The Effects of Nutrition on the Transcriptome and Epigenome: Alternative Breeding Strategy

A substantial challenge currently facing the food animal industry is developing strategies to secure a global and safe food supply to meet the population demands. Current methods in animal genetics are focused on genome-wide association studies aimed at the identification of genes affecting production and reproduction traits to be used in marker-assisted selection. Recently, we demonstrated in sheep and cattle that maternal diet before and during the different stages of pregnancy can induce transcriptomic and epigenetic changes in the fetus and offspring, which can lead to subsequent postnatal altered phenotypes such as growth and body composition effects and diseases. In sheep, we evaluated the effects of different maternal diets on the transcriptome of fetal tissues using RNA-Seq analysis. For example, in muscle, a total of 224 and 823 genes showed differential expression (FDR < 0.05) between dried corn distiller’s grains (DG) vs. corn (CN), and hay (HY) vs. CN, respectively. Expression analysis of nine imprinted genes and three DNA methylatransferase genes showed significant effects of the different maternal diets on the expression and DNA methylation of these genes. In cattle, we showed that a subtle difference in methionine supplementation in maternal diet before pregnancy was sufficient to cause significant changes in the transcriptome of the embryos. These findings provide evidence that maternal diet before and during pregnancy can modulate gene expression in fetuses. Thus, in addition to marker-assisted selection strategies currently used in animal breeding, nutrition-assisted selection provides an alternative or complementary strategy that can be used in breeding schemes.