Using Transcriptomics to Investigate Pathways Influencing Female Fertility in Beef Cattle

Abstract

Female fertility and reproductive success are the main drivers of economic efficiency in cattle operations. Herein, we performed two independent studies to investigate the molecular basis of fertility in beef cattle. First, we used a transcriptomics approach to identify differentially expressed genes (DEGs) in the endometrium of beef heifers classified as fertile (n = 7) or sub-fertile (n = 5). We identified 798 DEGs between groups involved with biological processes and pathways important for early pregnancy establishment. Further, we used public RNA-Seq data from uterine luminal epithelial cells of cows to identify expression quantitative trait loci (eQTLs). These eQTLs (4,676 cis and 7,682 trans eQTL, FDR < 0.05) modulated the expression of transcription factors and genes previously reported as differentially expressed and associated with pregnancy outcomes in Bos indicus-influenced crossbred cows. Over-represented pathways affected by eQTLregulated genes included metabolism, immune response, and hormone signaling (estrogen and GnRH) (p-value < 0.01). Interestingly, some of the eQTLs overlapped with 13 reproduction-related traits from the CattleQTLdb (FDR < 0.05). Altogether, this work unveils potential novel candidate genes and regulatory variants affecting female fertility in beef cattle. However, further research is required to validate both DEGs and eQTLs reported here.