Runs of homozygosity provide a genome landscape picture of inbreeding and genetic history of European autochthonous and commercial pig breeds
Аутори
Schiavo, GiussepinaBovo, 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
Чланак у часопису (Објављена верзија)
Метаподаци
Приказ свих података о документуАпстракт
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.
Кључне речи:
autozygosity / population genomics / selection signature / single nucleotide polymorphism / sus scrofaИзвор:
Animal Genetics, 04-2021, 52, 155-170Издавач:
- Blackwell Publishing Ltd
Финансирање / пројекти:
- Diversity of local pig breeds and production systems for high quality traditional products and sustainable pork chains (EU-H2020-634476)
Институција/група
RIStocarTY - JOUR AU - 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 . .