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| A genome scan of recent positive selection signatures in three sheep populations |
| ZHAO Fu-ping, WEI Cai-hong, ZHANG Li, LIU Jia-sen, WANG Guang-kai, ZENG Tao, DU Li-xin |
1、National Center for Molecular Genetics and Breeding of Animal, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, P.R.China
2、Institute of Animal Science, Inner Mongolia Academy of Agricultural & Animal Husbandry Sciences, Hohhot 010031, P.R.China
3、College of Animal Science and Technology, Sichuan Agricultural University, Ya’an 625014, P.R.China |
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摘要 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.
Abstract 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.
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Received: 18 November 2014
Accepted:
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| Fund: This work was supported by the National Natural Science Foundation of China (31200927), the National Modern Agricultural Industry Technology Fund for Scientists in the Sheep Industry System of China (CARS-39-04B), and the Agricultural Science and Technology Innovation Program, China (ASTIP-IAS-TS-6). |
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Corresponding Authors:
DU Li-xin,Tel: +86-10-62819997, E-mail: lxdu@263.net
E-mail: lxdu@263.net
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| About author: ZHAO Fu-ping, E-mail: zhaofuping@caas.cn; WEI Cai-hong,E-mail: weicaihong@caas.cn;* These authors contributed equally to this study |
Cite this article:
ZHAO Fu-ping, WEI Cai-hong, ZHANG Li, LIU Jia-sen, WANG Guang-kai, ZENG Tao, DU Li-xin.
2016.
A genome scan of recent positive selection signatures in three sheep populations. Journal of Integrative Agriculture, 15(1): 162-174.
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