scholarly journals Differential Expression and Functional Analysis of CircRNA in the Ovaries of Low and High Fecundity Hanper Sheep

Animals ◽  
2021 ◽  
Vol 11 (7) ◽  
pp. 1863
Author(s):  
Aiju Liu ◽  
Xiaoyong Chen ◽  
Menghe Liu ◽  
Limeng Zhang ◽  
Xiaofei Ma ◽  
...  
Keyword(s):  
Litter Size ◽  
Luteal Phase ◽  
Production Efficiency ◽  
Follicular Development ◽  
Mapk Signaling ◽  
Follicular Phase ◽  
Differentially Expressed ◽  
Low Fertility ◽  
High Fecundity ◽  
Phase Versus

Litter size is a considerable quality that determines the production efficiency of mutton sheep. Therefore, revealing the molecular regulation of high and low fertility may aid the breeding process to develop new varieties of mutton sheep. CircRNAs are the important factors regulating follicular development, but their mechanism role in the regulation of litter size in Hanper sheep is not clear. In the present study, ovarian tissues from the follicular (F) or luteal phase (L) of Hanper sheep that were either consecutive monotocous (M) or polytocous were collected. Then, we performed transcriptome sequencing to screen for differentially expressed circRNAs (DE-circRNAs) and elucidate their function. In total, 4256 circRNA derived from 2184 host genes were identified in which 183 (146 were upregulated, while 37 were downregulated) were differentially expressed in monotocous sheep in the follicular phase versus polytocous sheep in the follicular phase (MF vs. PF). Moreover, 34 circRNAs (14 were upregulated, while 20 were downregulated) were differentially expressed in monotocous sheep in the luteal phase versus polytocous sheep in the luteal sheep (ML vs. PL). This was achieved through DE-circRNAs function enrichment annotation analysis by GESA, GO, and KEGG, which function through the EGF-EGFR-RAS-JNK, TGF-β and thyroid hormone signaling pathway to affect the litter size of Hanper sheep in MF vs. PF and ML vs. PL. STEM results showed that MAPK signaling pathways play a key role in MF vs. PF and ML vs. PL. Through WGCNA analysis, AKT3 was a core gene in MF vs. PF and ML vs. PL. Moreover, competitive endogenous RNA (ceRNA) network analysis revealed the target binding sites for miRNA such as oar-miR-27a, oar-miR-16b, oar-miR-200a/b/c, oar-miR-181a, oar-miR-10a/b, and oar-miR-432 in the identified DE-cirRNAs.

scholarly journals Genome-Wide Analyses Reveal Genetic Convergence of Prolificacy between Goats and Sheep

Genes ◽  
2021 ◽  
Vol 12 (4) ◽  
pp. 480
Author(s):  
Lin Tao ◽  
Xiaoyun He ◽  
Yanting Jiang ◽  
Yufang Liu ◽  
Yina Ouyang ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Litter Size ◽  
Luteal Phase ◽  
Antigen Processing ◽  
Osteoclast Differentiation ◽  
Follicular Phase ◽  
Comparative Genomic ◽  
Genome Replication ◽  
Viral Genome Replication ◽  
Transcriptomic Level

The litter size of domestic goats and sheep is an economically important trait that shows variation within breeds. Strenuous efforts have been made to understand the genetic mechanisms underlying prolificacy in goats and sheep. However, there has been a paucity of research on the genetic convergence of prolificacy between goats and sheep, which likely arose because of similar natural and artificial selection forces. Here, we performed comparative genomic and transcriptomic analyses to identify the genetic convergence of prolificacy between goats and sheep. By combining genomic and transcriptomic data for the first time, we identified this genetic convergence in (1) positively selected genes (CHST11 and SDCCAG8), (2) differentially expressed genes (SERPINA14, RSAD2, and PPIG at follicular phase, and IGF1, GPRIN3, LIPG, SLC7A11, and CHST15 at luteal phase), and (3) biological pathways (genomic level: osteoclast differentiation, ErbB signaling pathway, and relaxin signaling pathway; transcriptomic level: the regulation of viral genome replication at follicular phase, and protein kinase B signaling and antigen processing and presentation at luteal phase). These results indicated the potential physiological convergence and enhanced our understanding of the overlapping genetic makeup underlying litter size in goats and sheep.

scholarly journals Large-Scale Metadata Analysis of Ovary Based Multi-Omics Datasets for Understanding the Genes Regulating Litter Size

2020 ◽  
Author(s):  
Ayyappa Kumar Sista Kameshwar ◽  
Julang Li
Keyword(s):  
Gene Expression ◽  
Differentially Expressed Genes ◽  
Litter Size ◽  
Large Scale ◽  
Expression Patterns ◽  
Genetic Selection ◽  
Follicular Development ◽  
Oocyte Quality ◽  
Differentially Expressed ◽  
Metadata Analysis

Abstract Background : Litter size is a very important production index in the livestock industry, which is controlled by various complex physiological processes. To understand and reveal the common gene expression patterns involved in controlling prolificacy, we have performed a large-scale metadata analysis of five genome-wide transcriptome datasets of pig and sheep ovary samples obtained from high and low litter groups, respectively. We analyzed separately each transcriptome dataset using GeneSpring v14.8 software by implementing standard, generic analysis pipelines and further compared the list of most significant and differentially expressed genes obtained from each dataset to identify genes that are found to be common and significant across all the studies. Results : We have observed a total of 62 differentially expressed genes common among more than two gene expression datasets. The KEGG pathway analysis of most significant genes has shown that they are involved in metabolism, the biosynthesis of lipids, cholesterol and steroid hormones, immune system, cell growth and death, cancer-related pathways and signal transduction pathways. Of these 62 genes, we further narrowed the list to the 25 most significant genes by focusing on the ones with fold change >1.5 and p<0.05. These genes are CYP11A1, HSD17B2, STAR, SCARB1, IGSF8, MSMB, SERPINA1 , FAM46C, HEXA, PTTG1, TIMP1, FAM167B, CCNG1, FAXDC2, HMGCS1, L2HGDH, Lipin1, MME, MSMO1, PARM1, PTGFR, SLC22A4, SLC35F5, CCNA2, CENPU, CEP55, RASSF2, and SLC16A3 . Conclusions : Interestingly, comparing the list of genes with the list of genes obtained from our literature search analysis, we found only three genes in common. These genes are HEXA, PTTG1, and TIMP1. Our finding points to the potential of a few genes that may be important for ovarian follicular development and oocyte quality. Future studies revealing the function of these genes will further our understanding of how litter size is controlled in the ovary while also providing insight on genetic selection of high litter gilts.

scholarly journals The expression and mutation of <i>BMPR1B</i> and its association with litter size in small-tail Han sheep (<i>Ovis aries</i>)

2021 ◽  
Vol 64 (1) ◽  
pp. 211-221
Author(s):  
Yu-Liang Wen ◽  
Xiao-Fei Guo ◽  
Lin Ma ◽  
Xiao-Sheng Zhang ◽  
Jin-Long Zhang ◽  
...  
Keyword(s):  
Litter Size ◽  
Quantitative Polymerase Chain Reaction ◽  
Follicular Development ◽  
Follicular Phase ◽  
Ovis Aries ◽  
Negative Effects ◽  
Single Nucleotide ◽  
Ovarian Granulosa Cell ◽  
Polymerase Chain ◽  
Genotype And Allele Frequencies

Abstract. Previous studies have shown that BMPR1B promotes follicular development and ovarian granulosa cell proliferation, thereby affecting ovulation in mammals. In this study, the expression and polymorphism of the BMPR1B gene associated with litter size in small-tail Han (STH) sheep were determined. The expression of BMPR1B was detected in 14 tissues of STH sheep during the follicular phase as well as in the hypothalamic–pituitary–gonadal (HPG) axis of monotocous and polytocous STH sheep during the follicular and luteal phases using quantitative polymerase chain reaction (qPCR). Sequenom MassARRAY® single nucleotide polymorphism (SNP) technology was also used to detect the polymorphism of SNPs in seven sheep breeds. Here, BMPR1B was highly expressed in hypothalamus, ovary, uterus, and oviduct tissue during the follicular phase, and BMPR1B was expressed significantly more in the hypothalamus of polytocous ewes than in monotocous ewes during both the follicular and luteal phases (P<0.05). For genotyping, we found that genotype and allele frequencies of three loci of the BMPR1B gene were extremely significantly different (P<0.01) between the monotocous and polytocous groups. Association analysis results showed that the g.29380965A>G locus had significant negative effects on the litter size of STH sheep, and the combination of g.29380965A>G and FecB (Fec – fecundity and B – Booroola; A746G) at the BMPR1B gene showed that the litter size of AG–GG, AA–GG, and GG–GG genotypes was significantly higher compared with other genotypes (P<0.05). This is the first study to find a new molecular marker affecting litter size and to systematically analyze the expression of BMPR1B in different fecundity and physiological periods of STH sheep.

scholarly journals Transcriptome Profile of Key CircRNAs and MiRNAs in Oviduct that Affect Sheep Reproduction

2020 ◽  
Author(s):  
Zhifeng Li ◽  
Xiaoyun He ◽  
Xiaosheng Zhang ◽  
Jinlong Zhang ◽  
Xiaofei Guo ◽  
...  
Keyword(s):  
Insulin Secretion ◽  
Signaling Pathway ◽  
Luteal Phase ◽  
Target Genes ◽  
Follicular Phase ◽  
Differentially Expressed ◽  
Kegg Analysis ◽  
Non Coding Rna ◽  
Comparison Groups ◽  
Host Genes

Abstract Background: CircRNA and miRNA, as classes of non-coding RNA, have been found to play pivotal roles in sheep reproduction. There are many reports of circRNA and miRNA in ovary and uterus, but few in oviduct. In this study, RNA-Seq was performed to analyze the expression profile of circRNA and miRNA in oviduct between follicular phase and luteal phase in FecBBB (MM) and FecB++ (WW) sheep.Results: The result showed that 15 circRNAs were found differentially expressed between the follicular phase and luteal phase of FecBBB genotype (MF VS. ML), no circRNAs were found differentially expressed between the follicular phase and luteal phase of FecB++ genotype (WF VS. WL). 9 and 1 differentially expressed miRNAs were identified in MF VS. ML, and WF VS. WL, respectively. GO and KEGG analysis showed that the host genes of circRNAs in MF VS. ML were mainly involved in the Rap1 signaling pathway and PI3K-Akt signaling pathway. GO and KEGG analysis of miRNAs showed that the predicted target genes were mainly involved in the Insulin secretion and Rap1 signaling pathway in MF VS. ML. In WF VS. WL, the result showed that the predicted target genes were mainly involved in the TGF-β signaling pathway, Insulin secretion and Rap1 signaling pathway. In 3 comparison groups, GO and KEGG analysis indicated that a number of host genes and target genes (XPR1, LPAR3, SLC7A11, RAB3A, PLCB3, CREB3L4, LPAR1, LPAR2, FGF18, TACR3, BMP6, SMAD4, SKP1) were found to influence sheep reproduction. Conclusion: The results of the study will help to elucidate the regulatory mechanisms of circRNAs and miRNAs in sheep reproduction. And, this study will enrich the sheep circRNA and miRNA databases, which provide a basis for further research on sheep reproduction.

scholarly journals Peripheral concentrations of inhibin A, ovarian steroids, and gonadotropins associated with follicular development throughout the estrous cycle of the sow

Reproduction ◽  
2010 ◽  
Vol 139 (1) ◽  
pp. 153-161 ◽  
Author(s):  
Michiko Noguchi ◽  
Koji Yoshioka ◽  
Seigo Itoh ◽  
Chie Suzuki ◽  
Sachiko Arai ◽  
...  
Keyword(s):  
Estrous Cycle ◽  
Luteal Phase ◽  
Inverse Relationship ◽  
Plasma Concentrations ◽  
Follicular Development ◽  
Follicular Phase ◽  
Follicular Growth ◽  
Inhibin A ◽  
Ovarian Steroids ◽  
Feedback Regulator

We investigated changes in peripheral concentrations of inhibin A, total inhibin, steroids, and gonadotropins throughout the intact estrous cycle of the sow in relation to ovarian changes determined by daily transrectal ultrasonography. All visible follicles of 3 mm or more in diameter were classified as small (≥3 and <6 mm) or large (≥6 mm). Follicular recruitment was identified in two periods of the cycle: one from the late luteal to the follicular phase, characterized by an increase in the number of small follicles followed by the appearance of large follicles; and another during the early luteal phase, consisting only of increased numbers of small follicles. Plasma concentrations of inhibin A increased (P<0.05), coinciding with the two periods of follicle emergence. Estradiol (E2) levels increased (P<0.05) during the follicular phase, but not during the early luteal phase. An inverse relationship (P<0.01) between the patterns of inhibin and FSH concentrations was noted around the two periods of follicle emergence, but there was no relationship (P≥0.1) between the patterns of plasma E2and FSH during the early luteal phase. In conclusion, measurement of plasma inhibin A levels combined with ultrasonographic examination of the ovaries revealed two periods of synchronous follicular growth during the sow's estrous cycle. The results strongly suggest that inhibin A functions as a negative feedback regulator of FSH secretion throughout the estrous cycle, whereas E2appears to influence FSH secretion only during the follicular phase.

scholarly journals Identification of circular RNAs in the ovarian follicles of Meishan and Duroc sows during the follicular phase

2020 ◽  
Vol 13 (1) ◽  
Author(s):  
Su Xie ◽  
Mengxun Li ◽  
Yansen Chen ◽  
Yi Liu ◽  
Lipeng Ma ◽  
...  
Keyword(s):  
Follicular Development ◽  
Ovarian Follicles ◽  
Follicular Phase ◽  
Differentially Expressed ◽  
Circular Rnas ◽  
Rna Seq ◽  
Rt Pcr ◽  
Reverse Transcription Pcr ◽  
New Perspective

Abstract Circular RNAs (circRNAs) are a newly discovered class of endogenous non-coding RNAs that play an important role in growth and development by regulating gene expression and participating in a variety of biological processes. However, the role of circRNAs in porcine follicles remains unclear. Therefore, this study examined middle-sized ovarian follicles obtained from Meishan and Duroc sows at day 4 of the follicular phase. High-throughput RNA sequencing (RNA-seq) was utilized to construct circRNAs, and differential expression was identified. The findings were validated using reverse transcription PCR (RT-PCR) and DNA sequencing, GO and KEGG analyses were performed, and potential miRNA targets were identified. The RNA-seq identified a total of 15,866 circRNAs, with 244 differentially expressed in the Meishan relative to the Duroc (111 up-regulated and 133 down-regulated). The RT-PCR finding confirmed the RNA-seq results, and quantitative real-time PCR (qPCR) analysis examining a subset of the circRNAs showed that they are resistant to RNase R digestion. Bioinformatics analysis (GO and KEGG) showed that the host genes associated with the differentially expressed circRNAs are involved in reproduction and follicular development signaling pathways. Furthermore, many of the circRNAs were found to interact with miRNAs that are associated with follicular development. This study presents a new perspective for studying circRNAs and provides a valuable resource for further examination into the potential roles of circRNAs in porcine follicular development.

scholarly journals Identification and Characterization of Hypothalamic Alternative Splicing Events and Variants in Ovine Fecundity-Related Genes

Animals ◽  
2020 ◽  
Vol 10 (11) ◽  
pp. 2111
Author(s):  
Zhuangbiao Zhang ◽  
Jishun Tang ◽  
Xiaoyun He ◽  
Ran Di ◽  
Xiaosheng Zhang ◽  
...  
Keyword(s):  
Alternative Splicing ◽  
Luteal Phase ◽  
Follicular Phase ◽  
Differentially Expressed ◽  
Nucleotide Polymorphisms ◽  
Rna Seq ◽  
Single Nucleotide ◽  
Galectin 3 ◽  
First Time

Previous studies revealed that alternative splicing (AS) events and gene variants played key roles in reproduction; however, their location and distribution in hypothalamic fecundity-related genes in sheep without the FecB mutation remain largely unknown. Therefore, in this study, we described the hypothalamic AS events and variants in differentially expressed genes (DEGs) in Small Tail Han sheep without the FecB mutation at polytocous sheep in the follicular phase vs. monotocous sheep in the follicular phase (PF vs. MF) and polytocous sheep in the luteal phase vs. monotocous sheep in the luteal phase (PL vs. ML) via an RNA-seq study for the first time. We found 39 DEGs with AS events (AS DEGs) in PF vs. MF, while 42 AS DEGs were identified in PL vs. ML. No DEGs with single nucleotide polymorphisms (SNPs) were observed in PF vs. MF, but five were identified in PL vs. ML. We also performed a correlation analysis of transcriptomics and proteomics, and the results suggested several key DEGs/differentially expressed proteins (DEPs), such as galectin 3 (LGALS3) in PF vs. MF and aspartoacylase (ASPA) and transthyretin (TTR) in PL vs. ML, could be candidate genes influencing ovine litter size. In addition, further analyses suggested that AS events, SNPs and miRNA-binding sites existed in key DEGs/DEPs, such as ASPA and TTR. All in all, this study provides a new insight into ovine and even other mammalian reproduction.

scholarly journals Transcriptome analysis reveals that long noncoding RNAs contribute to developmental differences between medium-sized ovarian follicles of Meishan and Duroc sows

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Mengxun Li ◽  
Yi Liu ◽  
Su Xie ◽  
Lipeng Ma ◽  
Zhichao Zhao ◽  
...  
Keyword(s):  
Signaling Pathway ◽  
Litter Size ◽  
Target Genes ◽  
Hormone Secretion ◽  
Follicular Development ◽  
Akt Signaling ◽  
Developmental Differences ◽  
Differentially Expressed ◽  
Akt Signaling Pathway ◽  
Potential Target

AbstractOvulation rate is an extremely important factor affecting litter size in sows. It differs greatly among pig breeds with different genetic backgrounds. Long non-coding RNAs (lncRNAs) can regulate follicle development, granulosa cell growth, and hormone secretion, which in turn can affect sow litter size. In this study, we identified 3554 lncRNAs and 25,491 mRNAs in M2 follicles of Meishan and Duroc sows. The lncRNA sequence and open reading frame lengths were shorter than mRNAs, and lncRNAs had fewer exons, were less abundant, and more conserved than protein-coding RNAs. Furthermore, 201 lncRNAs were differentially expressed (DE) between breeds, and quantitative trait loci analysis of DE lncRNAs were performed. A total of 127 DE lncRNAs were identified in 119 reproduction trait-related loci. In addition, the potential target genes of lncRNAs in cis or trans configurations were predicted. Gene ontology and Kyoto Encyclopedia of Genes and Genomes pathway analysis revealed that some potential target genes were involved in follicular development and hormone secretion-related biological processes or pathways, such as progesterone biosynthetic process, estrogen metabolic process, ovarian steroidogenesis, and PI3K-Akt signaling pathway. Furthermore, we also screened 19 differentially expressed lncRNAs in the PI3K-Akt signaling pathway as candidates. This study provides new insights into the roles of lncRNAs in follicular growth and development in pigs.

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