Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip

2019
Authors
Munoz, Maria
Bozzi, Riccardo

Garcia-Casco, Juan
Nunez, Yolanda
Ribani, A.
Franci, O.
Garcia, Fabian
Skrlep, Martin

Schiavo, Giuseppina
Bovo, Samuele

Utzeri, Valerio J.
Charneca, R.

Martins, Jose M.

Quintanilla, Raquel
Tibau, J.
Margeta, Vladimir
Djurkin-Kusec, Ivona
Mercat, Marie J.
Riquet, Juliette
Estelle, Jordi

Zimmer, Christoph
Razmaite, Violeta

Araujo, Jose P.

Radović, Čedomir

Savić, Radomir

Karolyi, Danijel

Gallo, Maurizio
Čandek-Potokar, Marjeta

Fernandez, Ana I

Fontanesi, Luca

Ovilo, Cristina

Article (Published version)
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Show full item recordAbstract
Genetic characterization of local breeds is essential to preserve their genomic variability, to advance conservation policies and to contribute to their promotion and sustainability. Genomic diversity of twenty European local pig breeds and a small sample of Spanish wild pigs was assessed using high density SNP chips. A total of 992 DNA samples were analyzed with the GeneSeek Genomic Profiler (GGP) 70 K HD porcine genotyping chip. Genotype data was employed to compute genetic diversity, population differentiation and structure, genetic distances, linkage disequilibrium and effective population size. Our results point out several breeds, such as Turopolje, Apulo Calabrese, Casertana, Mora Romagnola and Lithuanian indigenous wattle, having the lowest genetic diversity, supported by low heterozygosity and very small effective population size, demonstrating the need of enhanced conservation strategies. Principal components analysis showed the clustering of the individuals of the same breed..., with few breeds being clearly isolated from the rest. Several breeds were partially overlapped, suggesting genetic closeness, which was particularly marked in the case of Iberian and Alentejana breeds. Spanish wild boar was also narrowly related to other western populations, in agreement with recurrent admixture between wild and domestic animals. We also searched across the genome for loci under diversifying selection based on F-S(T) outlier tests. Candidate genes that may underlie differences in adaptation to specific environments and productive systems and phenotypic traits were detected in potentially selected genomic regions.
Source:
Scientific Reports, 2019, 9Publisher:
- Nature Publishing Group, London
Funding / projects:
DOI: 10.1038/s41598-019-49830-6
ISSN: 2045-2322
PubMed: 31537860
WoS: 000486567800022
Scopus: 2-s2.0-85072394238
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Poljoprivredni fakultetTY - JOUR AU - Munoz, Maria AU - Bozzi, Riccardo AU - Garcia-Casco, Juan AU - Nunez, Yolanda AU - Ribani, A. AU - Franci, O. AU - Garcia, Fabian AU - Skrlep, Martin AU - Schiavo, Giuseppina AU - Bovo, Samuele AU - Utzeri, Valerio J. AU - Charneca, R. AU - Martins, Jose M. AU - Quintanilla, Raquel AU - Tibau, J. AU - Margeta, Vladimir AU - Djurkin-Kusec, Ivona AU - Mercat, Marie J. AU - Riquet, Juliette AU - Estelle, Jordi AU - Zimmer, Christoph AU - Razmaite, Violeta AU - Araujo, Jose P. AU - Radović, Čedomir AU - Savić, Radomir AU - Karolyi, Danijel AU - Gallo, Maurizio AU - Čandek-Potokar, Marjeta AU - Fernandez, Ana I AU - Fontanesi, Luca AU - Ovilo, Cristina PY - 2019 UR - http://aspace.agrif.bg.ac.rs/handle/123456789/4915 AB - Genetic characterization of local breeds is essential to preserve their genomic variability, to advance conservation policies and to contribute to their promotion and sustainability. Genomic diversity of twenty European local pig breeds and a small sample of Spanish wild pigs was assessed using high density SNP chips. A total of 992 DNA samples were analyzed with the GeneSeek Genomic Profiler (GGP) 70 K HD porcine genotyping chip. Genotype data was employed to compute genetic diversity, population differentiation and structure, genetic distances, linkage disequilibrium and effective population size. Our results point out several breeds, such as Turopolje, Apulo Calabrese, Casertana, Mora Romagnola and Lithuanian indigenous wattle, having the lowest genetic diversity, supported by low heterozygosity and very small effective population size, demonstrating the need of enhanced conservation strategies. Principal components analysis showed the clustering of the individuals of the same breed, with few breeds being clearly isolated from the rest. Several breeds were partially overlapped, suggesting genetic closeness, which was particularly marked in the case of Iberian and Alentejana breeds. Spanish wild boar was also narrowly related to other western populations, in agreement with recurrent admixture between wild and domestic animals. We also searched across the genome for loci under diversifying selection based on F-S(T) outlier tests. Candidate genes that may underlie differences in adaptation to specific environments and productive systems and phenotypic traits were detected in potentially selected genomic regions. PB - Nature Publishing Group, London T2 - Scientific Reports T1 - Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip VL - 9 DO - 10.1038/s41598-019-49830-6 ER -
@article{ author = "Munoz, Maria and Bozzi, Riccardo and Garcia-Casco, Juan and Nunez, Yolanda and Ribani, A. and Franci, O. and Garcia, Fabian and Skrlep, Martin and Schiavo, Giuseppina and Bovo, Samuele and Utzeri, Valerio J. and Charneca, R. and Martins, Jose M. and Quintanilla, Raquel and Tibau, J. and Margeta, Vladimir and Djurkin-Kusec, Ivona and Mercat, Marie J. and Riquet, Juliette and Estelle, Jordi and Zimmer, Christoph and Razmaite, Violeta and Araujo, Jose P. and Radović, Čedomir and Savić, Radomir and Karolyi, Danijel and Gallo, Maurizio and Čandek-Potokar, Marjeta and Fernandez, Ana I and Fontanesi, Luca and Ovilo, Cristina", year = "2019", abstract = "Genetic characterization of local breeds is essential to preserve their genomic variability, to advance conservation policies and to contribute to their promotion and sustainability. Genomic diversity of twenty European local pig breeds and a small sample of Spanish wild pigs was assessed using high density SNP chips. A total of 992 DNA samples were analyzed with the GeneSeek Genomic Profiler (GGP) 70 K HD porcine genotyping chip. Genotype data was employed to compute genetic diversity, population differentiation and structure, genetic distances, linkage disequilibrium and effective population size. Our results point out several breeds, such as Turopolje, Apulo Calabrese, Casertana, Mora Romagnola and Lithuanian indigenous wattle, having the lowest genetic diversity, supported by low heterozygosity and very small effective population size, demonstrating the need of enhanced conservation strategies. Principal components analysis showed the clustering of the individuals of the same breed, with few breeds being clearly isolated from the rest. Several breeds were partially overlapped, suggesting genetic closeness, which was particularly marked in the case of Iberian and Alentejana breeds. Spanish wild boar was also narrowly related to other western populations, in agreement with recurrent admixture between wild and domestic animals. We also searched across the genome for loci under diversifying selection based on F-S(T) outlier tests. Candidate genes that may underlie differences in adaptation to specific environments and productive systems and phenotypic traits were detected in potentially selected genomic regions.", publisher = "Nature Publishing Group, London", journal = "Scientific Reports", title = "Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip", volume = "9", doi = "10.1038/s41598-019-49830-6" }
Munoz, M., Bozzi, R., Garcia-Casco, J., Nunez, Y., Ribani, A., Franci, O., Garcia, F., Skrlep, M., Schiavo, G., Bovo, S., Utzeri, V. J., Charneca, R., Martins, J. M., Quintanilla, R., Tibau, J., Margeta, V., Djurkin-Kusec, I., Mercat, M. J., Riquet, J., Estelle, J., Zimmer, C., Razmaite, V., Araujo, J. P., Radović, Č., Savić, R., Karolyi, D., Gallo, M., Čandek-Potokar, M., Fernandez, A. I., Fontanesi, L.,& Ovilo, C.. (2019). Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip. in Scientific Reports Nature Publishing Group, London., 9. https://doi.org/10.1038/s41598-019-49830-6
Munoz M, Bozzi R, Garcia-Casco J, Nunez Y, Ribani A, Franci O, Garcia F, Skrlep M, Schiavo G, Bovo S, Utzeri VJ, Charneca R, Martins JM, Quintanilla R, Tibau J, Margeta V, Djurkin-Kusec I, Mercat MJ, Riquet J, Estelle J, Zimmer C, Razmaite V, Araujo JP, Radović Č, Savić R, Karolyi D, Gallo M, Čandek-Potokar M, Fernandez AI, Fontanesi L, Ovilo C. Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip. in Scientific Reports. 2019;9. doi:10.1038/s41598-019-49830-6 .
Munoz, Maria, Bozzi, Riccardo, Garcia-Casco, Juan, Nunez, Yolanda, Ribani, A., Franci, O., Garcia, Fabian, Skrlep, Martin, Schiavo, Giuseppina, Bovo, Samuele, Utzeri, Valerio J., Charneca, R., Martins, Jose M., Quintanilla, Raquel, Tibau, J., Margeta, Vladimir, Djurkin-Kusec, Ivona, Mercat, Marie J., Riquet, Juliette, Estelle, Jordi, Zimmer, Christoph, Razmaite, Violeta, Araujo, Jose P., Radović, Čedomir, Savić, Radomir, Karolyi, Danijel, Gallo, Maurizio, Čandek-Potokar, Marjeta, Fernandez, Ana I, Fontanesi, Luca, Ovilo, Cristina, "Genomic diversity, linkage disequilibrium and selection signatures in European local pig breeds assessed with a high density SNP chip" in Scientific Reports, 9 (2019), https://doi.org/10.1038/s41598-019-49830-6 . .