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Freitas FAO, Brito LF, Fanalli SL, Gonçales JL, da Silva BPM, Durval MC, Ciconello FN, de Oliveira CS, Nascimento LE, Gervásio IC, Gomes JD, Moreira GCM, Silva-Vignato B, Coutinho LL, de Almeida VV, Cesar ASM. Identification of eQTLs using different sets of single nucleotide polymorphisms associated with carcass and body composition traits in pigs. BMC Genomics 2024; 25:14. [PMID: 38166730 PMCID: PMC10759680 DOI: 10.1186/s12864-023-09863-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024] Open
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.
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Affiliation(s)
- Felipe André Oliveira Freitas
- Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, 13416-000, SP, Brazil
- Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907, USA
- Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635- 900, SP, Brazil
| | - Simara Larissa Fanalli
- Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635- 900, SP, Brazil
| | - Janaína Lustosa Gonçales
- Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, 13416-000, SP, Brazil
| | | | - Mariah Castro Durval
- Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635- 900, SP, Brazil
| | - Fernanda Nery Ciconello
- Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, 13416-000, SP, Brazil
| | | | | | - Izally Carvalho Gervásio
- Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, 13416-000, SP, Brazil
| | - Julia Dezen Gomes
- Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, 13416-000, SP, Brazil
| | | | - Bárbara Silva-Vignato
- Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635- 900, SP, Brazil
| | - Luiz Lehmann Coutinho
- Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, 13416-000, SP, Brazil
| | - Vivian Vezzoni de Almeida
- College of Veterinary Medicine and Animal Science, Federal University of Goiás, Goiânia, 74001-970, GO, Brazil
| | - Aline Silva Mello Cesar
- Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, 13416-000, SP, Brazil.
- Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635- 900, SP, Brazil.
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