RNA Sequencing of Equine Endometrium during Maternal Recognition of Pregnancy

Equine maternal recognition of pregnancy (MRP) is a process that remains unknown. Traditional gene expression analyses have failed to reveal any possible candidates for the mechanism responsible, therefore, we evaluated equine endometrium via RNA Sequencing during MRP (which occurs around day 12 post-ovulation, PO). The objective was to evaluate endometrial gene expression changes based upon pregnancy status. This experiment utilized a cross-over design with each mare serving as as a pregnant and non-mated control (n=3/day) on days 9, 11, and 13 PO. Mares were randomly assigned to a collection day and each provided endometrial samples for a pregnant and non-mated cycle. Samples were snap frozen and stored until RNA isolation. Large RNA was isolated with Tri Reagent. Sequencing libraries were prepared using the Illumina TruSeq RNA Sample Preparation kit and sent to the University of California, Berkely, for RNASeq. Sequence reads were mapped and annotated using CLCBio software. Differential gene expression was analyzed using SAS via student’s paired t-test for comparing pregnancy status within days following calculation and application of the false discovery rate. On day 9 there were 203 genes, on day 11 there were 320 genes, and on day 13 there were 146 genes identified as significantly differentially expressed. Seven genes were differentially expressed across all three days. These RNASeq data are the first to identify differentially or uniquely expressed genes in equine endometrium during early pregnancy. These results may lead to the identification of pathways involved in maternal recognition of pregnancy in the mare.