A genome-wide detection of selection signatures in conserved and commercial pig breeds maintained in Poland
Abstract Background Identification of selection signatures can provide a direct insight into the mechanism of artificial selection and allow further disclosure of the candidate genes related to the animals’ phenotypic variation. Domestication and subsequent long-time selection have resulted in exten...
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| Format: | Article |
| Language: | English |
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BMC
2018-10-01
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| Series: | BMC Genetics |
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| Online Access: | http://link.springer.com/article/10.1186/s12863-018-0681-0 |
| _version_ | 1817981132538380288 |
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| author | Artur Gurgul Igor Jasielczuk Katarzyna Ropka-Molik Ewelina Semik-Gurgul Klaudia Pawlina-Tyszko Tomasz Szmatoła Magdalena Szyndler-Nędza Monika Bugno-Poniewierska Tadeusz Blicharski Karolina Szulc Ewa Skrzypczak Jędrzej Krupiński |
| author_facet | Artur Gurgul Igor Jasielczuk Katarzyna Ropka-Molik Ewelina Semik-Gurgul Klaudia Pawlina-Tyszko Tomasz Szmatoła Magdalena Szyndler-Nędza Monika Bugno-Poniewierska Tadeusz Blicharski Karolina Szulc Ewa Skrzypczak Jędrzej Krupiński |
| author_sort | Artur Gurgul |
| collection | DOAJ |
| description | Abstract Background Identification of selection signatures can provide a direct insight into the mechanism of artificial selection and allow further disclosure of the candidate genes related to the animals’ phenotypic variation. Domestication and subsequent long-time selection have resulted in extensive phenotypic changes in domestic pigs, involving a number of traits, like behavior, body composition, disease resistance, reproduction and coat color. In this study, based on genotypes obtained from PorcineSNP60 Illumina assay we attempt to detect both diversifying and within-breed selection signatures in 530 pigs belonging to four breeds: Polish Landrace, Puławska, Złotnicka White and Złotnicka Spotted, of which the last three are a subject of conservative breeding and substantially represent the native populations. Results A two largely complementary statistical methods were used for signatures detection, including: pairwise FST and relative extended haplotype homozygosity (REHH) test. Breed-specific diversifying selection signals included several genes involved in processes connected with fertility, growth and metabolism which are potentially responsible for different phenotypes of the studied breeds. The diversifying selection signals also comprised PPARD gene that was previously found to have a large effect on the shape of the external ear in pigs or two genes encoding neuropeptide Y receptors (Y2 and Y5) involved in fat deposition and stress response which are important features differentiating the studied breeds. REHH statistics allowed detecting several within-breed selection signatures overlapping with genes connected with a range of functions including, among others: metabolic pathways, immune system response or implantation and development of the embryo. Conclusions The study provides many potential candidate genes with implication for traits selected in the individual breeds and gives strong basis for further studies aiming at identification of sources of variation among the studied pig breeds. |
| first_indexed | 2024-04-13T23:01:45Z |
| format | Article |
| id | doaj.art-75e5eb4ce0e8487e87820e730d8c86a4 |
| institution | Directory Open Access Journal |
| issn | 1471-2156 |
| language | English |
| last_indexed | 2024-04-13T23:01:45Z |
| publishDate | 2018-10-01 |
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| series | BMC Genetics |
| spelling | doaj.art-75e5eb4ce0e8487e87820e730d8c86a42022-12-22T02:25:49ZengBMCBMC Genetics1471-21562018-10-0119111710.1186/s12863-018-0681-0A genome-wide detection of selection signatures in conserved and commercial pig breeds maintained in PolandArtur Gurgul0Igor Jasielczuk1Katarzyna Ropka-Molik2Ewelina Semik-Gurgul3Klaudia Pawlina-Tyszko4Tomasz Szmatoła5Magdalena Szyndler-Nędza6Monika Bugno-Poniewierska7Tadeusz Blicharski8Karolina Szulc9Ewa Skrzypczak10Jędrzej Krupiński11National Research Institute of Animal Production, Department of Animal Molecular BiologyNational Research Institute of Animal Production, Department of Animal Molecular BiologyNational Research Institute of Animal Production, Department of Animal Molecular BiologyNational Research Institute of Animal Production, Department of Animal Molecular BiologyNational Research Institute of Animal Production, Department of Animal Molecular BiologyNational Research Institute of Animal Production, Department of Animal Molecular BiologyNational Research Institute of Animal Production, Department of Pig BreedingNational Research Institute of Animal Production, Department of Animal Molecular BiologyInstitute of Genetics and Animal Breeding, Department of Genomics and BiodiversityPoznań University of Life Sciences, Faculty of Veterinary Medicine and Animal SciencePoznań University of Life Sciences, Faculty of Veterinary Medicine and Animal ScienceNational Research Institute of Animal Production, Department of Horse BreedingAbstract Background Identification of selection signatures can provide a direct insight into the mechanism of artificial selection and allow further disclosure of the candidate genes related to the animals’ phenotypic variation. Domestication and subsequent long-time selection have resulted in extensive phenotypic changes in domestic pigs, involving a number of traits, like behavior, body composition, disease resistance, reproduction and coat color. In this study, based on genotypes obtained from PorcineSNP60 Illumina assay we attempt to detect both diversifying and within-breed selection signatures in 530 pigs belonging to four breeds: Polish Landrace, Puławska, Złotnicka White and Złotnicka Spotted, of which the last three are a subject of conservative breeding and substantially represent the native populations. Results A two largely complementary statistical methods were used for signatures detection, including: pairwise FST and relative extended haplotype homozygosity (REHH) test. Breed-specific diversifying selection signals included several genes involved in processes connected with fertility, growth and metabolism which are potentially responsible for different phenotypes of the studied breeds. The diversifying selection signals also comprised PPARD gene that was previously found to have a large effect on the shape of the external ear in pigs or two genes encoding neuropeptide Y receptors (Y2 and Y5) involved in fat deposition and stress response which are important features differentiating the studied breeds. REHH statistics allowed detecting several within-breed selection signatures overlapping with genes connected with a range of functions including, among others: metabolic pathways, immune system response or implantation and development of the embryo. Conclusions The study provides many potential candidate genes with implication for traits selected in the individual breeds and gives strong basis for further studies aiming at identification of sources of variation among the studied pig breeds.http://link.springer.com/article/10.1186/s12863-018-0681-0FSTPigPolish landracePuławskaREHHSelection signatures |
| spellingShingle | Artur Gurgul Igor Jasielczuk Katarzyna Ropka-Molik Ewelina Semik-Gurgul Klaudia Pawlina-Tyszko Tomasz Szmatoła Magdalena Szyndler-Nędza Monika Bugno-Poniewierska Tadeusz Blicharski Karolina Szulc Ewa Skrzypczak Jędrzej Krupiński A genome-wide detection of selection signatures in conserved and commercial pig breeds maintained in Poland BMC Genetics FST Pig Polish landrace Puławska REHH Selection signatures |
| title | A genome-wide detection of selection signatures in conserved and commercial pig breeds maintained in Poland |
| title_full | A genome-wide detection of selection signatures in conserved and commercial pig breeds maintained in Poland |
| title_fullStr | A genome-wide detection of selection signatures in conserved and commercial pig breeds maintained in Poland |
| title_full_unstemmed | A genome-wide detection of selection signatures in conserved and commercial pig breeds maintained in Poland |
| title_short | A genome-wide detection of selection signatures in conserved and commercial pig breeds maintained in Poland |
| title_sort | genome wide detection of selection signatures in conserved and commercial pig breeds maintained in poland |
| topic | FST Pig Polish landrace Puławska REHH Selection signatures |
| url | http://link.springer.com/article/10.1186/s12863-018-0681-0 |
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