Gestational Feed Restriction Induces Differential Expression of Novel Long Non-Coding RNAs in Offspring Skeletal Muscle

Fetal programming via maternal nutrition during gestation plays a key role in shaping skeletal muscle development, directly affecting meat quality and production efficiency. This study examines how maternal feed restriction at different gestational stages alters the expression of novel long non-coding RNAs (lncRNAs) in the skeletal muscle of goat offspring. LncRNAs are emerging as important regulators of biological processes, including myogenesis, yet their role in fetal programming remains largely unexplored. Using RNA sequencing (RNA-Seq), we analyzed lncRNA expression in the Longissimus thoracis muscle of kids born to goats exposed to two feeding regimens: early gestation restriction (50% of maintenance from day 8–84 of gestation, then 100% until parturition; RM, n=6) and late gestation restriction (100% from day 8–84, then 50% until parturition; MR, n=8). RNA-Seq data underwent quality control, alignment, transcript assembly, and differential expression analysis using Cufflinks and FEELnc pipelines. Three differentially expressed (DE; FDR = 0.05) lncRNAs were identified and classified based on genomic context and potential regulatory function. The upregulated lncRNA_10996.1 in the RM group was linked to ENSCHIG00000020055 and ENSCHIG00000024132. Downregulated lncRNA_1180.1 and lncRNA_7992.1 were associated with ZNF546, PSMC4, SNORA65, ZNF79, LRSAM1, and ENSCHIG00000023017. These results suggest that maternal nutrition-induced shifts in lncRNA expression may influence muscle development through regulatory interactions with protein-coding genes. Our findings identify candidate lncRNAs as potential biomarkers and contribute novel insights into the molecular mechanisms underlying fetal programming in livestock. Overall design: RNA-Seq profilling of Longissimus thoracis muscle from newborn male goat kids.60 nulliparous Saanen dairy goats underwent estrous synchronization using prostaglandin administered at a 7-day interval, followed by artificial insemination with semen from a single male.The day of the insemination was considered the day 0 of the pregnancy and the beginning of the experiment. All the animals were kept under the same diet and management conditions for an adaptation period of 7 days. After that, the animals were randomly assigned to one of two feeding regimens: Restriction-Maintenance (RM) group (n = 6): fed 50% of maintenance requirements from days 8–84 of gestation, followed by 100% from day 85 to parturition. Maintenance-Restriction (MR) group (n = 8): fed 100% of maintenance requirements from days 8–84, followed by 50% from day 85 to parturition. Both groups received the same diet composition; only the timing of the restriction varied according to gestational stage.