Abstract
Selective signatures in whole genome can help us understand the mechanisms of selection and target causal variants for breeding program. In present study, we performed Extended Haplotype Homozygosity (EHH) tests to identify significant core regions harboring such signals in Chinese Holstein, and then verified the biological significance of these identified regions based on commonly-used bioinformatics analyses. Results showed a total of 125 significant regions in entire genome containing some of important functional genes such as LEP, ABCG2, CSN1S1, CSN3 and TNF based on the Gene Ontology database. Some of these annotated genes involved in the core regions overlapped with those identified in our previous GWAS as well as those involved in a recently constructed candidate gene database for cattle, further indicating these genes under positive selection maybe underlie milk production traits and other important traits in Chinese Holstein. Furthermore, in the enrichment analyses for the second level GO terms and pathways, we observed some significant terms over represented in these identified regions as compared to the entire bovine genome. This indicates that some functional genes associated with milk production traits, as reflected by GO terms, could be clustered in core regions, which provided promising evidence for the exploitability of the core regions identified by EHH tests. Findings in our study could help detect functional candidate genes under positive selection for further genetic and breeding research in Chinese Holstein.
Highlights
When a novel beneficial mutation have been under the force of selection over a long period of time, it will show some obvious features such as unusually long-range linkage disequilibrium (LD)and a high population frequency, which represents a detectable " signature of selection" [1,2]
This indicates that some functional genes associated with milk production traits, as reflected by gene ontology (GO) terms, could be clustered in core regions, which provided promising evidence for the exploitability of the core regions identified by extended haplotype homozygosity (EHH) tests
Two different types of enrichment analyses relevant to the significant core regions were performed i.e., gene ontology (GO) term enrichment analyses and pathway enrichment analyses
Summary
When a novel beneficial mutation have been under the force of selection over a long period of time, it will show some obvious features such as unusually long-range linkage disequilibrium (LD)and a high population frequency, which represents a detectable " signature of selection" [1,2]. Identifying signatures of recent positive selection could help us target causal variants for breeding and be potential to provide straightforward insights into the mechanisms of evolution. Score (iHS) and the extended haplotype homozygosity (EHH) test [5,6] based on haplotype lengths; FST test [7] for population differentiation detection These methods have been successfully implemented in many studies to exploit strong signatures of mutations under positive selection in humans and in domestic animals, e.g., genes resistance to malaria [6,8], in response to milk yield in dairy cattle [5,9] and related to pigmentation [10].
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