TY  - JOUR
AU  - Zorc, Minja
AU  - Škorput, Dubravko
AU  - Gvozdanović, Kristina
AU  - Margeta, Polona
AU  - Karolyi, Danijel
AU  - Luković, Zoran
AU  - Salajpal, Krešimir
AU  - Savić, Radomir
AU  - Muñoz, Maria
AU  - Bovo, Samuele
AU  - Djurkin Kušec, Ivona
AU  - Radović, Čedomir
PY  - 2022
UR  - http://aspace.agrif.bg.ac.rs/handle/123456789/6076
AB  - The importance of local breeds as genetic reservoirs of valuable genetic variation is well established. Pig breeding in Central and South-Eastern Europe has a long tradition that led to the formation of several local pig breeds. In the present study, genetic diversity parameters were analysed in six autochthonous pig breeds from Slovenia, Croatia and Serbia (Banija spotted, Black Slavonian, Turopolje pig, Swallow-bellied Mangalitsa, Moravka and Krskopolje pig). Animals from each of these breeds were genotyped using microsatellites and single nucleotide polymorphisms (SNPs). The results obtained with these two marker systems and those based on pedigree data were compared. In addition, we estimated inbreeding levels based on the distribution of runs of homozygosity (ROH) and identified genomic regions under selection pressure using ROH islands and the integrated haplotype score (iHS). Results: The lowest heterozygosity values calculated from microsatellite and SNP data were observed in the Turopolje pig. The observed heterozygosity was higher than the expected heterozygosity in the Black Slavonian, Moravka and Turopolje pig. Both types of markers allowed us to distinguish clusters of individuals belonging to each breed. The analysis of admixture between breeds revealed potential gene flow between the Mangalitsa and Moravka, and between the Mangalitsa and Black Slavonian, but no introgression events were detected in the Banija spotted and Turopolje pig. The distribution of ROH across the genome was not uniform. Analysis of the ROH islands identified genomic regions with an extremely high frequency of shared ROH within the Swallow-bellied Mangalitsa, which harboured genes associated with cholesterol biosynthesis, fatty acid metabolism and daily weight gain. The iHS approach to detect signatures of selection revealed candidate regions containing genes with potential roles in reproduction traits and disease resistance. Conclusions: Based on the estimation of population parameters obtained from three data sets, we showed the existence of relationships among the six pig breeds analysed here. Analysis of the distribution of ROH allowed us to estimate the level of inbreeding and the extent of homozygous regions in these breeds. The iHS analysis revealed genomic regions potentially associated with phenotypic traits and allowed the detection of genomic regions under selection pressure.
PB  - BioMed Central Ltd
T2  - Genetics Selection Evolution
T1  - Genetic diversity and population structure of six autochthonous pig breeds from Croatia, Serbia, and Slovenia
IS  - 1
SP  - 30
VL  - 54
DO  - 10.1186/s12711-022-00718-6
ER  - 

@article{
author = "Zorc, Minja and Škorput, Dubravko and Gvozdanović, Kristina and Margeta, Polona and Karolyi, Danijel and Luković, Zoran and Salajpal, Krešimir and Savić, Radomir and Muñoz, Maria and Bovo, Samuele and Djurkin Kušec, Ivona and Radović, Čedomir",
year = "2022",
abstract = "The importance of local breeds as genetic reservoirs of valuable genetic variation is well established. Pig breeding in Central and South-Eastern Europe has a long tradition that led to the formation of several local pig breeds. In the present study, genetic diversity parameters were analysed in six autochthonous pig breeds from Slovenia, Croatia and Serbia (Banija spotted, Black Slavonian, Turopolje pig, Swallow-bellied Mangalitsa, Moravka and Krskopolje pig). Animals from each of these breeds were genotyped using microsatellites and single nucleotide polymorphisms (SNPs). The results obtained with these two marker systems and those based on pedigree data were compared. In addition, we estimated inbreeding levels based on the distribution of runs of homozygosity (ROH) and identified genomic regions under selection pressure using ROH islands and the integrated haplotype score (iHS). Results: The lowest heterozygosity values calculated from microsatellite and SNP data were observed in the Turopolje pig. The observed heterozygosity was higher than the expected heterozygosity in the Black Slavonian, Moravka and Turopolje pig. Both types of markers allowed us to distinguish clusters of individuals belonging to each breed. The analysis of admixture between breeds revealed potential gene flow between the Mangalitsa and Moravka, and between the Mangalitsa and Black Slavonian, but no introgression events were detected in the Banija spotted and Turopolje pig. The distribution of ROH across the genome was not uniform. Analysis of the ROH islands identified genomic regions with an extremely high frequency of shared ROH within the Swallow-bellied Mangalitsa, which harboured genes associated with cholesterol biosynthesis, fatty acid metabolism and daily weight gain. The iHS approach to detect signatures of selection revealed candidate regions containing genes with potential roles in reproduction traits and disease resistance. Conclusions: Based on the estimation of population parameters obtained from three data sets, we showed the existence of relationships among the six pig breeds analysed here. Analysis of the distribution of ROH allowed us to estimate the level of inbreeding and the extent of homozygous regions in these breeds. The iHS analysis revealed genomic regions potentially associated with phenotypic traits and allowed the detection of genomic regions under selection pressure.",
publisher = "BioMed Central Ltd",
journal = "Genetics Selection Evolution",
title = "Genetic diversity and population structure of six autochthonous pig breeds from Croatia, Serbia, and Slovenia",
number = "1",
pages = "30",
volume = "54",
doi = "10.1186/s12711-022-00718-6"
}

Zorc, M., Škorput, D., Gvozdanović, K., Margeta, P., Karolyi, D., Luković, Z., Salajpal, K., Savić, R., Muñoz, M., Bovo, S., Djurkin Kušec, I.,& Radović, Č.. (2022). Genetic diversity and population structure of six autochthonous pig breeds from Croatia, Serbia, and Slovenia. in Genetics Selection Evolution
BioMed Central Ltd., 54(1), 30.
https://doi.org/10.1186/s12711-022-00718-6

Zorc M, Škorput D, Gvozdanović K, Margeta P, Karolyi D, Luković Z, Salajpal K, Savić R, Muñoz M, Bovo S, Djurkin Kušec I, Radović Č. Genetic diversity and population structure of six autochthonous pig breeds from Croatia, Serbia, and Slovenia. in Genetics Selection Evolution. 2022;54(1):30.
doi:10.1186/s12711-022-00718-6 .

Zorc, Minja, Škorput, Dubravko, Gvozdanović, Kristina, Margeta, Polona, Karolyi, Danijel, Luković, Zoran, Salajpal, Krešimir, Savić, Radomir, Muñoz, Maria, Bovo, Samuele, Djurkin Kušec, Ivona, Radović, Čedomir, "Genetic diversity and population structure of six autochthonous pig breeds from Croatia, Serbia, and Slovenia" in Genetics Selection Evolution, 54, no. 1 (2022):30,
https://doi.org/10.1186/s12711-022-00718-6 . .

TY  - JOUR
AU  - Bovo, Samuele
AU  - Schiavo, Giuseppina
AU  - Ribani, Anisa
AU  - Utzeri, Valerio J.
AU  - Taurisano, Valeria
AU  - Ballan, Mohamad
AU  - Muñoz, Maria
AU  - Alves, Estefania
AU  - Araujo, Jose P.
AU  - Bozzi, Riccardo
AU  - Charneca, Rui
AU  - Di Palma, Federica
AU  - Djurkin Kušec, Ivona
AU  - Etherington, Graham
AU  - Fernandez, Ana I.
AU  - García, Fabián
AU  - García‑Casco, Juan
AU  - Karolyi, Danijel
AU  - Gallo, Maurizio
AU  - Martins, José Manuel
AU  - Mercat, Marie‑José
AU  - Núñez, Yolanda
AU  - Quintanilla, Raquel
AU  - Radović, Čedomir
AU  - Razmaite, Violeta
AU  - Riquet, Juliette
AU  - Savić, Radomir
AU  - Škrlep, Martin
AU  - Usai, Graziano
AU  - Zimmer, Christoph
AU  - Ovilo, Cristina
AU  - Fontanesi, Luca
PY  - 2021
UR  - http://aspace.agrif.bg.ac.rs/handle/123456789/5807
AB  - 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
PB  - Nature Research
T2  - Scientific Reports
T1  - Describing variability in pig genes involved in coronavirus infections for a One Health perspective in conservation of animal genetic resources
IS  - 1
SP  - 3359
VL  - 11
DO  - 10.1038/s41598-021-82956-0
ER  - 

@article{
author = "Bovo, Samuele and Schiavo, Giuseppina and Ribani, Anisa and Utzeri, Valerio J. and Taurisano, Valeria and Ballan, Mohamad and Muñoz, Maria and Alves, Estefania and Araujo, Jose P. and Bozzi, Riccardo and Charneca, Rui and Di Palma, Federica and Djurkin Kušec, Ivona and Etherington, Graham and Fernandez, Ana I. and García, Fabián and García‑Casco, Juan and Karolyi, Danijel and Gallo, Maurizio and Martins, José Manuel and Mercat, Marie‑José and Núñez, Yolanda and Quintanilla, Raquel and Radović, Čedomir and Razmaite, Violeta and Riquet, Juliette and Savić, Radomir and Škrlep, Martin and Usai, Graziano and Zimmer, Christoph and Ovilo, Cristina and Fontanesi, Luca",
year = "2021",
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",
publisher = "Nature Research",
journal = "Scientific Reports",
title = "Describing variability in pig genes involved in coronavirus infections for a One Health perspective in conservation of animal genetic resources",
number = "1",
pages = "3359",
volume = "11",
doi = "10.1038/s41598-021-82956-0"
}

Bovo, S., Schiavo, G., Ribani, A., Utzeri, V. J., Taurisano, V., Ballan, M., Muñoz, M., Alves, E., Araujo, J. P., Bozzi, R., Charneca, R., Di Palma, F., Djurkin Kušec, I., Etherington, G., Fernandez, A. I., García, F., García‑Casco, J., Karolyi, D., Gallo, M., Martins, J. M., Mercat, M., Núñez, Y., Quintanilla, R., Radović, Č., Razmaite, V., Riquet, J., Savić, R., Škrlep, M., Usai, G., Zimmer, C., Ovilo, C.,& Fontanesi, L.. (2021). Describing variability in pig genes involved in coronavirus infections for a One Health perspective in conservation of animal genetic resources. in Scientific Reports
Nature Research., 11(1), 3359.
https://doi.org/10.1038/s41598-021-82956-0

Bovo S, Schiavo G, Ribani A, Utzeri VJ, Taurisano V, Ballan M, Muñoz M, Alves E, Araujo JP, Bozzi R, Charneca R, Di Palma F, Djurkin Kušec I, Etherington G, Fernandez AI, García F, García‑Casco J, Karolyi D, Gallo M, Martins JM, Mercat M, Núñez Y, Quintanilla R, Radović Č, Razmaite V, Riquet J, Savić R, Škrlep M, Usai G, Zimmer C, Ovilo C, Fontanesi L. Describing variability in pig genes involved in coronavirus infections for a One Health perspective in conservation of animal genetic resources. in Scientific Reports. 2021;11(1):3359.
doi:10.1038/s41598-021-82956-0 .

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, Fontanesi, Luca, "Describing variability in pig genes involved in coronavirus infections for a One Health perspective in conservation of animal genetic resources" in Scientific Reports, 11, no. 1 (2021):3359,
https://doi.org/10.1038/s41598-021-82956-0 . .