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- Title
Identification of selective sweeps reveals divergent selection between Chinese Holstein and Simmental cattle populations.
- Authors
Minhui Chen; Dunfei Pan; Hongyan Ren; Jinluan Fu; Junya Li; Guosheng Su; Aiguo Wang; Li Jiang; Qin Zhang; Jian-Feng Liu
- Abstract
Background: The identification of signals left by recent positive selection provides a feasible approach for targeting genomic variants that underlie complex traits and fitness. A better understanding of the selection mechanisms that occurred during the evolution of species can also be gained. In this study, we simultaneously detected the genomewide footprints of recent positive selection that occurred within and between Chinese Holstein and Simmental populations, which have been subjected to artificial selection for distinct purposes. We conducted analyses using various complementary approaches, including LRH, XP-EHH and FST, based on the Illumina 770K high-density single nucleotide polymorphism (SNP) array, to enable more comprehensive detection. Results: We successfully constructed profiles of selective signals in both cattle populations. To further annotate these regions, we identified a set of novel functional genes related to growth, reproduction, immune response and milk production. There were no overlapping candidate windows between the two breeds. Finally, we investigated the distribution of SNPs that had low FST values across five distinct functional regions in the genome. In the low-minor allele frequency bin, we found a higher proportion of low-FST SNPs in the exons of the bovine genome, which indicates strong purifying selection of the exons. Conclusions: The selection signatures identified in these two populations demonstrated positive selection pressure on a set of important genes with potential functions that are involved in many biological processes. We also demonstrated that in the bovine genome, exons were under strong purifying selection. Our findings provide insight into the mechanisms of artificial selection and will facilitate follow-up functional studies of potential candidate genes that are related to various economically important traits in cattle.
- Subjects
ARTIFICIAL insemination of cattle; BIOMETRIC identification; LIVESTOCK; CATTLE breeds; SELECTION indexes (Animal breeding)
- Publication
Genetics Selection Evolution, 2016, Vol 48, p1
- ISSN
0999-193X
- Publication type
Article
- DOI
10.1186/s12711-016-0254-5