Identification of eQTLs using different sets of single nucleotide polymorphisms associated with carcass and body composition traits in pigs.

Freitas, Felipe André Oliveira; Brito, Luiz F; Fanalli, Simara Larissa; Gonçales, Janaína Lustosa; da Silva, Bruna Pereira Martins; Durval, Mariah Castro; Ciconello, Fernanda Nery; de Oliveira, Camila Sabino; Nascimento, Lucas Echevarria; Gervásio, Izally Carvalho; Gomes, Julia Dezen; Costa Monteiro Moreira, Gabriel; Silva-Vignato, Bárbara; Coutinho, Luiz Lehmann; de Almeida, Vivian Vezzoni; Cesar, Aline Silva Mello

doi:10.1186/s12864-023-09863-8

Article (Scientific journals)

Identification of eQTLs using different sets of single nucleotide polymorphisms associated with carcass and body composition traits in pigs.

Freitas, Felipe André Oliveira; Brito, Luiz F; Fanalli, Simara Larissa et al.

2024 • In BMC Genomics, 25 (1), p. 14

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https://hdl.handle.net/2268/341477

DOI
10.1186/s12864-023-09863-8

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38166730

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Keywords :

Expression quantitative trait loci; LD pruning; Sus scrofa; Transcriptomic; Swine/genetics; Animals; Phenotype; Muscle, Skeletal/metabolism; Genome-Wide Association Study; Body Composition/genetics; Quantitative Trait Loci; Polymorphism, Single Nucleotide; Body Composition; Muscle, Skeletal; Swine; Biotechnology; Genetics

Abstract :

[en] 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.

Disciplines :

Genetics & genetic processes

Author, co-author :

Freitas, Felipe André Oliveira; 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

Brito, Luiz F; 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

Fanalli, Simara Larissa; Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635- 900, SP, Brazil

Gonçales, Janaína Lustosa; Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, 13416-000, SP, Brazil

da Silva, Bruna Pereira Martins; Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, 13416-000, SP, Brazil

Durval, Mariah Castro; Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635- 900, SP, Brazil

Ciconello, Fernanda Nery; Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, 13416-000, SP, Brazil

de Oliveira, Camila Sabino; Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, 13416-000, SP, Brazil

Nascimento, Lucas Echevarria; Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, 13416-000, SP, Brazil

Gervásio, Izally Carvalho; Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, 13416-000, SP, Brazil

More authors (6 more)

Language :

English

Title :

Identification of eQTLs using different sets of single nucleotide polymorphisms associated with carcass and body composition traits in pigs.

Publication date :

2024

Journal title :

BMC Genomics

eISSN :

1471-2164

Publisher :

BioMed Central Ltd, England

Volume :

Issue :

Pages :

Peer reviewed :

Peer Reviewed verified by ORBi

Additional URL :

https://link.springer.com/content/pdf/10.1186/s12864-023-09863-8.pdf

Funders :

CNPq - Conselho Nacional de Desenvolvimento Científico e Tecnológico
CAPES - Coordenação de Aperfeicoamento de Pessoal de Nível Superior
FAPESP - Fundação de Amparo à Pesquisa do Estado de São Paulo

Funding text :

We thank the collaborative efforts between the University of S\u00E3o Paulo, Iowa State University, Federal University of Goi\u00E1s, and Purdue University. We are also grateful to DB Gen\u00E9tica Su\u00EDna (Patos de Minas, MG, Brazil) for providing help and financial support for carrying out this research project.

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