Population genomic analyses based on 1 million SNPs in commercial egg layers.
Identifying signatures of selection can provide valuable insight about the genes or genomic regions that are or have been under selective pressure, which can lead to a better understanding of genotype-phenotype relationships. A common strategy for selection signature detection is to compare samples...
| Main Authors: | , , , , , , |
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| Format: | Article |
| Language: | English |
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Public Library of Science (PLoS)
2014-01-01
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| Series: | PLoS ONE |
| Online Access: | http://europepmc.org/articles/PMC3989219?pdf=render |
| _version_ | 1818387332398579712 |
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| author | Mahmood Gholami Malena Erbe Christian Gärke Rudolf Preisinger Annett Weigend Steffen Weigend Henner Simianer |
| author_facet | Mahmood Gholami Malena Erbe Christian Gärke Rudolf Preisinger Annett Weigend Steffen Weigend Henner Simianer |
| author_sort | Mahmood Gholami |
| collection | DOAJ |
| description | Identifying signatures of selection can provide valuable insight about the genes or genomic regions that are or have been under selective pressure, which can lead to a better understanding of genotype-phenotype relationships. A common strategy for selection signature detection is to compare samples from several populations and search for genomic regions with outstanding genetic differentiation. Wright's fixation index, FST, is a useful index for evaluation of genetic differentiation between populations. The aim of this study was to detect selective signatures between different chicken groups based on SNP-wise FST calculation. A total of 96 individuals of three commercial layer breeds and 14 non-commercial fancy breeds were genotyped with three different 600K SNP-chips. After filtering a total of 1 million SNPs were available for FST calculation. Averages of FST values were calculated for overlapping windows. Comparisons of these were then conducted between commercial egg layers and non-commercial fancy breeds, as well as between white egg layers and brown egg layers. Comparing non-commercial and commercial breeds resulted in the detection of 630 selective signatures, while 656 selective signatures were detected in the comparison between the commercial egg-layer breeds. Annotation of selection signature regions revealed various genes corresponding to productions traits, for which layer breeds were selected. Among them were NCOA1, SREBF2 and RALGAPA1 associated with reproductive traits, broodiness and egg production. Furthermore, several of the detected genes were associated with growth and carcass traits, including POMC, PRKAB2, SPP1, IGF2, CAPN1, TGFb2 and IGFBP2. Our approach demonstrates that including different populations with a specific breeding history can provide a unique opportunity for a better understanding of farm animal selection. |
| first_indexed | 2024-12-14T04:08:16Z |
| format | Article |
| id | doaj.art-9592d525b2054458950a9fb6d8145b6c |
| institution | Directory Open Access Journal |
| issn | 1932-6203 |
| language | English |
| last_indexed | 2024-12-14T04:08:16Z |
| publishDate | 2014-01-01 |
| publisher | Public Library of Science (PLoS) |
| record_format | Article |
| series | PLoS ONE |
| spelling | doaj.art-9592d525b2054458950a9fb6d8145b6c2022-12-21T23:17:45ZengPublic Library of Science (PLoS)PLoS ONE1932-62032014-01-0194e9450910.1371/journal.pone.0094509Population genomic analyses based on 1 million SNPs in commercial egg layers.Mahmood GholamiMalena ErbeChristian GärkeRudolf PreisingerAnnett WeigendSteffen WeigendHenner SimianerIdentifying signatures of selection can provide valuable insight about the genes or genomic regions that are or have been under selective pressure, which can lead to a better understanding of genotype-phenotype relationships. A common strategy for selection signature detection is to compare samples from several populations and search for genomic regions with outstanding genetic differentiation. Wright's fixation index, FST, is a useful index for evaluation of genetic differentiation between populations. The aim of this study was to detect selective signatures between different chicken groups based on SNP-wise FST calculation. A total of 96 individuals of three commercial layer breeds and 14 non-commercial fancy breeds were genotyped with three different 600K SNP-chips. After filtering a total of 1 million SNPs were available for FST calculation. Averages of FST values were calculated for overlapping windows. Comparisons of these were then conducted between commercial egg layers and non-commercial fancy breeds, as well as between white egg layers and brown egg layers. Comparing non-commercial and commercial breeds resulted in the detection of 630 selective signatures, while 656 selective signatures were detected in the comparison between the commercial egg-layer breeds. Annotation of selection signature regions revealed various genes corresponding to productions traits, for which layer breeds were selected. Among them were NCOA1, SREBF2 and RALGAPA1 associated with reproductive traits, broodiness and egg production. Furthermore, several of the detected genes were associated with growth and carcass traits, including POMC, PRKAB2, SPP1, IGF2, CAPN1, TGFb2 and IGFBP2. Our approach demonstrates that including different populations with a specific breeding history can provide a unique opportunity for a better understanding of farm animal selection.http://europepmc.org/articles/PMC3989219?pdf=render |
| spellingShingle | Mahmood Gholami Malena Erbe Christian Gärke Rudolf Preisinger Annett Weigend Steffen Weigend Henner Simianer Population genomic analyses based on 1 million SNPs in commercial egg layers. PLoS ONE |
| title | Population genomic analyses based on 1 million SNPs in commercial egg layers. |
| title_full | Population genomic analyses based on 1 million SNPs in commercial egg layers. |
| title_fullStr | Population genomic analyses based on 1 million SNPs in commercial egg layers. |
| title_full_unstemmed | Population genomic analyses based on 1 million SNPs in commercial egg layers. |
| title_short | Population genomic analyses based on 1 million SNPs in commercial egg layers. |
| title_sort | population genomic analyses based on 1 million snps in commercial egg layers |
| url | http://europepmc.org/articles/PMC3989219?pdf=render |
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