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Background  Maternal nutrition has been highlighted as one of the main factors affecting intra-uterine environment. The increase in nutritional requirements by beef cows during late gestation can cause nutritional deficiency in the fetus and impact the fetal regulation of genes associated with myogenesis and immune response.    Methods  Forty days before the expected calving date, cows were assigned to one of two diets: 100% (control) or 70% (restricted group) of the daily energy requirement. Muscle samples were collected from 12 heifers and 12 steers, and blood samples were collected from 12 steers. The objective of this work was to identify and to assess the biological relevance of differentially expressed genes (DEG) in the skeletal muscle and blood of beef calves born from cows that experienced [or not] a 30% energy restriction during the last 40 days of gestation.    Results  A total of 160, 164, and 346 DEG ( q -value< 0.05) were identified in the skeletal muscle for the effects of diet, sex, and diet-by-sex interaction, respectively. For blood, 452, 1392, and 155 DEG were identified for the effects of diet, time, and diet-by-time interaction, respectively. For skeletal muscle, results based on diet identified genes involved in muscle metabolism. In muscle, from the 10 most DEG down-regulated in the energy-restricted group (REST), we identified 5 genes associated with muscle metabolism and development:  SLCO3A1 ,  ATP6V0D1 ,  SLC2A1 ,  GPC4 , and  RASD2 . In blood, among the 10 most DEG, we found genes related to response to stress up-regulated in the REST after weaning, such as  SOD3  and  INO80D , and to immune response down-regulated in the REST after vaccination, such as  OASL, KLRF1 , and  LOC104968634.Conclusion  In conclusion, maternal energy restriction during late gestation may limit the expression of genes in the muscle and increase expression in the blood of calves. In addition, enrichment analysis showed that a short-term maternal energy restriction during pregnancy affects the expression of genes related to energy metabolism and muscle contraction, and immunity and stress response in the blood. Therefore, alterations in the intra-uterine environment can modify prenatal development with lasting consequences to adult life.    Electronic supplementary material  The online version of this article (10.1186/s12864-018-5089-8) contains supplementary material, which is available to authorized users.

Impact of energy restriction during late gestation on the muscle and blood transcriptome of beef calves after preconditioning