Single-Cell RNA-Seq Revealed the Gene Expression Pattern during the In Vitro Maturation of Donkey Oocytes

Differential transcript usage across mammalian oocytes at the germinal vesicle and metaphase II stages

Ongoing progress in mRNA-Sequencing technologies has significantly contributed to the refinement of assisted reproductive technologies. However, the prior investigations have predominantly concentrated on alterations in overall gene expression levels, thereby leaving a considerable gap in our understanding of the influence of transcript isoform expression on fundamental cellular mechanisms of oocytes. Given the efficacy of differential transcript usage (DTU) analysis to address such knowledge, we conducted comprehensive DTU analysis utilizing mRNA-Seq datasets of germinal vesicle (GV) and metaphase II (MII) oocytes across six mammalian species from the SRA database, including cow, donkey, horse, human, mouse, and pig. To further illuminate the roles of these genes, we also conducted a rigorous Gene Ontology (GO) term enrichment analysis. While the DTU analysis of each species exhibited several genes with alterations in their transcript isoform usage, referred to as DTU genes, this study focused on only ten cross-species DTU genes sharing among a minimum of five distinct species (FDR≤0.05). These cross-species DTU genes were as follows: ABCF1, CDC6, CFAP36, CNOT10, DNM3, IWS1, NBN, NDEL1, RAD50 and ZCCHC17. GO term enrichment analysis unveiled the alignment of these cross-species DTU gene functions with RNA and cell-cycle control mechanisms across diverse mammalian species, thereby suggesting their vital roles during oocyte maturation. Further exploration of the transcript isoforms of these genes hence bore the potential to uncover novel transcript isoform markers for future reproductive technologies in both human and animal contexts.

Transcriptome analyses reveal transcriptional profiles of horse oocytes before and after in vitro maturation

Oocyte in vitro maturation is necessary for the study and application of animal-assisted reproduction technology in animal reproduction and breeding. The comprehensive transcriptional profile of equine oocyte maturated in vitro has not been fully mined yet, which makes many key transcriptional events still unidentified. Here, Smart-seq2 was performed to analyse the gene expression pattern and the underlying regulatory mechanism of horse germinal vesicle (GV) and in vitro metaphase II (MII) oocytes. The results showed that 6402 genes (2640 up-regulated and 3762 down-regulated in MII samples compared to GV) and 4021 lncRNA transcripts (1210 up-regulated and 2811 down-regulated in MII samples compared to GV) were differentially expressed in GV and MII oocytes. Further, GO and KEGG analysis found that differentially expressed mRNAs and lncRNAs were mainly enriched in the pathways related to energy and lipid metabolism. In addition, LGALS3 was found a key gene in mediating the regulation of oocyte meiosis recovery and fertilization ability. This study provides novel knowledge about gene expression and energy metabolism during equine oocyte maturation and a reference for the further study and application of assisted reproductive technology in horse reproduction and breeding.

Exploring Genetic Markers: Mitochondrial DNA and Genomic Screening for Biodiversity and Production Traits in Donkeys

Donkeys (Equus asinus) play a pivotal role as essential livestock in arid and semi-arid regions, serving various purposes such as transportation, agriculture, and milk production. Despite their significance, donkey breeding has often been overlooked in comparison to other livestock species, resulting in limited genetic improvement programs. Preserving donkey genetic resources within each country necessitates the establishment of breed conservation programs, focusing on managing genetic diversity among populations. In recent years, significant strides have been made in sequencing and analyzing complete mitochondrial DNA (mtDNA) molecules in donkeys. Notably, numerous studies have honed in on the mitochondrial D-loop region, renowned for its remarkable variability and higher substitution rate within the mtDNA genome, rendering it an effective genetic marker for assessing genetic diversity in donkeys. Furthermore, genetic markers at the RNA/DNA level have emerged as indispensable tools for enhancing production and reproduction traits in donkeys. Traditional animal breeding approaches based solely on phenotypic traits, such as milk yields, weight, and height, are influenced by both genetic and environmental factors. To overcome these challenges, genetic markers, such as polymorphisms, InDel, or entire gene sequences associated with desirable traits in animals, have achieved widespread usage in animal breeding practices. These markers have proven increasingly valuable for facilitating the selection of productive and reproductive traits in donkeys. This comprehensive review examines the cutting-edge research on mitochondrial DNA as a tool for assessing donkey biodiversity. Additionally, it highlights the role of genetic markers at the DNA/RNA level, enabling the informed selection of optimal production and reproductive traits in donkeys, thereby driving advancements in donkey genetic conservation and breeding programs.

Advances in Oocyte Maturation In Vivo and In Vitro in Mammals

The quality and maturation of an oocyte not only play decisive roles in fertilization and embryo success, but also have long-term impacts on the later growth and development of the fetus. Female fertility declines with age, reflecting a decline in oocyte quantity. However, the meiosis of oocytes involves a complex and orderly regulatory process whose mechanisms have not yet been fully elucidated. This review therefore mainly focuses on the regulation mechanism of oocyte maturation, including folliculogenesis, oogenesis, and the interactions between granulosa cells and oocytes, plus in vitro technology and nuclear/cytoplasm maturation in oocytes. Additionally, we have reviewed advances made in the single-cell mRNA sequencing technology related to oocyte maturation in order to improve our understanding of the mechanism of oocyte maturation and to provide a theoretical basis for subsequent research into oocyte maturation.

Progesterone Promotes In Vitro Maturation of Domestic Dog Oocytes Leading to Successful Live Births

Gene-edited dogs are promising models for biomedical research because they have hundreds of genetic diseases that are similar to humans. A common method for producing gene-edited dogs is assisted reproductive technology (ART) using in vivo oocytes or embryos, but it is much more inefficient and has a higher cost. ART for dogs has lagged mostly because of the lack of an efficient in vitro maturation system. Because early maturation of canine oocytes occurs in follicles with extremely high concentrations of progesterone (P4), we hypothesize that P4 has an important role during maturation. In this study, we obtained ovaries of female dogs and collected cumulus−oocyte complexes, which were cultured in vitro in microdrops containing different P4 concentrations (0, 10, 40, 100 or 200 µg/mL). We found that 40 µg/mL P4 produced the highest oocyte maturation rate (29.7% ± 7.1%, p < 0.05). We also evaluated the quality of in vitro matured oocytes by in vitro fertilization and single-cell RNA sequencing, and both indicated an improvement in oocyte developmental potential. In conclusion, we successfully obtained the first live dogs using in vitro matured oocytes by adding P4 to optimize the in vitro maturation system of canine oocytes, and established a new and low-cost method to produce dogs via in vitro maturation and in vitro fertilization.

Embryo production by in vitro fertilization in wild ungulates: progress and perspectives

Wild ungulates are of fundamental importance for balancing ecosystems, as well as being the species of economic interest. Increasing concern over the accelerated population reduction of these species has resulted in the development of assisted reproduction techniques, such as in vitro fertilization (IVF), as a tool for conservation and multiplication. In the present scenario, IVF protocols were developed based on the methodologies used for domestic ungulates. Nevertheless, owing to the physiological and reproductive differences among the species, several factors associated with IVF and its relationship with the characteristics of the species of interest require clarification. In vitro conditions for the collection and selection of female and male gametes, oocyte maturation, sperm capacitation, co-incubation of gametes, and embryonic development can influence IVF results. Therefore, the present review considers the main advances in the methodologies already used for wild ungulates, emphasizing the strategies for improving the protocols to obtain better efficiency rates. Additionally, we discuss the conditions of each IVF stage, with emphasis on aspects related to in vitro manipulation and comparability with the protocols for domestic ungulates.

Comparative Transcriptomics Uncover the Uniqueness of Oocyte Development in the Donkey

The donkey is an important domestic animal, however the number of donkeys world-wide is currently declining. It is therefore important to protect their genetic resources and to elaborate the regulatory mechanisms of donkey reproduction, particularly, oocyte development. Here, we adopted comparative transcriptomic analysis and weighted gene co-expression network analysis (WGCNA) to uncover the uniqueness of donkey oocyte development compared to cattle, sheep, pigs, and mice, during the period from germinal vesicle (GV) to metaphase II (MII). Significantly, we selected 36 hub genes related to donkey oocyte development, including wee1-like protein kinase 2 (WEE2). Gene Ontology (GO) analysis suggested that these genes are involved in the negative regulation of cell development. Interestingly, we found that donkey specific differentially expressed genes (DEGs) were involved in RNA metabolism and apoptosis. Moreover, the results of WGCNA showed species-specific gene expression patterns. We conclude that, compared to other species, donkey oocytes express a large number of genes related to RNA metabolism to maintain normal oocyte development during the period from GV to MII.