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.
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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
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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)