Insights into the architecture of human-induced polygenic selection in Duroc pigs View Full Text


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Article Info

DATE

2022-09-21

AUTHORS

Zitao Chen, Jinyan Teng, Shuqi Diao, Zhiting Xu, Shaopan Ye, Dingjie Qiu, Zhe Zhang, Yuchun Pan, Jiaqi Li, Qin Zhang, Zhe Zhang

ABSTRACT

BackgroundAs one of the most utilized commercial composite boar lines, Duroc pigs have been introduced to China and undergone strongly human-induced selection over the past decades. However, the efficiencies and limitations of previous breeding of Chinese Duroc pigs are largely understudied. The objective of this study was to uncover directional polygenic selection in the Duroc pig genome, and investigate points overlooked in the past breeding process.ResultsHere, we utilized the Generation Proxy Selection Mapping (GPSM) on a dataset of 1067 Duroc pigs with 8,766,074 imputed SNPs. GPSM detected a total of 5649 putative SNPs actively under selection in the Chinese Duroc pig population, and the potential functions of the selection regions were mainly related to production, meat and carcass traits. Meanwhile, we observed that the allele frequency of variants related to teat number (NT) relevant traits was also changed, which might be influenced by genes that had pleiotropic effects. First, we identified the direction of selection on NT traits by G^\documentclass[12pt]{minimal} \usepackage{amsmath} \usepackage{wasysym} \usepackage{amsfonts} \usepackage{amssymb} \usepackage{amsbsy} \usepackage{mathrsfs} \usepackage{upgreek} \setlength{\oddsidemargin}{-69pt} \begin{document}$$\hat{G}$$\end{document}, and further pinpointed large-effect genomic regions associated with NT relevant traits by selection signature and GWAS. Combining results of NT relevant traits-specific selection signatures and GWAS, we found three common genome regions, which were overlapped with QTLs related to production, meat and carcass traits besides “teat number” QTLs. This implied that there were some pleiotropic variants underlying NT and economic traits. We further found that rs346331089 has pleiotropic effects on NT and economic traits, e.g., litter size at weaning (LSW), litter weight at weaning (LWW), days to 100 kg (D100), backfat thickness at 100 kg (B100), and loin muscle area at 100 kg (L100) traits.ConclusionsThe selected loci that we identified across methods displayed the past breeding process of Chinese Duroc pigs, and our findings could be used to inform future breeding decision. More... »

PAGES

99

Identifiers

URI

http://scigraph.springernature.com/pub.10.1186/s40104-022-00751-x

DOI

http://dx.doi.org/10.1186/s40104-022-00751-x

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PUBMED

https://www.ncbi.nlm.nih.gov/pubmed/36127741


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32 SNPs
33 allele frequencies
34 architecture
35 area
36 backfat thickness
37 boar line
38 breeding
39 breeding decisions
40 breeding process
41 carcass traits
42 carcasses
43 dataset
44 days
45 decades
46 decisions
47 direction
48 direction of selection
49 economic traits
50 effect
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52 findings
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56 genes
57 genome
58 genome regions
59 genomic regions
60 insights
61 limitations
62 lines
63 litter size
64 litter weight
65 loci
66 loin muscle area
67 mapping
68 meat
69 method
70 muscle area
71 number
72 objective
73 one
74 past decade
75 pig genome
76 pig population
77 pigs
78 pleiotropic effects
79 pleiotropic variants
80 point
81 polygenic selection
82 population
83 potential function
84 previous breeding
85 process
86 production
87 putative SNPs
88 region
89 relevant traits
90 results
91 selection
92 selection mapping
93 selection regions
94 selection signatures
95 signatures
96 size
97 study
98 thickness
99 total
100 traits
101 variants
102 weaning
103 weight
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