17The majority of pregnancy loss in ruminants occurs during the preimplantation stage, which is thus 18 the most critical period determining reproductive success. While ovulation rate is the major 19 determinant of litter size in sheep, interactions among the conceptus, corpus luteum and endometrium 20 are essential for pregnancy success. To evaluate the role of reproductive tract function in sheep 21 fertility, we performed a comparative transcriptome study by sequencing total RNA (mRNA and 22 miRNA) from corpus luteum (CL) and endometrium tissues collected during the preimplantation 23 stage of pregnancy in Finnsheep, Texel and F1 crosses. A total of 21,287 genes and 599 miRNAs 24were expressed in our dataset. Ten out of the top 25 most highly expressed genes were shared across 25 tissues, indicating the complementary functions of the CL and endometrium. Moreover, highly 26 expressed autosomal genes in the endometrium and CL were associated with biological processes 27 such as progesterone formation (STAR and HSD3B1) in the CL and facilitation of maternal 28 recognition of pregnancy, trophoblast elongation and implantation (LGALS15, CST3, CST6, and 29 EEF1A1) in the endometrium. In the CL, a group of sialic acid-binding immunoglobulin (Ig)-like 30 lectins (Siglecs), solute carriers (SLC13A5, SLC15A2, SLC44A5) and chemokines (CCL5, CXCL13, 31 CXCL9) were upregulated in Finnsheep, while several multidrug resistance-associated proteins 32(MRPs) were upregulated in Texel ewes. We also identified a novel ERV gene located in a reduced 33FecL locus that is associated with sheep prolificacy and is upregulated in prolific Finnsheep. 34Moreover, we report, for the first time in any species, several genes that are active in the CL during 35 early pregnancy (including SIGLEC13, SIGLEC14, SIGLEC6, MRP4, and CA5A). Importantly, 36 functional analysis of differentially expressed genes suggested that Finnsheep have a better immune 37