Identification of eQTLs using different sets of single nucleotide polymorphisms associated with carcass and body composition traits in pigs
Abstract Background Mapping expression quantitative trait loci (eQTLs) in skeletal muscle tissue in pigs is crucial for understanding the relationship between genetic variation and phenotypic expression of carcass traits in meat animals. Therefore, the primary objective of this study was to evaluate...
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BMC
2024-01-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-023-09863-8 |
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| author | Felipe André Oliveira Freitas Luiz F. Brito Simara Larissa Fanalli Janaína Lustosa Gonçales Bruna Pereira Martins da Silva Mariah Castro Durval Fernanda Nery Ciconello Camila Sabino de Oliveira Lucas Echevarria Nascimento Izally Carvalho Gervásio Julia Dezen Gomes Gabriel Costa Monteiro Moreira Bárbara Silva-Vignato Luiz Lehmann Coutinho Vivian Vezzoni de Almeida Aline Silva Mello Cesar |
| author_facet | Felipe André Oliveira Freitas Luiz F. Brito Simara Larissa Fanalli Janaína Lustosa Gonçales Bruna Pereira Martins da Silva Mariah Castro Durval Fernanda Nery Ciconello Camila Sabino de Oliveira Lucas Echevarria Nascimento Izally Carvalho Gervásio Julia Dezen Gomes Gabriel Costa Monteiro Moreira Bárbara Silva-Vignato Luiz Lehmann Coutinho Vivian Vezzoni de Almeida Aline Silva Mello Cesar |
| author_sort | Felipe André Oliveira Freitas |
| collection | DOAJ |
| description | Abstract Background Mapping expression quantitative trait loci (eQTLs) in skeletal muscle tissue in pigs is crucial for understanding the relationship between genetic variation and phenotypic expression of carcass traits in meat animals. Therefore, the primary objective of this study was to evaluate the impact of different sets of single nucleotide polymorphisms (SNP), including scenarios removing SNPs pruned for linkage disequilibrium (LD) and SNPs derived from SNP chip arrays and RNA-seq data from liver, brain, and skeletal muscle tissues, on the identification of eQTLs in the Longissimus lumborum tissue, associated with carcass and body composition traits in Large White pigs. The SNPs identified from muscle mRNA were combined with SNPs identified in the brain and liver tissue transcriptomes, as well as SNPs from the GGP Porcine 50 K SNP chip array. Cis- and trans-eQTLs were identified based on the skeletal muscle gene expression level, followed by functional genomic analyses and statistical associations with carcass and body composition traits in Large White pigs. Results The number of cis- and trans-eQTLs identified across different sets of SNPs (scenarios) ranged from 261 to 2,539 and from 29 to 13,721, respectively. Furthermore, 6,180 genes were modulated by eQTLs in at least one of the scenarios evaluated. The eQTLs identified were not significantly associated with carcass and body composition traits but were significantly enriched for many traits in the “Meat and Carcass” type QTL. The scenarios with the highest number of cis- (n = 304) and trans- (n = 5,993) modulated genes were the unpruned and LD-pruned SNP set scenarios identified from the muscle transcriptome. These genes include 84 transcription factor coding genes. Conclusions After LD pruning, the set of SNPs identified based on the transcriptome of the skeletal muscle tissue of pigs resulted in the highest number of genes modulated by eQTLs. Most eQTLs are of the trans type and are associated with genes influencing complex traits in pigs, such as transcription factors and enhancers. Furthermore, the incorporation of SNPs from other genomic regions to the set of SNPs identified in the porcine skeletal muscle transcriptome contributed to the identification of eQTLs that had not been identified based on the porcine skeletal muscle transcriptome alone. |
| first_indexed | 2024-03-08T16:23:21Z |
| format | Article |
| id | doaj.art-66923c9308f74f4ea2e997209e25d848 |
| institution | Directory Open Access Journal |
| issn | 1471-2164 |
| language | English |
| last_indexed | 2024-03-08T16:23:21Z |
| publishDate | 2024-01-01 |
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| series | BMC Genomics |
| spelling | doaj.art-66923c9308f74f4ea2e997209e25d8482024-01-07T12:12:16ZengBMCBMC Genomics1471-21642024-01-0125111810.1186/s12864-023-09863-8Identification of eQTLs using different sets of single nucleotide polymorphisms associated with carcass and body composition traits in pigsFelipe André Oliveira Freitas0Luiz F. Brito1Simara Larissa Fanalli2Janaína Lustosa Gonçales3Bruna Pereira Martins da Silva4Mariah Castro Durval5Fernanda Nery Ciconello6Camila Sabino de Oliveira7Lucas Echevarria Nascimento8Izally Carvalho Gervásio9Julia Dezen Gomes10Gabriel Costa Monteiro Moreira11Bárbara Silva-Vignato12Luiz Lehmann Coutinho13Vivian Vezzoni de Almeida14Aline Silva Mello Cesar15Luiz de Queiroz College of Agriculture, University of São PauloDepartment of Animal Sciences, Purdue UniversityFaculty of Animal Science and Food Engineering, University of São PauloLuiz de Queiroz College of Agriculture, University of São PauloLuiz de Queiroz College of Agriculture, University of São PauloFaculty of Animal Science and Food Engineering, University of São PauloLuiz de Queiroz College of Agriculture, University of São PauloLuiz de Queiroz College of Agriculture, University of São PauloLuiz de Queiroz College of Agriculture, University of São PauloLuiz de Queiroz College of Agriculture, University of São PauloLuiz de Queiroz College of Agriculture, University of São PauloUnit of Animal Genomics, GIGA-R and Faculty of Veterinary Medicine, University of Liège (B34)Faculty of Animal Science and Food Engineering, University of São PauloLuiz de Queiroz College of Agriculture, University of São PauloCollege of Veterinary Medicine and Animal Science, Federal University of GoiásLuiz de Queiroz College of Agriculture, University of São PauloAbstract Background Mapping expression quantitative trait loci (eQTLs) in skeletal muscle tissue in pigs is crucial for understanding the relationship between genetic variation and phenotypic expression of carcass traits in meat animals. Therefore, the primary objective of this study was to evaluate the impact of different sets of single nucleotide polymorphisms (SNP), including scenarios removing SNPs pruned for linkage disequilibrium (LD) and SNPs derived from SNP chip arrays and RNA-seq data from liver, brain, and skeletal muscle tissues, on the identification of eQTLs in the Longissimus lumborum tissue, associated with carcass and body composition traits in Large White pigs. The SNPs identified from muscle mRNA were combined with SNPs identified in the brain and liver tissue transcriptomes, as well as SNPs from the GGP Porcine 50 K SNP chip array. Cis- and trans-eQTLs were identified based on the skeletal muscle gene expression level, followed by functional genomic analyses and statistical associations with carcass and body composition traits in Large White pigs. Results The number of cis- and trans-eQTLs identified across different sets of SNPs (scenarios) ranged from 261 to 2,539 and from 29 to 13,721, respectively. Furthermore, 6,180 genes were modulated by eQTLs in at least one of the scenarios evaluated. The eQTLs identified were not significantly associated with carcass and body composition traits but were significantly enriched for many traits in the “Meat and Carcass” type QTL. The scenarios with the highest number of cis- (n = 304) and trans- (n = 5,993) modulated genes were the unpruned and LD-pruned SNP set scenarios identified from the muscle transcriptome. These genes include 84 transcription factor coding genes. Conclusions After LD pruning, the set of SNPs identified based on the transcriptome of the skeletal muscle tissue of pigs resulted in the highest number of genes modulated by eQTLs. Most eQTLs are of the trans type and are associated with genes influencing complex traits in pigs, such as transcription factors and enhancers. Furthermore, the incorporation of SNPs from other genomic regions to the set of SNPs identified in the porcine skeletal muscle transcriptome contributed to the identification of eQTLs that had not been identified based on the porcine skeletal muscle transcriptome alone.https://doi.org/10.1186/s12864-023-09863-8Sus scrofaExpression quantitative trait lociTranscriptomicLD pruning |
| spellingShingle | Felipe André Oliveira Freitas Luiz F. Brito Simara Larissa Fanalli Janaína Lustosa Gonçales Bruna Pereira Martins da Silva Mariah Castro Durval Fernanda Nery Ciconello Camila Sabino de Oliveira Lucas Echevarria Nascimento Izally Carvalho Gervásio Julia Dezen Gomes Gabriel Costa Monteiro Moreira Bárbara Silva-Vignato Luiz Lehmann Coutinho Vivian Vezzoni de Almeida Aline Silva Mello Cesar Identification of eQTLs using different sets of single nucleotide polymorphisms associated with carcass and body composition traits in pigs BMC Genomics Sus scrofa Expression quantitative trait loci Transcriptomic LD pruning |
| title | Identification of eQTLs using different sets of single nucleotide polymorphisms associated with carcass and body composition traits in pigs |
| title_full | Identification of eQTLs using different sets of single nucleotide polymorphisms associated with carcass and body composition traits in pigs |
| title_fullStr | Identification of eQTLs using different sets of single nucleotide polymorphisms associated with carcass and body composition traits in pigs |
| title_full_unstemmed | Identification of eQTLs using different sets of single nucleotide polymorphisms associated with carcass and body composition traits in pigs |
| title_short | Identification of eQTLs using different sets of single nucleotide polymorphisms associated with carcass and body composition traits in pigs |
| title_sort | identification of eqtls using different sets of single nucleotide polymorphisms associated with carcass and body composition traits in pigs |
| topic | Sus scrofa Expression quantitative trait loci Transcriptomic LD pruning |
| url | https://doi.org/10.1186/s12864-023-09863-8 |
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