Identification of eQTLs and differential gene expression associated with fetal programming in beef cattle

This study assessed differential gene expression and identified expression quantitative trait loci (eQTLs) from samples of Longissimus lumborum muscle from bulls at 15 months of age submitted to different prenatal nutrition. Upon confirmation of pregnancy, 126 dams were separated into three diet tre...

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Bibliographic Details
Published in:Journal of applied genetics 2022-12, Vol.63 (4), p.717-728
Main Authors: Polizel, Guilherme Henrique Gebim, Cesar, Aline Silva Mello, Cracco, Roberta Cavalcante, Fernandes, Arícia Christofaro, Reginato, Gustavo Morandini, Xavier, Pedro Luiz Porfirio, Mortari, Isabela, Furlan, Édison, Fukumasu, Heidge, Santana, Miguel Henrique de Almeida
Format: Article
Language:English
Subjects:
Animal Genetics and Genomics
Animal Genetics • Original Paper
Beef cattle
Biomedical and Life Sciences
Cattle
computer software
energy
Fetuses
Gene expression
gene expression regulation
Gene mapping
gene ontology
Gene set enrichment analysis
Genes
Genetic aspects
genotype
Genotypes
genotyping
Human Genetics
Life Sciences
Linkage analysis
Linkage disequilibrium
longissimus muscle
Metabolic pathways
Microbial Genetics and Genomics
Muscles
Nellore
Nutrition
Plant Genetics and Genomics
Pregnancy
Prenatal experience
principal component analysis
Principal components analysis
protein supplements
Quantitative trait loci
quantitative traits
sequence analysis
Skeletal muscle
transcriptome
Transcriptomes
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Summary:This study assessed differential gene expression and identified expression quantitative trait loci (eQTLs) from samples of Longissimus lumborum muscle from bulls at 15 months of age submitted to different prenatal nutrition. Upon confirmation of pregnancy, 126 dams were separated into three diet treatments varying the period of inclusion of energy protein supplementation (NP, PP, and FP). At calving, 63 males were genotyped with GGP LD BeadChip. The skeletal muscle of 15 bulls was sequenced (RNA-seq) at 15 months of age. The EdgeR package was used for differential gene expression and principal component analysis (PCA), and the Matrix eQTL package was used for the eQTLs analysis (R statistical). The functional enrichment analysis was performed using the MetaCore® software. No genes differentially expressed were found between treatments (FDR > 0.05); nevertheless, we found 179 cis-tag-eQTLs and 20,762 trans-tag-eQTLs (FDR 
ISSN:1234-1983
2190-3883
DOI:10.1007/s13353-022-00711-1