Identification of selective sweeps reveals divergent selection between Chinese Holstein and Simmental cattle populations

Genetics Selection Evolution, Oct 2016

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 genome-wide 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 F ST , 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 F ST values across five distinct functional regions in the genome. In the low-minor allele frequency bin, we found a higher proportion of low-F ST 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.

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Identification of selective sweeps reveals divergent selection between Chinese Holstein and Simmental cattle populations

Chen et al. Genet Sel Evol Identification of selective sweeps reveals divergent selection between Chinese Holstein and Simmental cattle populations Minhui Chen 0 2 3 Dunfei Pan 0 3 Hongyan Ren 1 Jinluan Fu 0 3 Junya Li 4 Guosheng Su 2 Aiguo Wang 0 3 Li Jiang 0 3 Qin Zhang 0 3 Jian‑Feng Liu 0 3 0 Department of Animal Genetics , Breeding and Reproduction , China Agricultural University , Beijing 100193 , China 1 National Natural Science Foun‐ dation of China , Beijing 100085 , China 2 Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University , AU‐Foulum, 8830 Tjele , Denmark 3 Department of Animal Genetics , Breeding and Reproduction , China Agri‐ cultural University , Beijing 100193 , China 4 Institute of Animal Science, Chinese Academy of Agricultural Science , Beijing 100193 , China 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. - Background The patterns of genetic variation are essential for understanding the history and structure of populations and the relationship between genotype and phenotype [1– 3]. To date, many studies have focused on the genomewide scanning of signals that were left by recent positive selection in many species, such as humans [4–7], plants [8], and domestic animals [9, 10]. Signatures of selection in a genome usually involve three typical genomic features, i.e., high-frequency derived alleles, long-range haplotypes with strong linkage disequilibrium (LD) and highly differentiated allele frequencies between populations [6]. Specifically, a selective sweep rapidly increases the frequency of the favorable causal variant, and strong LD persists between the causal variant and neighboring polymorphisms relative to neutral regions, which results in an unusually long-range haplotype with a high level of homozygosity [4, 5]. When geographically variable selective forces or directional © 2016 The Author(s). This article is distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons license, and indicate if changes were made. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/ publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated. selection with some economic purpose favor different variants in different regions, allele frequencies in such regions will differ greatly among populations [9]. To detect these genomic features that result from recent positive selection, various analytical methods have been proposed and successfully applied to many species. These approaches are largely considered as belonging to two different types. One type is based on LD patterns across genomes, such as the long-range haplotype (LRH) test [7], integrated haplotype homozygosity score (iHS) [5], cross population extended haplotype homozygosity (XP-EHH) test [4] and Rsb test [11]. The (...truncated)


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Minhui Chen, Dunfei Pan, Hongyan Ren, Jinluan Fu, Junya Li, Guosheng Su, Aiguo Wang, Li Jiang, Qin Zhang, Jian-Feng Liu. Identification of selective sweeps reveals divergent selection between Chinese Holstein and Simmental cattle populations, Genetics Selection Evolution, 2016, pp. 76, 48, DOI: 10.1186/s12711-016-0254-5