The high concentration of secondary branched wool follicles is a distinctive feature of the Merino sheep. At present, the molecular control of the development and branching of secondary wool follicles (SF) remains elusive. To reveal the potential genes associated with the development of hair follicles, we investigated the characteristics of prenatal and postnatal development of wool follicles, and the transcriptional expression profile in fetuses/lambs from dams under either maternal maintenance or sub-maintenance (75% maintenance) nutrition. The density of SF and the ratio of SF to primary wool follicles (PF) were reduced (p < 0.05) in fetuses from day 105 to 135 of gestation under sub-maintenance nutrition. Differentially expressed genes were enriched in the binding, single-organism process, cellular process, cell and cell part Gene Ontology (GO) functional categories and metabolism, apoptosis, and ribosome pathways. Four candidate genes, SFRP4, PITX1, BAMBI, and KRT16, which were involved in secondary wool follicles branching and development, were identified. Our results indicate that nutritional intervention imposed on pregnant ewes by short-term sub-maintenance nutrition could provide a strategy for the study of wool follicle development. Overall insight into the global gene expression associated with SF development can be used to investigate the underlying mechanisms of SF branching in Merino sheep.

In mammalian embryonic development, blastocyst hatching is essential for normal implantation and development of the fetus. We reported previously that blastocysts hatching out of the zona pellucida (ZP) exhibited site preferences that were associated with pregnancy outcomes. To characterize these site differences, we analyzed the transcriptomes in the following developing mouse blastocysts within 16 h of hatching: expanding (E), hatching from the A-site (A), B-site (B), and C-site (C), hatched (H), and non-hatching (N). By principal component analysis and hierarchical cluster analysis, we determined that the gene expression profiles of A and B blastocysts, which resulted in good fertility, clustered closely. C and N blastocysts, which resulted in poor fertility, clustered closely, but distantly from A and B. Embryos hatched at B- vs. C-sites, with good vs. poor pregnancy, showed 178 differentially expressed genes (DEGs), mainly involved in immunity, which correlated positively with birth rate. These DEGs were primarily regulated by transcription factors TCF24 and DLX3. During blastocyst hatching, immune-related genes were regulated, such as Ptgs1, Lyz2, Il-α, Cfb (upregulated) and Cd36 (downregulated). By immunofluorescence staining, we found C3 and IL-1β on the extra-luminal surface of the trophectoderm of the hatched blastocyst, suggesting that they play a role in maternal-fetal interactions. As the blastocysts developed from the expanding to the fully hatched state, 307 DEGs were either upregulated by transcription factor ATOH8 or downregulated by SPIC to switch on immune pathways. Based on the hatching outcome, we identified three transcription patterns in developing blastocysts, with complex changes in the transcriptional regulation network of failed hatched blastocysts vs. successfully hatched blastocysts. We developed a LASSO regression-based model using DEGs Lyz2, Cd36, Cfb, and Cyp17a1 to predict implantation success. This study revealed the diverse, multidimensional developmental fates of blastocysts during short-term hatching and indicated that the immune properties of the embryo had a major effect on blastocyst hatching outcomes. We suggest that transcriptional changes and their regulation during the development of the preimplantation blastocyst affect implantation. This study contributes to our understanding of the role of transcriptional changes in mammalian embryonic development during hatching and their effect on maternal-fetal interactions.