Transcriptional downregulation of ABC transporters is related to follicular degeneration after vitrification and in vitro culture of ovine ovarian tissue

Whole genome sequencing reveals that five genes are related to BW trait in sheep

BW is an important economic trait in sheep that influences growth and development. Currently, most studies have used a single approach to screen genes associated with BW traits in sheep. To address this limitation, we conducted a genome-wide association study (GWAS) covering four different BW periods: birth, weaning, 6 months, and 12 months. Five new candidate genes: MAP3K1, ANKRD55, ABCB1, MEF2C and TRNAW-CCA-87 were screened using a combination of GWAS and quantitative trait loci analysis in sheep. Additionally, five genes were subjected to Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway enrichment analyses. These genes were primarily enriched in pathways related to growth hormone and energy metabolism. The results demonstrated that the above genes potentially influenced the growth and development of sheep. The five new candidate genes are closely related to the BW trait in sheep, which will be valuable for understanding the genetic mechanisms underlying BW traits and for guiding sheep breeding.

Identification of copy number variation in Tibetan sheep using whole genome resequencing reveals evidence of genomic selection

BACKGROUND

Copy number variation (CNV) is an important source of structural variation in the mammalian genome. CNV assays present a new method to explore the genomic diversity of environmental adaptations in animals and plants and genes associated with complex traits. In this study, the genome-wide CNV distribution characteristics of 20 Tibetan sheep from two breeds (10 Oula sheep and 10 Panou sheep) were analysed using whole-genome resequencing to investigate the variation in the genomic structure of Tibetan sheep during breeding.

RESULTS

CNVs were detected using CNVnator, and the overlapping regions of CNVs between individual sheep were combined. Among them, a total of 60,429 CNV events were detected between the indigenous sheep breed (Oula) and the synthetic sheep breed (Panou). After merging the overlapping CNVs, 4927 CNV regions (CNVRs) were finally obtained. Of these, 4559 CNVRs were shared by two breeds, and there were 368 differential CNVRs. Deletion events have a higher percentage of occurrences than duplication events. Functional enrichment analysis showed that the shared CNVRs were significantly enriched in 163 GO terms and 62 KEGG pathways, which were mainly associated with organ development, neural regulation, immune regulation, digestion and metabolism. In addition, 140 QTLs overlapped with some of the CNVRs at more than 1 kb, such as average daily gain QTL, body weight QTL, and total lambs born QTL. Many of the CNV-overlapping genes such as PPP3CA, SSTR1 and FASN, overlap with the average daily weight gain and carcass weight QTL regions. Moreover, VST analysis showed that XIRP2, ABCB1, CA1, ASPA and EEF2 differed significantly between the synthetic breed and local sheep breed. The duplication of the ABCB1 gene may be closely related to adaptation to the plateau environment in Panou sheep, which deserves further study. Additionally, cluster analysis, based on all individuals, showed that the CNV clustering could be divided into two origins, indicating that some Tibetan sheep CNVs are likely to arise independently in different populations and contribute to population differences.

CONCLUSIONS

Collectively, we demonstrated the genome-wide distribution characteristics of CNVs in Panou sheep by whole genome resequencing. The results provides a valuable genetic variation resource and help to understand the genetic characteristics of Tibetan sheep. This study also provides useful information for the improvement and breeding of Tibetan sheep in the future.

Three-Dimensional Culture for In Vitro Folliculogenesis in the Aspect of Methods and Materials

In vitro ovarian follicle culture is a reproduction technique used to obtain fertilizable oocytes, for overcoming fertility issues due to premature ovarian failure. This requires the establishment of an in vitro culture model that is capable of better simulating the in vivo ovarian growth environment. Two-dimensional (2D) culture systems have been successfully set up in rodent models. However, they are not suitable for larger animal models as the follicles of larger animals cultured in 2D culture systems often lose their shape due to dysfunction in the gap junctions. Three-dimensional (3D) culture systems are more suitable for maintaining follicle architecture, and therefore are proposed for the successful in vitro culturing of follicles in various animal models. The role of different methods, scaffolds, and suspension cultures in supporting follicle development has been studied to provide direction for improving in vitro follicle culture technologies. The three major strategies for in vitro 3D follicle cultures are discussed in this article. First, the in vitro culture systems, such as microfluidics, hanging drop, hydrogels, and 3D-printing, are reviewed. We have focused on the 3D hydrogel system as it uses different materials for supporting follicular growth and oocyte maturation in several animal models and in humans. We have also discussed the criteria used for biomaterial evaluations such as solid concentration, elasticity, and rigidity. In addition, future research directions for advancing in vitro 3D follicle culture system are discussed. Impact statement A new frontier in assisted reproductive technology is in vitro tissue or follicle culture, particularly for fertility preservation. The in vitro three-dimensional (3D) culture technique enhances follicular development and provides mature oocytes, overcoming the limitations of traditional in vitro two-dimensional cultures. Polymer biomaterials have good compatibility and retain the physiological structure of follicles in the 3D culture system. Utilizing hybrid in vitro culture materials by merging matrix, hydrogel, and unique patterned materials may facilitate follicular growth in the future.