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. 2018 Nov 6;8(11):3617-3625.
doi: 10.1534/g3.118.200665.

Genomic Analysis To Identify Signatures of Artificial Selection and Loci Associated with Important Economic Traits in Duroc Pigs

Yunlong Ma  1 , Saixian Zhang  1 , Kaili Zhang  1 , Chengchi Fang  1 , Shengsong Xie  1 , Xiaoyong Du  1 , Xinyun Li  1 , Debin Ni  2 , Shuhong Zhao  2
Affiliations

Genomic Analysis To Identify Signatures of Artificial Selection and Loci Associated with Important Economic Traits in Duroc Pigs

Yunlong Ma et al. G3 (Bethesda). .

Abstract

Identifying genetic basis of domestication and improvement in livestock contributes to our understanding of the role of artificial selection in shaping the genome. Here we used whole-genome sequencing and the genotyping by sequencing approach to detect artificial selection signatures and identify the associated SNPs of two economic traits in Duroc pigs. A total of 38 candidate selection regions were detected by combining the fixation index and the Composite Likelihood Ratio methods. Further genome-wide association study revealed seven associated SNPs that were related with intramuscular fat content and feed conversion ratio traits, respectively. Enrichment analysis suggested that the artificial selection regions harbored genes, such as MSTN, SOD2, MC5R and CD83, which are responsible for economic traits including lean muscle mass, fertility and immunization. Overall, this study found a series of candidate genes putatively associated with the breeding improvement of Duroc pigs and the polygenic basis of adaptive evolution, which can provide important references and fundamental information for future breeding programs.

Keywords: Artificial selection signatures; Duroc pig; Economic traits; Genome-wide association study.

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Figures

Figure 1
Figure 1
Summary of the genomic regions underlying artificial selection in Duroc pigs. (A) Manhattan plot based on CLR tests. (B) Manhattan plot based on FST tests, the points in blue and red (black and orange) represent scores when EWB (AWB) was treated as reference population. (C) The lines illustrate the positions and lengths of candidate artificial selection regions (CASR).
Figure 2
Figure 2
Visualization of the signals revealed by genome-wide association analyses for IMF and FCR traits. (A, C) Manhattan plots present the association of the imputed SNPs with the IMF and FCR traits in 282 Duroc individuals, respectively. (B, D) The corresponding quantile-quantile plots.
Figure 3
Figure 3
Comparison of GWAS and candidate artificial selection regions (CASR) on SSC1 in Duroc. (A) The top Manhattan plot shows GWAS results for IMF trait. The middle plot shows the distribution of CLR scores calculated in sliding windows. The bottom plot is the distribution of FST scores when AWB (blue) and EWB (green) were treated as reference population, respectively. The red line is the significance threshold. (B) The positions of 31 gene models in this region are indicated: skyblue, minus-strand genes; red, positive-strand genes. The detailed gene list can be found in Supplementary Table S8.
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References

    1. Abbott A., 2012. Pig geneticists go the whole hog. Nature 491: 315–316. 10.1038/491315a - DOI - PubMed
    1. Ai H. S., Fang X. D., Yang B., Huang Z. Y., Chen H., et al. , 2015. Adaptation and possible ancient interspecies introgression in pigs identified by whole-genome sequencing. Nat. Genet. 47: 217–225. 10.1038/ng.3199 - DOI - PubMed
    1. Ashworth M. D., Ross J. W., Stein D. R., White F. J., DeSilva U. W., et al. , 2010. Endometrial caspase 1 and interleukin-18 expression during the estrous cycle and peri-implantation period of porcine pregnancy and response to early exogenous estrogen administration. Reprod. Biol. Endocrinol. 8: 33 10.1186/1477-7827-8-33 - DOI - PMC - PubMed
    1. Baati N., Feillet-Coudray C., Fouret G., Vernus B., Goustard B., et al. , 2017. Myostatin deficiency is associated with lipidomic abnormalities in skeletal muscles. Biochimica Et Biophysica Acta-Molecular and Cell Biology of Lipids 1862: 1044–1055. 10.1016/j.bbalip.2017.06.017 - DOI - PubMed
    1. Briggs H. M., Briggs D. M., 1969. Modern breeds of livestock, Macmillan, London.

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