A genome scan of recent positive selection signatures in three sheep populations
Domesticated sheep have been exposed to artificial selection for the production of fiber, meat, and milk as well as to natural selection. Such selections are likely to have imposed distinctive selection signatures on the sheep genome. Therefore, detecting selection signatures across the genome may h...
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KeAi Communications Co., Ltd.
2016-01-01
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| Series: | Journal of Integrative Agriculture |
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| Online Access: | http://www.sciencedirect.com/science/article/pii/S2095311915610802 |
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| author | Fu-ping ZHAO Cai-hong WEI Li ZHANG Jia-sen LIU Guang-kai WANG Tao ZENG Li-xin DU |
| author_facet | Fu-ping ZHAO Cai-hong WEI Li ZHANG Jia-sen LIU Guang-kai WANG Tao ZENG Li-xin DU |
| author_sort | Fu-ping ZHAO |
| collection | DOAJ |
| description | Domesticated sheep have been exposed to artificial selection for the production of fiber, meat, and milk as well as to natural selection. Such selections are likely to have imposed distinctive selection signatures on the sheep genome. Therefore, detecting selection signatures across the genome may help elucidate mechanisms of selection and pinpoint candidate genes of interest for further investigation. Here, detection of selection signatures was conducted in three sheep breeds, Sunite (n=66), German Mutton (n=159), and Dorper (n=93), using the Illumina OvineSNP50 Genotyping BeadChip array. Each animal provided genotype information for 43 273 autosomal single nucleotide polymorphisms (SNPs). We adopted two complementary haplotype-based statistics of relative extended haplotype homozygosity (REHH) and the cross-population extended haplotype homozygosity (XP-EHH) tests. In total, 707, 755, and 438 genomic regions subjected to positive selection were identified in Sunite, German Mutton, and Dorper sheep, respectively, and 42 of these regions were detected using both REHH and XP-EHH analyses. These genomic regions harbored many important genes, which were enriched in gene ontology terms involved in muscle development, growth, and fat metabolism. Fourteen of these genomic regions overlapped with those identified in our previous genome-wide association studies, further indicating that these genes under positive selection may underlie growth developmental traits. These findings contribute to the identification of candidate genes of interest and aid in understanding the evolutionary and biological mechanisms for controlling complex traits in Chinese and western sheep. |
| format | Article |
| id | doaj-art-b0205fd59b2f48a988852a53e283ebd6 |
| institution | Kabale University |
| issn | 2095-3119 |
| language | English |
| publishDate | 2016-01-01 |
| publisher | KeAi Communications Co., Ltd. |
| record_format | Article |
| series | Journal of Integrative Agriculture |
| spelling | doaj-art-b0205fd59b2f48a988852a53e283ebd62025-08-20T03:58:49ZengKeAi Communications Co., Ltd.Journal of Integrative Agriculture2095-31192016-01-0115116217410.1016/S2095-3119(15)61080-2A genome scan of recent positive selection signatures in three sheep populationsFu-ping ZHAO0Cai-hong WEI1Li ZHANG2Jia-sen LIU3Guang-kai WANG4Tao ZENG5Li-xin DU6National Center for Molecular Genetics and Breeding of Animal, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.ChinaNational Center for Molecular Genetics and Breeding of Animal, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.ChinaNational Center for Molecular Genetics and Breeding of Animal, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.ChinaInstitute of Animal Science, Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, P.R.ChinaNational Center for Molecular Genetics and Breeding of Animal, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.ChinaCollege of Animal Science and Technology, Sichuan Agricultural University, Ya'an 625014, P.R.ChinaNational Center for Molecular Genetics and Breeding of Animal, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China; Correspondence DU Li-xin, Tel: +86-10-62819997Domesticated sheep have been exposed to artificial selection for the production of fiber, meat, and milk as well as to natural selection. Such selections are likely to have imposed distinctive selection signatures on the sheep genome. Therefore, detecting selection signatures across the genome may help elucidate mechanisms of selection and pinpoint candidate genes of interest for further investigation. Here, detection of selection signatures was conducted in three sheep breeds, Sunite (n=66), German Mutton (n=159), and Dorper (n=93), using the Illumina OvineSNP50 Genotyping BeadChip array. Each animal provided genotype information for 43 273 autosomal single nucleotide polymorphisms (SNPs). We adopted two complementary haplotype-based statistics of relative extended haplotype homozygosity (REHH) and the cross-population extended haplotype homozygosity (XP-EHH) tests. In total, 707, 755, and 438 genomic regions subjected to positive selection were identified in Sunite, German Mutton, and Dorper sheep, respectively, and 42 of these regions were detected using both REHH and XP-EHH analyses. These genomic regions harbored many important genes, which were enriched in gene ontology terms involved in muscle development, growth, and fat metabolism. Fourteen of these genomic regions overlapped with those identified in our previous genome-wide association studies, further indicating that these genes under positive selection may underlie growth developmental traits. These findings contribute to the identification of candidate genes of interest and aid in understanding the evolutionary and biological mechanisms for controlling complex traits in Chinese and western sheep.http://www.sciencedirect.com/science/article/pii/S2095311915610802selection signature detectionsheep genomeREHH testXP-EHH testSNP chip |
| spellingShingle | Fu-ping ZHAO Cai-hong WEI Li ZHANG Jia-sen LIU Guang-kai WANG Tao ZENG Li-xin DU A genome scan of recent positive selection signatures in three sheep populations Journal of Integrative Agriculture selection signature detection sheep genome REHH test XP-EHH test SNP chip |
| title | A genome scan of recent positive selection signatures in three sheep populations |
| title_full | A genome scan of recent positive selection signatures in three sheep populations |
| title_fullStr | A genome scan of recent positive selection signatures in three sheep populations |
| title_full_unstemmed | A genome scan of recent positive selection signatures in three sheep populations |
| title_short | A genome scan of recent positive selection signatures in three sheep populations |
| title_sort | genome scan of recent positive selection signatures in three sheep populations |
| topic | selection signature detection sheep genome REHH test XP-EHH test SNP chip |
| url | http://www.sciencedirect.com/science/article/pii/S2095311915610802 |
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