Epigenetics

Influence of Maternal Nutrition on Alternative Splicing and Isoform Regulation in Skeletal Muscle of Beef Cattle Progeny

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Abstract

Maternal nutrition during gestation plays a critical role in fetal muscle development and long-term metabolic programming; however, its persistent molecular effects on offspring skeletal muscle remain incompletely understood. This study aimed to evaluate how maternal nutrition during gestation influences alternative splicing events and isoform regulation in the skeletal muscle of beef cattle progeny. A total of 126 pregnant Nellore cows were arranged into three groups of 42 animals each, balanced for age, body weight (BW), and body condition score. They were assigned to one of the three following dietary treatments: NP (mineral supplementation only at 0.03% of the BW per day), PP (protein-energy supplementation during late gestation at 0.3% of the BW per day), and FP (protein-energy supplementation throughout gestation at 0.3% of the BW per day). At 676 ± 28 days of age, muscle samples were collected from offspring for RNA sequencing. Differential gene expression (DGE) and differential mRNA transcript expression (DTE) analyses were performed using edgeR, while differential transcript usage (DTU) was evaluated using IsoformSwitchAnalyzeR. Functional overrepresentation analysis was conducted using g:Profiler. A total of 27,412 genes and 111,185 transcripts, including novel loci and isoforms, were identified. Gene-level differences were modest (16 genes), whereas transcript-level analyses revealed stronger effects. The FP vs. NP comparison exhibited the greatest impact, with 14 DTEs (FDR < 0.05 and |log₂FC| > 1) and 87 DTUs (FDR < 0.05 and |dIF| > 1), compared with 12 and 30 in PP vs. NP, and 10 and 3 in FP vs. PP, respectively. Isoform switching was observed in key genes, including SLC7A8, SLC25A30, SORBS3, and CDH13 genes, influencing coding potential, functional domains, and mRNA stability, with potential consequences for amino acid transport, cytoskeletal organization, and muscle regeneration. Enrichment analyses highlighted significant metabolic pathways related to amino acid and biotin metabolism, intracellular trafficking, and immune regulation. Overall, prenatal nutrition, particularly FP vs. NP comparison, modulates offspring skeletal muscle predominantly through transcript usage and alternative splicing events. These findings demonstrate that long-term molecular adaptation to maternal diet occurs primarily at the isoform level rather than through global gene expression changes, underscoring the importance of integrating DGE, DTE, and DTU analyses to fully understand prenatal nutritional programming mechanisms in livestock.

Keywords: 2026

How to Cite:

Brito, L., Cánovas, à., Carvalho, F., Cesar, A., Diniz, W., Ferraz, J., Fukumasu, H., Polizel, G., Ramà­rez-Zamudio, G. & Santana, M., (2026) “Influence of Maternal Nutrition on Alternative Splicing and Isoform Regulation in Skeletal Muscle of Beef Cattle Progeny”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2283465. doi: https://doi.org/10.31274/wcgalp.23500

Rights: 1