TY  - JOUR
AU  - Schiavo, Giussepina
AU  - Bovo, Samuele
AU  - Munoz, Maria
AU  - Ribani, Anisa
AU  - Alves, Estefania
AU  - Araujo, Jose P.
AU  - Bozzi, Riccardo
AU  - Čandek-Potokar, Marjeta
AU  - Charneca, Rui
AU  - Fernandez, Ana I.
AU  - Gallo, Maurizio
AU  - Garcia, Fabian
AU  - Karolyi, Danijel
AU  - Kušec, Goran
AU  - Martins, Jose Manuel
AU  - Mercat, Marie-Jose
AU  - Nunez, Yolanda
AU  - Quintanilla, Raquel
AU  - Radović, Čedomir
AU  - Razmaite, Violeta
AU  - Riquet, Juliette
AU  - Savić, Radomir
AU  - Usai, Graziano
AU  - Utzeri, Valerio J.
AU  - Zimmer, Christoph
AU  - Ovilo, Cristina
AU  - Fontanesi, Luca
PY  - 2021-04
UR  - http://r.istocar.bg.ac.rs/handle/123456789/925
AB  - 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.
PB  - Blackwell Publishing Ltd
T2  - Animal Genetics
T1  - Runs of homozygosity provide a genome landscape picture of inbreeding and genetic history of European autochthonous and commercial pig breeds
VL  - 52
SP  - 155
EP  - 170
DO  - 10.1111/age.13045
ER  - 

@article{
author = "Schiavo, Giussepina and Bovo, Samuele and Munoz, Maria and Ribani, Anisa and Alves, Estefania and Araujo, Jose P. and Bozzi, Riccardo and Čandek-Potokar, Marjeta and Charneca, Rui and Fernandez, Ana I. and Gallo, Maurizio and Garcia, Fabian and Karolyi, Danijel and Kušec, Goran and Martins, Jose Manuel and Mercat, Marie-Jose and Nunez, Yolanda and Quintanilla, Raquel and Radović, Čedomir and Razmaite, Violeta and Riquet, Juliette and Savić, Radomir and Usai, Graziano and Utzeri, Valerio J. and Zimmer, Christoph and Ovilo, Cristina and Fontanesi, Luca",
year = "2021-04",
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.",
publisher = "Blackwell Publishing Ltd",
journal = "Animal Genetics",
title = "Runs of homozygosity provide a genome landscape picture of inbreeding and genetic history of European autochthonous and commercial pig breeds",
volume = "52",
pages = "155-170",
doi = "10.1111/age.13045"
}

Schiavo, G., Bovo, S., Munoz, M., Ribani, A., Alves, E., Araujo, J. P., Bozzi, R., Čandek-Potokar, M., Charneca, R., Fernandez, A. I., Gallo, M., Garcia, F., Karolyi, D., Kušec, G., Martins, J. M., Mercat, M., Nunez, Y., Quintanilla, R., Radović, Č., Razmaite, V., Riquet, J., Savić, R., Usai, G., Utzeri, V. J., Zimmer, C., Ovilo, C.,& Fontanesi, L.. (2021-04). Runs of homozygosity provide a genome landscape picture of inbreeding and genetic history of European autochthonous and commercial pig breeds. in Animal Genetics
Blackwell Publishing Ltd., 52, 155-170.
https://doi.org/10.1111/age.13045

Schiavo G, Bovo S, Munoz M, Ribani A, Alves E, Araujo JP, Bozzi R, Čandek-Potokar M, Charneca R, Fernandez AI, Gallo M, Garcia F, Karolyi D, Kušec G, Martins JM, Mercat M, Nunez Y, Quintanilla R, Radović Č, Razmaite V, Riquet J, Savić R, Usai G, Utzeri VJ, Zimmer C, Ovilo C, Fontanesi L. Runs of homozygosity provide a genome landscape picture of inbreeding and genetic history of European autochthonous and commercial pig breeds. in Animal Genetics. 2021;52:155-170.
doi:10.1111/age.13045 .

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, "Runs of homozygosity provide a genome landscape picture of inbreeding and genetic history of European autochthonous and commercial pig breeds" in Animal Genetics, 52 (2021-04):155-170,
https://doi.org/10.1111/age.13045 . .