian Research Agency, Dadousis, Christos [0000-0002-7689-6443], Óvilo, Cristina [0000-0002-5738-8435], Fabbri, Maria Chiara [0000-0002-3224-745X], Araújo, José Pedro [0000-0002-1232-3160], Bovo, Samuele [0000-0002-5712-8211], Potokar, Marjeta Čandek [0000-0003-0231-126X], Charneca, Rui [0000-0002-3597-6746], Crovetti, Alessandro [0000-0002-4052-0794], García-Casco, Juan María [0000-0003-0851-608X], Karolyi, Danijel [0000-0003-0409-9071], Kušec, Goran [0000-0002-2900-4019], Mercat, Marie-José [0000-0002-3087-082X], Pugliese, Carolina [000-0002-3735-8714], Tinarelli, Silvia [0000-0001-8875-5456], Usai, Graziano [0000-0002-6002-2223], Fontanesi, Luca [00000000-0001-7050-3760-0001-7050-3760], Riccardo Bozzi [0000-0001-8854-0834], Dadousis C., Munoz M., Ovilo C., Fabbri M.C., Araujo J.P., Bovo S., Potokar M.C., Charneca R., Crovetti A., Gallo M., Garcia-Casco J.M., Karolyi D., Kusec G., Martins J.M., Mercat M.-J., Pugliese C., Quintanilla R., Radovic C., Razmaite V., Ribani A., Riquet J., Savic R., Schiavo G., Skrlep M., Tinarelli S., Usai G., Zimmer C., Fontanesi L., Bozzi R., Università degli Studi di Firenze = University of Florence (UniFI), Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria = National Institute for Agricultural and Food Research and Technology (INIA), Universidade de Évora, Department of Animal Science [Zagreb], Faculty of Agriculture [Zagreb] (UNIZG), University of Zagreb-University of Zagreb, Institut du Porc (IFIP), Institut de Recerca i Tecnologia Agroalimentàries = Institute of Agrifood Research and Technology (IRTA), Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Slovenian Research Agency (grant number P4-0133), European Project: 634476,H2020,H2020-SFS-2014-2,TREASURE(2015), Dadousis, Christos, Óvilo, Cristina, Fabbri, Maria Chiara, Araújo, José Pedro, Bovo, Samuele, Potokar, Marjeta Čandek, Charneca, Rui, Crovetti, Alessandro, García-Casco, Juan María, Karolyi, Danijel, Kušec, Goran, Mercat, Marie-José, Pugliese, Carolina, Tinarelli, Silvia, Usai, Graziano, Fontanesi, Luca, Riccardo Bozzi, Producció Animal, and Genètica i Millora Animal

Subjects
Pig, Genome, [SDV.BA.MVSA]Life Sciences [q-bio]/Animal biology/Veterinary medicine and animal Health, [SDV.BIO]Life Sciences [q-bio]/Biotechnology, Multidisciplinary, Swine, [SDV.BA]Life Sciences [q-bio]/Animal biology, Sus scrofa, SNP, DAPC, Admixture, Polymorphism, Single Nucleotide, pig, local breeds, wild boar, admixture, breed traceability, Plant Breeding, local pig, traceability, [SDV.BA.ZV]Life Sciences [q-bio]/Animal biology/Vertebrate Zoology, Genomic, Single Nucleotide Polymorphism, Animals, [SDE.BE]Environmental Sciences/Biodiversity and Ecology, Biological Specimen Banks
Abstract

13 Pág., Preserving diversity of indigenous pig (Sus scrofa) breeds is a key factor to (i) sustain the pork chain (both at local and global scales) including the production of high-quality branded products, (ii) enrich the animal biobanking and (iii) progress conservation policies. Single nucleotide polymorphism (SNP) chips offer the opportunity for whole-genome comparisons among individuals and breeds. Animals from twenty European local pigs breeds, reared in nine countries (Croatia: Black Slavonian, Turopolje; France: Basque, Gascon; Germany: Schwabisch-Hällisches Schwein; Italy: Apulo Calabrese, Casertana, Cinta Senese, Mora Romagnola, Nero Siciliano, Sarda; Lithuania: Indigenous Wattle, White Old Type; Portugal: Alentejana, Bísara; Serbia: Moravka, Swallow-Bellied Mangalitsa; Slovenia: Krškopolje pig; Spain: Iberian, Majorcan Black), and three commercial breeds (Duroc, Landrace and Large White) were sampled and genotyped with the GeneSeek Genomic Profiler (GGP) 70 K HD porcine genotyping chip. A dataset of 51 Wild Boars from nine countries was also added, summing up to 1186 pigs (~ 49 pigs/breed). The aim was to: (i) investigate individual admixture ancestries and (ii) assess breed traceability via discriminant analysis on principal components (DAPC). Albeit the mosaic of shared ancestries found for Nero Siciliano, Sarda and Moravka, admixture analysis indicated independent evolvement for the rest of the breeds. High prediction accuracy of DAPC mark SNP data as a reliable solution for the traceability of breed-specific pig products., This work has received funding from the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 634476 for the project with acronym TREASURE. The content of this article reflects only the authors’ view and the European Union Agency is not responsible for any use that may be made of the information it contains. MŠ and MČP received core-financing by the Slovenian Research Agency (grant number P4-0133).

Published
2022
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21. Describing variability in pig genes involved in coronavirus infections for a One Health perspective in conservation of animal genetic resources

Author

Giuseppina Schiavo, Valeria Taurisano, Raquel Quintanilla, Anisa Ribani, Juan García-Casco, Rui Charneca, Valerio Joe Utzeri, Marie-José Mercat, Estefania Alves, Fabián García, Graham J Etherington, Samuele Bovo, Juliette Riquet, Danijel Karolyi, Christoph Zimmer, Ivona Djurkin Kušec, Federica Di Palma, Ana Isabel Fernández, G. Usai, Violeta Razmaite, María Muñoz, Yolanda Núñez, José Pedro Araújo, Martin Škrlep, Radomir Savić, J.M. Martins, Maurizio Gallo, Luca Fontanesi, Čedomir Radović, Mohamad Ballan, Cristina Óvilo, Riccardo Bozzi, University of Bologna, Instituto Nacional de Investigación Agropecuaria (INIA), Centro de Investigação de Montanha [Bragança, Portugal] (CIMO), Instituto Politécnico de Bragança, Department of Agriculture, Food, Environment and Forestry (DAGRI), Università degli Studi di Firenze = University of Florence [Firenze] (UNIFI), Universidade de Évora, University of East Anglia [Norwich] (UEA), Josip Juraj Strossmayer University of Osijek, Earlham Institute [Norwich], University of Zagreb, Associazione Nazionale Allevatori Suini, Institut du Porc (IFIP), Institute of Agrifood Research and Technology (IRTA), Institute for Animal Husbandry, Lithuanian University of Health Sciences [Kaunas, Lithuania], Génétique Physiologie et Systèmes d'Elevage (GenPhySE ), Ecole Nationale Vétérinaire de Toulouse (ENVT), Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-Institut National Polytechnique (Toulouse) (Toulouse INP), Université Fédérale Toulouse Midi-Pyrénées-Université Fédérale Toulouse Midi-Pyrénées-École nationale supérieure agronomique de Toulouse [ENSAT]-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), University of Belgrade [Belgrade], Kmetijski Inštitut Slovenije (KIS), AGRIS sardegna, Bäuerliche Erzeugergemeinschaft Schwäbisch Hall (BESH), European Cooperation in Science and Technology (COST)Ministry of Foreign Affairs of ItalyUniversity of Bologna RFO 2016-2019 programmesItalian MIUR 2017 PigPhenomics projectEuropean Commission634476European Open Science Cloud (EOSC) Secretariat, project 'Application of animal genomics and data mining to predict and monitor novel coronavirus potential infections (VirAnimalOne)'EGI call for COVID-19 research projects (AnGen1H project)Por Fesr Emilia-Romagna 2014-2020 (actions 1.1.4 and 1.2.2-Bando per sostenere progetti di ricerca ed innovazione per lo sviluppo di soluzioni finalizzate al contrasto dell'epidemia da COVID-19-Project LIVESTOCK-STOP-COVI), European Project: 634476,H2020,H2020-SFS-2014-2,TREASURE(2015), Producció Animal, Genètica i Millora Animal, University of Bologna/Università di Bologna, Università degli Studi di Firenze = University of Florence (UniFI), Institut de Recerca i Tecnologia Agroalimentàries = Institute of Agrifood Research and Technology (IRTA), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National Polytechnique (Toulouse) (Toulouse INP), Université de Toulouse (UT)-Université de Toulouse (UT)-École nationale supérieure agronomique de Toulouse (ENSAT), Université de Toulouse (UT)-Université de Toulouse (UT)-Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement (INRAE), Università di Bologna, European Commission, Bovo, Samuele, Schiavo, Giuseppina, Ribani, Anisa, Utzeri, Valerio J, Taurisano, Valeria, Araujo, Jose P, Bozzi, Riccardo, Charneca, Rui, Di Palma, Federica, Djurkin Kušec, Ivona, Etherington, Graham, Fernandez, Ana I, Suárez García, Fabián, García-Casco, Juan, Karolyi, D 0000-003-0409-9071], Martins, José Manuel, Mercat, Marie-José, Núñez, Yolanda, Radović, Čedomir, Razmaite, Violeta, Riquet, Juliette, Savić, Radomir, Škrlep, Martin, Usai, Graziano, Ovilo, Cristina, Bovo S., Schiavo G., Ribani A., Utzeri V.J., Taurisano V., Ballan M., Munoz M., Alves E., Araujo J.P., Bozzi R., Charneca R., Di Palma F., Djurkin Kusec I., Etherington G., Fernandez A.I., Garcia F., Garcia-Casco J., Karolyi D., Gallo M., Martins J.M., Mercat M.-J., Nunez Y., Quintanilla R., Radovic C., Razmaite V., Riquet J., Savic R., Skrlep M., Usai G., Zimmer C., Ovilo C., and Fontanesi L.

Subjects
0301 basic medicine, Candidate gene, Population genetics, Swine, MESH: Coronavirus Infections, Sus scrofa, MESH: Angiotensin-Converting Enzyme 2, MESH: One Health, Breeding, MESH: INDEL Mutation, 0302 clinical medicine, Gene Frequency, INDEL Mutation, Receptors, Receptors, Viru, MESH: Animals, MESH: Serine Endopeptidases, MESH: Genetic Variation, MESH: High-Throughput Nucleotide Sequencing, MESH: Swine, 2. Zero hunger, Genetics, education.field_of_study, Multidisciplinary, MESH: Polymorphism, Single Nucleotide, Serine Endopeptidases, High-Throughput Nucleotide Sequencing, Single Nucleotide, Genomics, Virus, Serine Endopeptidase, One Health, 030220 oncology & carcinogenesis, Microsomal aminopeptidase, Medicine, Infectious diseases, Receptors, Virus, Angiotensin-Converting Enzyme 2, Coronavirus Infections, MESH: Whole Genome Sequencing, Human, Agricultural genetics, pig, local breed, whole genome sequencing, coronavirus, Science, Dipeptidyl Peptidase 4, Population, MESH: Genetics, Population, Context (language use), MESH: Breeding, CD13 Antigens, Biology, Polymorphism, Single Nucleotide, Article, 03 medical and health sciences, Animals, Genetics, Population, Humans, Whole Genome Sequencing, Genetic Variation, Genetic variation, MESH: Gene Frequency, Polymorphism, education, Data mining, Gene, CD13 Antigen, Animal breeding, Whole genome sequencing, MESH: Humans, Animal, Coronavirus Infection, Host (biology), Virus receptor, MESH: CD13 Antigens, MESH: Dipeptidyl Peptidase 4, MESH: Receptors, Virus, MESH: Sus scrofa, [SDV.GEN.GA]Life Sciences [q-bio]/Genetics/Animal genetics, 030104 developmental biology, Dipeptidyl peptidase IV, Next-generation sequencing, Genetic markers, Serine proteinase
Abstract

14 Pág. Departamento de ​Mejora Genética Animal, Coronaviruses silently circulate in human and animal populations, causing mild to severe diseases. Therefore, livestock are important components of a "One Health" perspective aimed to control these viral infections. However, at present there is no example that considers pig genetic resources in this context. In this study, we investigated the variability of four genes (ACE2, ANPEP and DPP4 encoding for host receptors of the viral spike proteins and TMPRSS2 encoding for a host proteinase) in 23 European (19 autochthonous and three commercial breeds and one wild boar population) and two Asian Sus scrofa populations. A total of 2229 variants were identified in the four candidate genes: 26% of them were not previously described; 29 variants affected the protein sequence and might potentially interact with the infection mechanisms. The results coming from this work are a first step towards a "One Health" perspective that should consider conservation programs of pig genetic resources with twofold objectives: (i) genetic resources could be reservoirs of host gene variability useful to design selection programs to increase resistance to coronaviruses; (ii) the described variability in genes involved in coronavirus infections across many different pig populations might be part of a risk assessment including pig genetic resources., This work has received funding from the University of Bologna RFO 2016-2019 programmes, the Italian MIUR 2017 PigPhenomics project, from the European Union’s Horizon 2020 research and innovation programme under grant agreement No. 634476 for the project with acronym TREASURE, from the European Open Science Cloud (EOSC) Secretariat, project “Application of animal genomics and data mining to predict and monitor novel coronavirus potential infections (VirAnimalOne)”, the EGI call for COVID-19 research projects (AnGen1H project) and from the Por Fesr Emilia-Romagna 2014-2020 (actions 1.1.4 and 1.2.2—Bando per sostenere progetti di ricerca ed innovazione per lo sviluppo di soluzioni finalizzate al contrasto dell’epidemia da COVID-19—Project LIVESTOCK-STOP-COVI). The content of this article reflects only the authors' view and the European Union Agency is not responsible for any use that may be made of the information it contains.

Published
2021
Full Text
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