Identification of Circular RNAs in Hypothalamus of Gilts during the Onset of Puberty

Characterization and Comparative Analysis of Whole-Transcriptome Sequencing in High- and Low-Fecundity Chongming White Goat Ovaries during the Estrus Phase

Reproductive performance is one of the most important economic traits in the goat industry. Increasing the number of goats is an effective measure to improve production efficiency and reduce production costs. Ovaries are important reproductive organs in female mammals that directly affect the estrous cycle and reproductive abilities. Understanding the complex transcription network of non-coding RNAs (lncRNAs, circRNAs, and miRNAs) and messenger RNA (mRNA) could lead to significant insights into the ovarian regulation of the reproductive processes of animals. However, the whole-transcriptome analysis of the non-coding RNAs and mRNA of the ovaries in Chongming white goats between high-fecundity (HP) and low-fecundity (LP) groups is limited. In this study, a whole-transcriptome sequencing approach was used to identify lncRNA, circRNA, miRNA, and mRNA expression in the ovaries of Chongming white goats during the estrus phase using RNA-Seq technology. More than 20,000 messenger RNAs (mRNAs), 10,000 long non-coding RNAs (lncRNAs), 3500 circular RNAs (circRNAs), and 1000 micro RNAs (miRNAs) were identified. A total of 1024 differential transcripts (724 mRNAs, 112 lncRNAs, 178 circRNAs, and 10 miRNAs) existing between the HP and the LP groups were revealed through a bioinformatics analysis. They were enriched in the prolactin signaling pathway, the Jak-STAT signaling pathway, and the GnRH signaling pathway, as well as various metabolic pathways. Differentially expressed mRNAs (such as LYPD6, VEGFA, NOS3, TNXB, and EPHA2) and miRNAs (such as miR-10a-5p) play key roles in the regulation of goat ovaries during the estrus phase. The enrichment of pathways related to reproduction, such as the Hippo, Hedgehog, PI3K-AKT, and MAPK signaling pathways, suggests that they might be involved in the prolificacy of goat ovaries. Overall, we identified several gene modules associated with goat fecundity and provided a basis for a molecular mechanism in the ovaries of Chongming white goats.

Transcriptomic Analysis Reveals Differentially Expressed Circular RNAs Associated with Fecundity in the Sheep Hypothalamus with Different FecB Genotypes

Circular RNAs (circRNAs) are a specific type of noncoding RNA, and some have defined roles in cellular and biological processes. However, little is known about the role of circRNAs in follicular development in sheep with FecB (fecundity Booroola) mutations. Here, the expression profiles of circRNAs were investigated using RNA sequencing (RNA-seq) in the follicular phase (F) and the luteal phase (L) of FecB mutant homozygous (BB) and wild-type (WW) Small Tail Han sheep. A total of 38,979 circRNAs were identified, and 314, 343, 336, and 296 of them were differentially expressed (DE) between BB_F and BB_L, WW_F and WW_L, BB_F and WW_F, and BB_L and WW_L, respectively. The length, type, and chromosome distribution of the circRNAs and the expression characteristic between the circRNAs and their host genes in the sheep hypothalamus were ascertained. Enrichment analysis showed that the host genes of DE circRNAs in the follicular and luteal phases were annotated to MAPK, gap junctions, progesterone-mediated oocyte maturation, oocyte meiosis, and other hormone-related signaling pathways, and the different FecB genotypes were annotated to the gap junctions, circadian entrainment, MAPK, and other hormone-related signaling pathways. The competing endogenous RNA network prediction revealed that the 129 target miRNAs might be bound to 336 DE circRNAs. oar_circ_0000523 and oar_circ_0028984, which were specifically expressed during the follicular phase in the BB genotype sheep, probably acted as miRNA sponges involved in the regulation of LH synthesis and secretion. This study reveals the expression profiles and characterization of circRNAs at two phases of follicular development considering different FecB genotypes, thereby providing an improved understanding of the roles of circRNAs in the sheep hypothalamus and their involvement in follicular development and ovulation.

Integrated Proteotranscriptomics of the Hypothalamus Reveals Altered Regulation Associated with the FecB Mutation in the BMPR1B Gene That Affects Prolificacy in Small Tail Han Sheep

The litter size and ovulation rate are different among ewes of different FecB genotypes in Small Tail Han sheep. These variants in reproductive phenotypes may be regulated by hormones released by the hypothalamic-pituitary-ovarian axis. However, there have been few reports on the hypothalamus regarding regulating an increase in ovulation in sheep with FecB mutation at different estrous stages. Thus, we examined the abundance of hypothalamus tissue protein profiles of six FecB mutant homozygous (BB) and six wild-type (WW) ewes at the luteal and follicular phases. We determined this abundance by tandem mass tag-based quantitative analysis and parallel reaction monitoring methods. Furthermore, an integrated proteotranscriptomic analysis was performed by the Data Integration Analysis for Biomarker discovery using the latent variable approaches for Omics studies (DIABLO) framework to examine biological processes and pathway alterations by the FecB mutant. The abundance of 154 proteins was different between the two estrous stages. Growth hormone and prolactin were particularly enriched in the neuroactive ligand-receptor interactions, the prolactin signaling pathway, and the PI3K-Akt signaling pathway which are related to hypothalamic function and reproduction. We combined proteome and transcriptome data from different estrous stages and genotypes. There is a high correlation (Pearson correlation coefficient = 0.99) between the two datasets in the first two components. We applied the traditional single-omic multivariate approach to obtain differentially abundant proteins and differentially expressed genes. The major fertility related biomarkers were selected using the two approaches mentioned above. Several key pathways (GABAergic synapse, neuroactive ligand-receptor interaction, estrogen and MAPK signaling pathways) were enriched, which are central to gonadotrophin-releasing hormone (GnRH) secretion and reproduction. A higher level of gamma-aminobutyric acid type A receptor subunit alpha1 (GABRA1) and gamma-aminobutyric acid type A receptor subunit beta2 (GABRB2) expression was observed in BB ewes as compared to WW ewes. This finding suggested that a greater production of GnRH during follicular development in BB ewes may explain the higher mature follicle number in mutant ewes. FKBP prolyl isomerase 1A (FKBP1A), which was a major feature factor in the proteome selected by DIABLO, was an important switch for activating the transforming growth factor beta (TGFβ) pathway, and its expression was higher in the WW ewes than in the BB ewes. We suggest that BB sheep maintain TGFβ pathway activity by reducing FKBP1A protein abundance. This innovative data integration in the hypothalamus may provide fresh insight into the mechanisms by which the FecB mutation affects sheep fertility, while providing novel biomarkers related to reproductive endocrinology in sheep breeding.

Determination of puberty in gilts: contrast of diagnostic methods

BACKGROUND

Early onset of a gilt´s puberty is needed for adequate economic performance in farms, because it indicates her reproductive performance and longevity. Therefore, an effective diagnosis is needed. Our purpose was to compare different procedures (external characteristics, blood progesterone analysis and ultrasonography diagnosis) to detect puberty in 70 gilts (Topigs TN70; 240 days old) on farm conditions. Postmortem examination was the standard reference. Multiple logistic regression analysis was used to identify which combination of independent variables (predictors) best predicts the status of gilts.

RESULTS

Puberty (46/70 gilts; 65.71%) was characterized by the presence of follicles larger than 6 mm, corpus albicans, corpus rubrum, and corpus luteum (postmortem examination). Vaginal length, body condition, backfat, carcass weight and progesterone blood concentration were significantly higher in pubertal than prepubertal gilts (P < 0.05). Two types of ultrasonography equipment (DELTA and W3) were compared and performed by the same senior technician (V1). The results obtained by two technicians with different levels of experience (V1 and V2, a junior technician) using W3 were also compared. Ultrasonography provided better results than other diagnostic techniques, although the effectiveness of the ultrasonography changed with technological improvements and with increased expertise of technicians. The most accurate results were found by V1/DELTA (Nagelkerke´s R² = 0.846; Sensitivity = 0.956; Specificity = 0.958; Positive predictive value = 0.978; Negative predictive value = 0.920; Area under ROC curve = 0.957). Results using the W3 equipment could be improved when used in conjunction with vaginal length (V1; Nagelkerke´s R² = 0.834; Sensitivity = 0.933; Specificity = 0.958; Positive predictive value = 0.977; Negative predictive value = 0.885; Area under ROC curve = 0.972) or progesterone concentration (V2; Nagelkerke´s R² = 0.780; Sensitivity = 0.955; Specificity = 0.826; Positive predictive value = 0.915; Negative predictive value = 0.905; Area under ROC curve = 0.970).

CONCLUSIONS

Ultrasonography provided better results than other diagnostic techniques. The effectiveness of the ultrasonography changes with technological improvements and with increased expertise of technicians. Results using the W3 equipment could be improved when used along with vaginal length (V1) or progesterone concentration (V2). Accuracy parameters are a guide to choose puberty diagnosis, but the farms must also evaluate effect on gilts, ease and cost of administration.

Transcriptome Sequencing-Based Mining of Genes Associated With Pubertal Initiation in Dolang Sheep

Improving the fertility of sheep is an important goal in sheep breeding as it greatly increases the productivity. Dolang sheep is a typical representative breed of lamb in Xinjiang and is the main local sheep breed and meat source in the region. To explore the genes associated with the initiation of puberty in Dolang sheep, the hypothalamic tissues of Dolang sheep prepubertal, pubertal, and postpubertal periods were collected for RNA-seq analysis on the Illumina platform, generating 64.08 Gb clean reads. A total of 575, 166, and 648 differentially expressed genes (DEGs) were detected in prepuberty_vs._puberty, postpuberty_vs._prepuberty, and postpuberty_vs._puberty analyses, respectively. Based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses, the related genes involved in the initiation of puberty in Dolang sheep were mined. Ten genes that have direct or indirect functions in the initiation of puberty in Dolang sheep were screened using the GO and KEGG results. Additionally, quantitative real-time PCR was used to verify the reliability of the RNA-Seq data. This study provided a new approach for revealing the mechanism of puberty initiation in sheep and provided a theoretical basis and candidate genes for the breeding of early-pubertal sheep by molecular techniques, and at the same time, it is also beneficial for the protection, development, and utilization of the fine genetic resources of Xinjiang local sheep.