Comprehensive Genome and Transcriptome Analysis Identifies SLCO3A1 Associated with Aggressive Behavior in Pigs
Copy number variation (CNV) represents a significant reservoir of genetic diversity within the genome and exhibits a strong association with economically valuable traits in livestock. The manifestation of aggressive behavior in pigs has detrimental effects on production efficiency, immune competency...
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| Format: | Article |
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MDPI AG
2023-09-01
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| Series: | Biomolecules |
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| Online Access: | https://www.mdpi.com/2218-273X/13/9/1381 |
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| author | Chunlei Zhang Huan Yang Qinglei Xu Mingzheng Liu Xiaohuan Chao Jiahao Chen Bo Zhou Yang Liu |
| author_facet | Chunlei Zhang Huan Yang Qinglei Xu Mingzheng Liu Xiaohuan Chao Jiahao Chen Bo Zhou Yang Liu |
| author_sort | Chunlei Zhang |
| collection | DOAJ |
| description | Copy number variation (CNV) represents a significant reservoir of genetic diversity within the genome and exhibits a strong association with economically valuable traits in livestock. The manifestation of aggressive behavior in pigs has detrimental effects on production efficiency, immune competency, and meat quality. Nevertheless, the impact of CNV on the aggressive behavior of pigs remains elusive. In this investigation, we employed an integrated analysis of genome and transcriptome data to investigate the interplay between CNV, gene expression changes, and indicators of aggressive behavior in weaned pigs. Specifically, a subset of pigs comprising the most aggressive pigs (MAP, <i>n</i> = 12) and the least aggressive pigs (LAP, <i>n</i> = 11) was purposefully selected from a herd of 500 weaned pigs following a mixing procedure based on their composite aggressive score (CAS). Subsequently, we thoroughly analyzed copy number variation regions (CNVRs) across the entire genome using next-generation sequencing techniques, ultimately revealing the presence of 6869 CNVRs. Using genome-wide association study (GWAS) analysis and evaluating variance-stabilizing transformation (V<sub>ST</sub>) values, we successfully identified distinct CNVRs that distinguished the MAP and LAP counterparts. Among the prioritized CNVRs, CNVR-4962 (designated as the top-ranked <i>p</i>-value and V<sub>ST</sub> value, No. 1) was located within the Solute Carrier Organic Anion Transporter Family Member 3A1 (SLCO3A1) gene. The results of our analyses indicated a significantly higher (<i>p</i> < 0.05) copy number of <i>SLCO3A1</i> in the MAP compared to the LAP. Furthermore, this increased copy number exhibited a positive correlation with the CAS of the pigs (<i>p</i> < 0.05). Furthermore, we integrated genomic data with transcriptomic data from the temporal lobe to facilitate the examination of expression quantitative trait loci (eQTL). Importantly, these observations were consistent with the mRNA expression pattern of <i>SLCO3A1</i> in the temporal lobe of both MAP and LAP (<i>p</i> < 0.05). Consequently, our findings strongly suggest that CNVs affecting <i>SLCO3A1</i> may influence gene expression through a dosage effect. These results highlight the potential of <i>SLCO3A1</i> as a candidate gene associated with aggressive traits in pig breeding programs. |
| first_indexed | 2024-03-10T22:59:23Z |
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| id | doaj.art-760b117232ec4929abc308e42795bad8 |
| institution | Directory Open Access Journal |
| issn | 2218-273X |
| language | English |
| last_indexed | 2024-03-10T22:59:23Z |
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| spelling | doaj.art-760b117232ec4929abc308e42795bad82023-11-19T09:46:13ZengMDPI AGBiomolecules2218-273X2023-09-01139138110.3390/biom13091381Comprehensive Genome and Transcriptome Analysis Identifies SLCO3A1 Associated with Aggressive Behavior in PigsChunlei Zhang0Huan Yang1Qinglei Xu2Mingzheng Liu3Xiaohuan Chao4Jiahao Chen5Bo Zhou6Yang Liu7College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, ChinaCollege of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, ChinaCollege of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, ChinaCollege of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, ChinaCollege of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, ChinaCollege of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, ChinaCollege of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, ChinaCollege of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, ChinaCopy number variation (CNV) represents a significant reservoir of genetic diversity within the genome and exhibits a strong association with economically valuable traits in livestock. The manifestation of aggressive behavior in pigs has detrimental effects on production efficiency, immune competency, and meat quality. Nevertheless, the impact of CNV on the aggressive behavior of pigs remains elusive. In this investigation, we employed an integrated analysis of genome and transcriptome data to investigate the interplay between CNV, gene expression changes, and indicators of aggressive behavior in weaned pigs. Specifically, a subset of pigs comprising the most aggressive pigs (MAP, <i>n</i> = 12) and the least aggressive pigs (LAP, <i>n</i> = 11) was purposefully selected from a herd of 500 weaned pigs following a mixing procedure based on their composite aggressive score (CAS). Subsequently, we thoroughly analyzed copy number variation regions (CNVRs) across the entire genome using next-generation sequencing techniques, ultimately revealing the presence of 6869 CNVRs. Using genome-wide association study (GWAS) analysis and evaluating variance-stabilizing transformation (V<sub>ST</sub>) values, we successfully identified distinct CNVRs that distinguished the MAP and LAP counterparts. Among the prioritized CNVRs, CNVR-4962 (designated as the top-ranked <i>p</i>-value and V<sub>ST</sub> value, No. 1) was located within the Solute Carrier Organic Anion Transporter Family Member 3A1 (SLCO3A1) gene. The results of our analyses indicated a significantly higher (<i>p</i> < 0.05) copy number of <i>SLCO3A1</i> in the MAP compared to the LAP. Furthermore, this increased copy number exhibited a positive correlation with the CAS of the pigs (<i>p</i> < 0.05). Furthermore, we integrated genomic data with transcriptomic data from the temporal lobe to facilitate the examination of expression quantitative trait loci (eQTL). Importantly, these observations were consistent with the mRNA expression pattern of <i>SLCO3A1</i> in the temporal lobe of both MAP and LAP (<i>p</i> < 0.05). Consequently, our findings strongly suggest that CNVs affecting <i>SLCO3A1</i> may influence gene expression through a dosage effect. These results highlight the potential of <i>SLCO3A1</i> as a candidate gene associated with aggressive traits in pig breeding programs.https://www.mdpi.com/2218-273X/13/9/1381CNVaggressive behavior<i>SLCO3A1</i>animal welfaredosage effect |
| spellingShingle | Chunlei Zhang Huan Yang Qinglei Xu Mingzheng Liu Xiaohuan Chao Jiahao Chen Bo Zhou Yang Liu Comprehensive Genome and Transcriptome Analysis Identifies SLCO3A1 Associated with Aggressive Behavior in Pigs Biomolecules CNV aggressive behavior <i>SLCO3A1</i> animal welfare dosage effect |
| title | Comprehensive Genome and Transcriptome Analysis Identifies SLCO3A1 Associated with Aggressive Behavior in Pigs |
| title_full | Comprehensive Genome and Transcriptome Analysis Identifies SLCO3A1 Associated with Aggressive Behavior in Pigs |
| title_fullStr | Comprehensive Genome and Transcriptome Analysis Identifies SLCO3A1 Associated with Aggressive Behavior in Pigs |
| title_full_unstemmed | Comprehensive Genome and Transcriptome Analysis Identifies SLCO3A1 Associated with Aggressive Behavior in Pigs |
| title_short | Comprehensive Genome and Transcriptome Analysis Identifies SLCO3A1 Associated with Aggressive Behavior in Pigs |
| title_sort | comprehensive genome and transcriptome analysis identifies slco3a1 associated with aggressive behavior in pigs |
| topic | CNV aggressive behavior <i>SLCO3A1</i> animal welfare dosage effect |
| url | https://www.mdpi.com/2218-273X/13/9/1381 |
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