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Jie Yang
South China Agricultural University
Corresponding Author
ORCiD: https://orcid.org/0000-0002-7031-2160
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Background: In the process of pig breeding, the average daily gain (ADG), days to 100 kg (AGE), and backfat thickness (BFT) are directly related to growth rate and fatness. However, the genetic mechanisms involved are not well understood. As an essential source of genetic diversity, copy number variation (CNV) that can affect a variety of complex traits and diseases, has gradually been thrust into the limelight. In this study, we reported the genome-wide CNVs of Duroc pigs by SNP genotyping data of 6,627 Duroc pigs. Moreover, we also performed CNV region (CNVR) based association analysis for growth and fatness traits in two Duroc populations.
Results: Our study identified a total of 835 nonredundant CNVRs in American and Canadian Duroc pigs, which covered 226.73 Mb (~ 10.00%) of the pig autosomal genome. Among them, we identified 682 CNVRs in the American Duroc pigs and 424 CNVRs in the Canadian Duroc pigs, and 271 CNVRs were detected in both populations. Experimentally, 77.8% of randomly selected CNVRs were validated by quantitative PCR (qPCR). We also identified 24 significant CNVRs for growth and fatness traits though CNVR-based association analysis. Among these, six and three CNVRs in American and Canadian Duroc pigs were found to be associated with both ADG and AGE traits, respectively. Notably, four CNVRs showed both significant in ADG, AGE, and BFT, indicating that these CNVRs may play a pleiotropic role in regulating pig growth and fat deposition. Besides, further bioinformatics analysis determined a subset of potential candidate genes, such as PDGFRB, INSIG1, GPER1, PDGFA, and LPCAT1.
Conclusions: The present study provides a necessary supplement to the CNV map of the Duroc genome through a large-scale population genotyping. Also, the CNVR-based association results provide a meaningful way to elucidate the genetic mechanisms of complex traits. The identified CNVRs can be used as molecular markers for genetic improvement in molecular-guided breeding of modern commercial pigs
Keywords
Copy number variation, CNVR-based association, Growth, Fatness, Duroc pigs
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This is a list of supplementary files associated with this preprint. Click to download.
- Additionalfile1TableS1.xlsx
Additional file 1 Table S1 Format: .xlsx Title: Overview of CNVRs for two Duroc populations. Description: The data provided chromosomes, physical position, and other details of CNVRs detected in the Duroc population.
- Additionalfile2TableS2.xlsx
Additional file 2 Table S2 Format: .xlsx Title: Information of CNVRs shared by two Duroc populations. Description: The data provided chromosomes, physical position, and other details of CNVRs shared between the two Duroc populations.
- Additionalfile3TableS3.xlsx
Additional file 3 Table S3 Format: .xlsx Title: Identified CNVRs compared with previous studies. Description: The data provided comparative results with other CNVR studies, mainly including CNVRs identified in other studies, their position in the pig genome, and overlapping bases.
- Additionalfile4TableS4.xlsx
Additional file 4 Table S4 Format: .xlsx Title: qPCR primer and probe sequence information. Description: The data provided primers designed according to CNVR co-localized genes, including chromosomes, gene names, forward and reverse sequences.
- Additionalfile5TableS5.xlsx
Additional file 5 Table S5 Format: .xlsx Title: Trait-related QTLs overlapped with significant CNVRs. Description: The data provided ID, chromosomes, physical position, and overlapping length of QTLs with their corresponding overlapped CNVRs.
- Additionalfile6TableS6.xlsx
Additional file 6 Table S6 Format: .xlsx Title: Information of genes in the significant CNVRs. Description: The data provided chromosomes, physical position, and all overlapped genes of significant CNVRs associated with corresponding traits.
- Additionalfile7TableS7.xlsx
Additional file 7 Table S7. Format: .xlsx Title: KEGG and GO Enrichment Analysis for significant CNVRs gene set by KOBAS. Description: The data provided significant GO terms and KEGG pathways obtained by enrichment analysis.
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A new preprint design is coming!
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This is a preprint, a preliminary version of a manuscript that has not completed peer review at a journal. Research Square does not conduct peer review prior to posting preprints. The posting of a preprint on this server should not be interpreted as an endorsement of its validity or suitability for dissemination as established information or for guiding clinical practice.
Research
Jie Yang
South China Agricultural University
Corresponding Author
ORCiD: https://orcid.org/0000-0002-7031-2160
Badges
Prescreen
This manuscript passed our Prescreen assessment
Complete author information
Appropriate declaration statements
Potential risks to human health
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CURRENT STATUS: Posted
View the published article at BMC Genomics.
Version 1
Posted 08 Oct, 2020
No community comments so far
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Comments: 0
PDF Downloads: ...
HTML Views: ...
Subject Areas
Animal Science
License:
This work is licensed under a CC BY 4.0 License. Read Full License
View the published article at BMC Genomics.
Background: In the process of pig breeding, the average daily gain (ADG), days to 100 kg (AGE), and backfat thickness (BFT) are directly related to growth rate and fatness. However, the genetic mechanisms involved are not well understood. As an essential source of genetic diversity, copy number variation (CNV) that can affect a variety of complex traits and diseases, has gradually been thrust into the limelight. In this study, we reported the genome-wide CNVs of Duroc pigs by SNP genotyping data of 6,627 Duroc pigs. Moreover, we also performed CNV region (CNVR) based association analysis for growth and fatness traits in two Duroc populations.
Results: Our study identified a total of 835 nonredundant CNVRs in American and Canadian Duroc pigs, which covered 226.73 Mb (~ 10.00%) of the pig autosomal genome. Among them, we identified 682 CNVRs in the American Duroc pigs and 424 CNVRs in the Canadian Duroc pigs, and 271 CNVRs were detected in both populations. Experimentally, 77.8% of randomly selected CNVRs were validated by quantitative PCR (qPCR). We also identified 24 significant CNVRs for growth and fatness traits though CNVR-based association analysis. Among these, six and three CNVRs in American and Canadian Duroc pigs were found to be associated with both ADG and AGE traits, respectively. Notably, four CNVRs showed both significant in ADG, AGE, and BFT, indicating that these CNVRs may play a pleiotropic role in regulating pig growth and fat deposition. Besides, further bioinformatics analysis determined a subset of potential candidate genes, such as PDGFRB, INSIG1, GPER1, PDGFA, and LPCAT1.
Conclusions: The present study provides a necessary supplement to the CNV map of the Duroc genome through a large-scale population genotyping. Also, the CNVR-based association results provide a meaningful way to elucidate the genetic mechanisms of complex traits. The identified CNVRs can be used as molecular markers for genetic improvement in molecular-guided breeding of modern commercial pigs
Figure 1
Figure 2
Figure 3
Figure 4
Figure 5
Figure 6
This is a list of supplementary files associated with this preprint. Click to download.
- Additionalfile1TableS1.xlsx
Additional file 1 Table S1 Format: .xlsx Title: Overview of CNVRs for two Duroc populations. Description: The data provided chromosomes, physical position, and other details of CNVRs detected in the Duroc population.
- Additionalfile2TableS2.xlsx
Additional file 2 Table S2 Format: .xlsx Title: Information of CNVRs shared by two Duroc populations. Description: The data provided chromosomes, physical position, and other details of CNVRs shared between the two Duroc populations.
- Additionalfile3TableS3.xlsx
Additional file 3 Table S3 Format: .xlsx Title: Identified CNVRs compared with previous studies. Description: The data provided comparative results with other CNVR studies, mainly including CNVRs identified in other studies, their position in the pig genome, and overlapping bases.
- Additionalfile4TableS4.xlsx
Additional file 4 Table S4 Format: .xlsx Title: qPCR primer and probe sequence information. Description: The data provided primers designed according to CNVR co-localized genes, including chromosomes, gene names, forward and reverse sequences.
- Additionalfile5TableS5.xlsx
Additional file 5 Table S5 Format: .xlsx Title: Trait-related QTLs overlapped with significant CNVRs. Description: The data provided ID, chromosomes, physical position, and overlapping length of QTLs with their corresponding overlapped CNVRs.
- Additionalfile6TableS6.xlsx
Additional file 6 Table S6 Format: .xlsx Title: Information of genes in the significant CNVRs. Description: The data provided chromosomes, physical position, and all overlapped genes of significant CNVRs associated with corresponding traits.
- Additionalfile7TableS7.xlsx
Additional file 7 Table S7. Format: .xlsx Title: KEGG and GO Enrichment Analysis for significant CNVRs gene set by KOBAS. Description: The data provided significant GO terms and KEGG pathways obtained by enrichment analysis.
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