Genome-wide analysis of miRNAs in the ovaries of Jining Grey and Laiwu Black goats to explore the regulation of fecundity

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.

Characterization of MicroRNA expression profiles in the ovarian tissue of goats during the sexual maturity period

BACKGROUND

The ovary is an important reproductive organ in mammals, and its development directly affects the sexual maturity and reproductive capacity of individuals. MicroRNAs (miRNAs) are recognized as regulators of reproductive physiological processes in various animals and have been shown to regulate ovarian development through typical targeting and translational repression. However, little is known about the regulatory role of miRNAs in ovarian tissue development during sexual maturity in goats. To comprehensively profile the different physiological stages of sexual maturation in goats, we performed small-RNA sequencing of ovarian tissue samples collected at four specific time points (1 day after birth (D1), 2 months old (M2), 4 months old (M4), and 6 months old (M6)). In addition, we used ELISAs to measure serum levels of reproductive hormones to study their temporal changes.

RESULTS

The results showed that serum levels of gonadotropin-releasing hormone, follicle-stimulating hormone, luteinizing hormone, oestradiol, progesterone, oxytocin, and prolactin were lower in goats at the D1 stage than at the other three developmental stages (P < 0.05). The secretion patterns of these seven hormones show a similar trend, with hormone levels reaching their peaks at 4 months of age. A total of 667 miRNAs were detected in 20 libraries, and 254 differentially expressed miRNAs and 3 groups of miRNA clusters that had unique expression patterns were identified (|log2-fold change|> 1, FDR < 0.05) in the 6 comparison groups. RT‒qPCR was employed to confirm that the expression pattern of the 15 selected miRNAs was consistent with the Illumina sequencing results. Gene ontology analyses revealed significant enrichment of GO terms such as cell proliferation regulation, epithelial cell development, and amino acid transport, as well as important signaling pathways including the MAPK signaling pathway, the PI3K-Akt signaling pathway, and the oestrogen signaling pathway. Further miRNA‒mRNA regulation network analysis revealed that 8 differentially expressed miRNAs (chi-miR-1343, chi-miR-328-3p, chi-miR-877-3p, chi-miR-296-3p, chi-miR-128-5p, chi-miR-331-3p, chi-miR-342-5p and chi-miR-34a) have important regulatory roles in ovarian cell proliferation, hormone secretion and metabolism-related biological processes.

CONCLUSIONS

Overall, our study investigated the changes in serum hormone and miRNA levels in the ovaries. These data provide a valuable resource for understanding the molecular regulatory mechanisms of miRNAs in ovarian tissue during the sexual maturity period in goats.

Identification and analysis of differentially expressed microRNAs in endometrium to explore the regulation of sheep fecundity

BACKGROUND

MicroRNAs (miRNAs) play an important regulatory role in mammalian reproduction. Currently, most studies are primarily concentrated on ovarian miRNAs, ignoring the influence of endometrial miRNAs on the fecundity of female sheep. To uncover potential regulators of sheep fecundity, RNA-seq was used to comparatively analyze miRNA expression profiles of endometrium between high prolificacy sheep (HP, litter size = 3) and low prolificacy sheep (LP, litter size = 1) with FecB genotype.

RESULTS

Firstly, genomic features of miRNAs from endometrium were analyzed. Furthermore, 58 differentially expressed (DE) miRNAs were found in the endometrium of Hu sheep with different litter size. A co-expression network of DE miRNAs and target genes has been constructed, and hub genes related litter size are included, such as DE miRNA unconservative_NC_019472.2_1229533 and unconservative_NC_019481.2_1637827 target to estrogen receptor α (ESR1) and unconservative_NC_019481.2_1637827 targets to transcription factor 7 (TCF7). Moreover, functional annotation analysis showed that the target genes (NRCAM and NEGR1) of the DE miRNAs were significantly enriched in cell adhesion molecules (CAMs) signaling pathway, which was related to uterine receptivity.

CONCLUSION

Taken together, this study provides a new valuable resource for understanding the molecular mechanisms underlying Hu sheep prolificacy.

Comprehensive analysis on the regulation of differentially expressed of mRNA and ncRNA in different ovarian stages of ark shell Scapharca broughtonii

BACKGROUND

Ovarian development is an important prerequisite and basis for animal reproduction. In many vertebrates, it is regulated by multiple genes and influenced by sex steroid hormones and environmental factors. However, relative information is limited in shellfish. To explore the biological functions and molecular mechanisms of mRNA and non-coding RNA that regulate ovarian development in Scapharca broughtonii, we performed whole transcriptome sequencing analysis on ovaries at three developmental stages. Furthermore, the biological processes involved in the differential expression of mRNA and ncRNA were analyzed.

RESULTS

A total of 11,342 mRNAs, 6897 lncRNAs, 135 circRNAs, and 275 miRNAs were differentially expressed. By mapping the differentially expressed RNAs from the three developmental stages of Venn diagram, multiple groups of shared mRNAs and lncRNAs were found to be associated with ovarian development, with some mRNA and ncRNA functions associated with steroid hormone. In addition, we constructed and visualized the lncRNA/circRNA-miRNA-mRNA network based on ceRNA targeting relationships.

CONCLUSIONS

These findings may facilitate our further understanding the mRNA and ncRNAs roles in the regulation of shellfish reproduction.

Construction of a circRNA- lincRNA-lncRNA-miRNA-mRNA ceRNA regulatory network identifies genes and pathways linked to goat fertility

Background: There is growing interest in the genetic improvement of fertility traits in female goats. With high-throughput genotyping, single-cell RNA sequencing (scRNA-seq) is a powerful tool for measuring gene expression profiles. The primary objective was to investigate comparative transcriptome profiling of granulosa cells (GCs) of high- and low-fertility goats, using scRNA-seq. Methods: Thirty samples from Ji'ning Gray goats (n = 15 for high fertility and n = 15 for low fertility) were retrieved from publicly available scRNA-seq data. Functional enrichment analysis and a literature mining approach were applied to explore modules and hub genes related to fertility. Then, interactions between types of RNAs identified were predicted, and the ceRNA regulatory network was constructed by integrating these interactions with other gene regulatory networks (GRNs). Results and discussion: Comparative transcriptomics-related analyses identified 150 differentially expressed genes (DEGs) between high- and low-fertility groups, based on the fold change (≥5 and ≤-5) and false discovery rate (FDR <0.05). Among these genes, 80 were upregulated and 70 were downregulated. In addition, 81 mRNAs, 58 circRNAs, 8 lincRNAs, 19 lncRNAs, and 55 miRNAs were identified by literature mining. Furthermore, we identified 18 hub genes (SMAD1, SMAD2, SMAD3, SMAD4, TIMP1, ERBB2, BMP15, TGFB1, MAPK3, CTNNB1, BMPR2, AMHR2, TGFBR2, BMP4, ESR1, BMPR1B, AR, and TGFB2) involved in goat fertility. Identified biological networks and modules were mainly associated with ovary signature pathways. In addition, KEGG enrichment analysis identified regulating pluripotency of stem cells, cytokine-cytokine receptor interactions, ovarian steroidogenesis, oocyte meiosis, progesterone-mediated oocyte maturation, parathyroid and growth hormone synthesis, cortisol synthesis and secretion, and signaling pathways for prolactin, TGF-beta, Hippo, MAPK, PI3K-Akt, and FoxO. Functional annotation of identified DEGs implicated important biological pathways. These findings provided insights into the genetic basis of fertility in female goats and are an impetus to elucidate molecular ceRNA regulatory networks and functions of DEGs underlying ovarian follicular development.

Comparison of alternative splicing (AS) events in adipose tissue of polled dorset versus small tail han sheep

Background

During the alternative splicing (AS), the exons of primary transcripts are spliced in various arrangements, resulting in structurally and functionally distinct mRNAs and proteins. This study aimed to examine genes with AS events from Small Tail Han sheep and Dorset sheep to explore the mechanism of adipose developments.

Methods

This study identified the genes with AS events in adipose tissues of two different sheep with next-generation sequencing. In this paper, genes with significantly different AS events were performed gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses.

Results

364 genes with 411 A S events showed significant differences in adipose tissues between the two breeds; 108 genes with 120 A S events were extremely significant differences between the two breeds. We identified several novel genes that are related with adipose growth and development. The results of KEGG and GO analysis indicated that oocyte meiosis, mitogen-activated protein kinase (Wnt), mitogen-activated protein kinase (MAPK) signaling pathway, etc. Were closely related to the adipose tissue developments.

Conclusions

This paper revealed that the genes with AS events are important for adipose tissues in sheep, exploring the mechanisms of AS events associated with adipose tissue developments in sheep of different breeds.

Impact of FecB Mutation on Ovarian DNA Methylome in Small-Tail Han Sheep

Booroola fecundity (FecB) gene, a mutant of bone morphogenetic protein 1B (BMPR-1B) that was discovered in Booroola Merino, was the first prolificacy gene identified in sheep related to increased ovulation rate and litter size. The mechanism of FecB impact on reproduction is unclear.

METHODS

In this study, adult Han ewes with homozygous FecB(B)/FecB(B) mutations (Han BB group) and ewes with FecB(+)/FecB(+) wildtype (Han ++ group) were selected. Methylated DNA immunoprecipitation and high-throughput sequencing (MeDIP-seq) was used to identify differences in methylated genes in ovary tissue.

RESULTS

We examined differences in DNA methylation patterns between HanBB and Han ++ sheep. In both sheep, methylated reads were mainly distributed at the gene body regions, CpG islands and introns. The differentially methylated genes were enriched in neurotrophy in signaling pathway, Gonadotropin Releasing Hormone (GnRH) signaling pathway, Wnt signaling pathway, oocyte meiosis, vascular endothelial growth factor (VEGF) signaling pathway, etc. Differentially-methylated genes were co-analyzed with differentially-expressed mRNAs. Several genes which could be associated with female reproduction were identified, such as FOXP3 (forkhead box P3), TMEFF2 (Transmembrane Protein with EGF Like and Two Follistatin Like Domains 2) and ADAT2 (Adenosine Deaminase TRNA Specific 2).

CONCLUSIONS

We constructed a MeDIP-seq based methylomic study to investigate the ovarian DNA methylation differences between Small-Tail Han sheep with homozygous FecB mutant and wildtype, and successfully identified FecB gene-associated differentially-methylated genes. This study has provided information with which to understand the mechanisms of FecB gene-induced hyperprolificacy in sheep.

Integrative Analysis of miRNAs Involved in Fat Deposition in Different Pig Breeds

BACKGROUND

miRNAs are a set of small, noncoding RNAs that bind to partially complementary sequences on target mRNAs. This leads to the post-transcriptional regulation of gene expression. Many studies have shown that microRNAs play critical roles in adipose cell differentiation and fat metabolism. The aim of this study was to explore the regulatory functions of miRNAs in fat deposition for the prevention and therapy of lipid metabolism-related diseases.

METHODS

The significant differences in the fat deposition of Laiwu (LW) pigs and Large White (LY) pigs were studied. To investigate the genetic relationships of miRNAs that regulate fat deposition, we performed a genome-wide analysis of miRNAs derived from subcutaneous adipose tissue of LW and LY pigs using RNA-seq.

RESULTS

There were 39 known miRNAs and 56 novel miRNAs significantly differential expressed between the two breeds of pigs. In the analysis of the Gene Ontology and KEGG pathways, predicted targets of these differentially expressed miRNAs were involved in several fat-associated pathways, such as the peroxisome proliferator-activated receptor (PPAR), mitogen-activated protein kinases (MAPK) and Wnt signaling pathways. In addition, ssc-miR-133a-3p, ssc-miR-486 and ssc-miR-1 each had a great impact on the development of porcine subcutaneous fat through the PPAR signaling pathway.

CONCLUSIONS

We explored the role of differentially expressed miRNAs and studied the mechanisms of adipogenesis and fat deposition between two different pig breeds. In addition, these results also contribute to research relevant to human obesity.

Integrated analysis of the expression profiles of the lncRNA-miRNA-mRNA ceRNA network in granulosa and cumulus cells from yak ovaries

Background

Growing oocytes acquire the ability to mature through two-way communication between gametes and surrounding somatic cumulus cells (CCs). Granulosa cells (GCs) support oocyte growth, regulate meiosis progression, and modulate global oocyte transcription activity. However, the proliferation and differentiation of the yak ovary in GCs and CCs remain unclear. To characterize the important roles of long non-coding RNA, (lncRNA), microRNA (miRNA), and messenger RNA (mRNA), whole-transcriptome analysis was performed. Real-time quantitative fluorescence PCR was performed to verify the selected RNA sequences.

Results

Important gene ontology terms and Kyoto Encyclopedia of Genes and Genomes pathways related to differentiation and oocyte development were identified for the target genes of differentially expressed lncRNAs, miRNAs, and mRNAs. In total,6223 mRNAs (2197 upregulated, 4026 downregulated), 643 lncRNAs (204 upregulated, 479 downregulated), and 559 miRNAs (311 upregulated, 248 downregulated) were significantly altered between the two groups. Target genes involved in cell adhesion, cell differentiation, regulation of developmental processes, cell proliferation, embryo development, signal transduction, apoptosis, and aromatic compound biosynthetic processes were significantly enriched. These RNAs were involved in ECM-receptor interaction, MAPK signaling, Hippo signaling, PI3K-Akt signaling, cell cycle, cell adhesion, leukocyte trans-endothelial migration, and actin cytoskeleton regulation.

Conclusions

A comprehensive analysis of the co-expression network of competing endogenous RNAs (ceRNAs) will facilitate the understanding of the process of granulosa cell proliferation and differentiation and offer a theoretical basis for the development of oocytes.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12864-022-08848-3.

Differential regulation of mRNAs and lncRNAs related to lipid metabolism in Duolang and Small Tail Han sheep

The function of long non-coding RNA (lncRNA) can be achieved through the regulation of target genes, and the deposition of fat is regulated by lncRNA. Fat has an important effect on meat quality. However, there are relatively few studies on lncRNAs in the subcutaneous adipose tissue of Duolang sheep and Small Tail Han sheep. In this study, RNA-Seq technology and bioinformatics methods were used to identify and analyze the lncRNA and mRNA in the subcutaneous adipose tissue of the two breeds of sheep. The results showed that 107 lnRNAs and 1329 mRNAs were differentially expressed. The differentially expressed genes and lncRNA target genes were significantly enriched in the biosynthesis of unsaturated fatty acids signaling pathway, fatty acid metabolism, adipocyte differentiation and other processes related to fat deposition. Among them, LOC105616076, LOC114118103, LOC105607837, LOC101116622, and LOC105603235 target FADS1, SCD, ELOVL6, HSD17B12 and HACD2, respectively. They play a key regulatory role in the biosynthesis of unsaturated fatty acids. This study lays a foundation for the study of the molecular mechanism of lncRNA on fat development, and has reference value for studying the differences in fat deposition between Duolang sheep and Small Tail Han sheep.

Genome-wide detection of selective signals for fecundity traits in goats (Capra hircus)

Fecundity in livestock is an economically important complex quantitative trait that is influenced by both genetics and the environment. However, the underlying genetic mechanism of reproductive performance in goats has not been well investigated. To investigate the genomic basis of fecundity in goats, genomic sequencing data of the Jining grey goat (a high prolificacy breed in China) were collected, as well as data for other commonly available goat breeds, and a mass of genomic variants were generated after variation calling. We screened the Jining grey goat (20 individuals) using a selective sweep with the Asian wild goat population (5 individuals), and potential candidate genes were proposed, such as STIM1, ESR1, LRRC14B and SLC9A3. Among, STIM1 is a most promising one associated with high reproductive capacity. When compared to Chinese domestic goats with low fecundity (17 individuals), the genes including MLLT10, SPIRE2, TCF25, ZNF276 and FANCA were screened, and the SPIRE2 gene was thought to be associated with fecundity traits. Meanwhile, the functional enrichment of these candidate genes revealed that they were involved in biological processes of mammary gland morphogenesis, uterus development, gastrulation, mesoderm morphogenesis and formation, and blood vessel development, which might undergo natural or artificial selection during reproductive trait formation in goats. Thus, our findings could enrich the genetic basis of reproductive trait selection during goat domestication, which may serve to improve goat breeding practices.

Changthangi Pashmina Goat Genome: Sequencing, Assembly, and Annotation

Pashmina goats produce the world's finest and the most costly animal fiber (Pashmina) with an average fineness of 11-13 microns and have more evolved mechanisms than any known goat breed around the globe. Despite the repute of Pashmina goat for producing the finest and most sought-after animal fiber, meager information is available in the public domain about Pashmina genomics and transcriptomics. Here we present a 2.94 GB genome sequence from a male Changthangi white Pashmina goat. We generated 294.8 GB (>100X coverage) of the whole-genome sequence using the Illumina HiSeq 2500 sequencer. All cleaned reads were mapped to the goat reference genome (2,922,813,246 bp) which covers 97.84% of the genome. The Unaligned reads were used for de novo assembly resulting in a total of 882 MB non-reference contigs. De novo assembly analysis presented in this study provides important insight into the adaptation of Pashmina goats to cold stress and helps enhance our understanding of this complex phenomenon. A comparison of the Pashmina goat genome with a wild goat genome revealed a total of 2,823 high impact single nucleotide variations and small insertions and deletions, which may be associated with the evolution of Pashmina goats. The Pashmina goat genome sequence provided in this study may improve our understanding of complex traits found in Pashmina goats, such as annual fiber cycling, defense mechanism against hypoxic, survival secret in extremely cold conditions, and adaptation to a sparse diet. In addition, the genes identified from de novo assembly could be utilized in differentiating Pashmina fiber from other fibers to avoid falsification at marketing practices.

Genome-wide transcriptome profiling uncovers differential miRNAs and lncRNAs in ovaries of Hu sheep at different developmental stages

Ovary development is an important determinant of the procreative capacity of female animals. Here, we performed genome-wide sequencing of long non-coding RNAs (lncRNAs) and mRNAs on ovaries of 1, 3 and 8 months old Hu sheep to assess their expression profiles and roles in ovarian development. We identified 37,309 lncRNAs, 45,404 messenger RNAs (mRNAs) and 330 novel micro RNAs (miRNAs) from the transcriptomic analysis. Six thousand, seven hundred and sixteen (6716) mRNAs and 1972 lncRNAs were significantly and differentially expressed in ovaries of 1 month and 3 months old Hu sheep (H1 vs H3). These mRNAs and target genes of lncRNAs were primarily enriched in the TGF-β and PI3K-Akt signalling pathways which are closely associated with ovarian follicular development and steroid hormone biosynthesis regulation. We identified MSTRG.162061.1, MSTRG.222844.7, MSTRG.335777.1, MSTRG.334059.16, MSTRG.188947.6 and MSTRG.24344.3 as vital genes in ovary development by regulating CTNNB1, CCNA2, CDK2, CDC20, CDK1 and EGFR expressions. A total of 2903 mRNAs and 636 lncRNAs were differentially expressed in 3 and 8 months old ovaries of Hu sheep (H3 vs H8); and were predominantly enriched in PI3K-Akt, progesterone-mediated oocyte maturation, estrogen metabolism, ovulation from the ovarian follicle and oogenesis pathways. These lncRNAs were also found to regulate FGF7, PRLR, PTK2, AMH and INHBA expressions during follicular development. Our result indicates the identified genes participate in the development of the final stages of follicles and ovary development in Hu sheep.

MicroRNAs as Biomarkers for Animal Health and Welfare in Livestock

MicroRNAs (miRNAs) are small and highly conserved non-coding RNA molecules that orchestrate a wide range of biological processes through the post-transcriptional regulation of gene expression. An intriguing aspect in identifying these molecules as biomarkers is derived from their role in cell-to-cell communication, their active secretion from cells into the extracellular environment, their high stability in body fluids, and their ease of collection. All these features confer on miRNAs the potential to become a non-invasive tool to score animal welfare. There is growing interest in the importance of miRNAs as biomarkers for assessing the welfare of livestock during metabolic, environmental, and management stress, particularly in ruminants, pigs, and poultry. This review provides an overview of the current knowledge regarding the potential use of tissue and/or circulating miRNAs as biomarkers for the assessment of the health and welfare status in these livestock species.

Integrated analysis of lncRNA, miRNA and mRNA reveals novel insights into the fertility regulation of large white sows

Background

Improving sow fertility is extremely important as it can lead to increased reproductive efficiency and thus profitability for swine producers. There are considerable differences in fertility rates among individual animals, but the underlying molecular mechanisms remain unclear. In this study, by using different types of RNA libraries, we investigated the complete transcriptome of ovarian tissue during the luteal (L) and follicular (F) phases of the estrous cycle in Large White pigs with high (H) and low (L) fecundity, and performed a comprehensive analysis of long noncoding RNAs (lncRNAs), mRNAs and micro RNAs (miRNAs) from 16 samples by combining RNA sequencing (RNA-seq) with bioinformatics.

Results

In total, 24,447 lncRNAs, 27,370 mRNAs, and 216 known miRNAs were identified in ovarian tissues. The genomic features of lncRNAs, such as length distribution and number of exons, were further analyzed. We selected a threshold of P < 0.05 and |log₂ (fold change)| ≥ 1 to obtain the differentially expressed lncRNAs, miRNAs and mRNAs by pairwise comparison (LH vs. LL, FH vs. FL). Bioinformatics analysis of these differentially expressed RNAs revealed multiple significantly enriched pathways (P < 0.05) that were closely involved in the reproductive process, such as ovarian steroidogenesis, lysosome, steroid biosynthesis, and the estrogen and GnRH signaling pathways. Moreover, bioinformatics screening of differentially expressed miRNAs that share common miRNA response elements (MREs) with lncRNAs and their downstream mRNA targets were performed. Finally, we constructed lncRNA–miRNA–mRNA regulation networks. The key genes in these networks were verified by Reverse Transcription Real-time Quantitative PCR (RT-qRCR), which were consistent with the results from RNA-Seq data.

Conclusions

These results provide further insights into the fertility of pigs andcan contribute to further experimental investigation of the functions of these genes.

A Preliminary Study on the Characteristics of microRNAs in Ovarian Stroma and Follicles of Chuanzhong Black Goat during Estrus

microRNAs (miRNAs) play a significant role in ovarian follicular maturity, but miRNA expression patterns in ovarian stroma (OS), large follicles (LF), and small follicles (SF) have been rarely explored. We herein aimed to identify miRNAs, their target genes and signaling pathways, as well as their interaction networks in OS, LF, and SF of Chuanzhong black goats at the estrus phase using small RNA-sequencing. We found that the miRNA expression profiles of LF and SF were more similar than those of OS—32, 16, and 29 differentially expressed miRNAs were identified in OS vs. LF, OS vs. SF, and LF vs. SF, respectively. Analyses of functional enrichment and the miRNA-targeted gene interaction network suggested that miR-182 (SMC3), miR-122 (SGO1), and miR-206 (AURKA) were involved in ovarian organogenesis and hormone secretion by oocyte meiosis. Furthermore, miR-202-5p (EREG) and miR-485-3p (FLT3) were involved in follicular maturation through the MAPK signaling pathway, and miR-2404 (BMP7 and CDKN1C) played a key role in follicular development through the TGF-β signaling pathway and cell cycle; nevertheless, further research is warranted. To our knowledge, this is the first study to investigate miRNA expression patterns in OS, LF, and SF of Chuanzhong black goats during estrus. Our findings provide a theoretical basis to elucidate the role of miRNAs in follicular maturation. These key miRNAs might provide candidate biomarkers for the diagnosis of follicular maturation and will assist in developing new therapeutic targets for female goat infertility.

Unconservative_15_2570409 suppresses progesterone receptor expression in the granulosa cells of Hu sheep

Female fertility potential depends on the number of mature follicles; however, the underlying molecular mechanisms remain unclear. Based on previously generated miRNA and mRNA sequencing data of healthy ovarian follicles (>5 mm in diameter) isolated from Hu sheep with different prolificacy, we investigated the roles of a novel miRNA (unconservative_15_2570409) and the progesterone receptor (PGR) gene in follicular development. During the periovulatory phase, the expression of unconservative_15_2570409 and PGR was lower and higher, respectively, in the >5 mm follicles of high prolificacy (HP) ewes than in those of low prolificacy (LP) ewes and in the >3 mm follicles than in the smaller follicles of the HP ewes. Subsequently, the granulosa cells (GCs) of Hu sheep were used as an in vitro model. PGR overexpression significantly increased the mRNA expression of steroidogenic acute regulatory protein (StAR), 3-beta-hydroxysteroid dehydrogenase/isomerase (3β-HSD), and cytochrome P450 family 19 subfamily A member 1 (CYP19A1), which promoted the secretion of progesterone (P₄) and estradiol (E₂). PGR knockdown significantly downregulated the levels of StAR and 3β-HSD mRNA and decreased the production of P₄, whereas no effects on CYP19A1 mRNA expression and E₂ levels were observed. We also found the negative regulatory effect of unconservative_15_2570409 on the mRNA and protein expression of PGR by targeting the 3'-untranslated region. The regulation of PGR levels resulted in a corresponding change in the ADAMTS1, PPAR-γ, and CTSL gene transcripts, which are important for follicular maturation and ovulation. Additionally, PGR, ADAMTS1, and PPAR-γ were predominantly localized in the GCs. Collectively, our results suggest that by regulating PGR expression and consequently affecting the expression of target genes and steroidogenesis, unconservative_15_2570409 plays a role in follicular development during the periovulatory stage, which provides novel insights into the molecular mechanisms affecting Hu sheep prolificacy.

Comparative DNA methylome analysis of estrus ewes reveals the complex regulatory pathways of sheep fecundity

BACKGROUND/AIMS

Sheep are important livestock with variant ovulation rate and fertility. Dorset sheep is a typical breed with low prolificacy, whereas Small Tail Han sheep with FecB mutation (HanBB) have hyperprolificacy. Our previous studies have revealed the gene expression difference between the ovaries from Dorset and HanBB sheep contributes to the difference of fecundity, however, what leads to these gene expression difference remains unclear. DNA methylation, an important epigenetic process, plays a crucial role in gene expression regulation.

METHODS

In the present study, we constructed a methylated DNA immunoprecipitation combined with high throughput sequencing (MeDIP-seq) strategy to investigate the differentially methylated genes between the Dorset and HanBB ovaries.

RESULTS

Our findings suggest the genes involved in immune response, branched-chain amino acid metabolism, cell growth and cell junction were differentially methylated in or around the gene body regions.

CONCLUSIONS

These findings provide prospective insights on the epigenetic basis of sheep fecundity.

Long non-coding RNA366.2 controls endometrial epithelial cell proliferation and migration by upregulating WNT6 as a ceRNA of miR-1576 in sheep uterus

Long non-coding RNAs (lncRNAs) play an important regulatory role in mammalian fecundity. Currently, most studies are primarily concentrated on ovarian lncRNAs, ignoring the influence of uterine lncRNAs on the fecundity of female sheep. In this study, we found a higher density of uterine glands and endometrial microvessel density (MVD) in high prolificacy group of Hu sheep compared to low prolificacy groups (p < 0.05) as well as an increased level of serum placental growth factor (PLGF). Hundreds of differentially expressed (DE) lncRNAs were identified in Hu sheep with different fecundity by RNA sequencing (RNA-seq), and their targets were enriched in some signaling pathways involved in endometrial functions, such as the estrogen signaling pathway, nuclear factor kappa B (NF-κB) signaling pathway, oxytocin signaling pathway, and Wnt signaling pathway. Furthermore, the underlying mechanisms of competitive endogenous RNA (ceRNA) of lncRNA366.2-miR-1576- WNT6 were determined by bioinformatics analysis. Functionally, our results indicated that lncRNA366.2 promoted endometrial epithelial cell (EEC) proliferation, migration, and growth factor expression by sponging miR-1576 to upregulate WNT6 expression and activate the Wnt/β-catenin pathway. Taken together, our research indicated the regulatory mechanism of the lncRNA366.2-miR-1576-WNT6 in EEC proliferation and migration. Furthermore, this study provides a new theoretical reference for the identification of candidate genes related to fecundity.

Genomic Signatures of Selection Associated With Litter Size Trait in Jining Gray Goat

Litter size (LS), an important economic trait in livestock, is so complicate that involves many aspects of reproduction, the underlying mechanism of which particularly in goat has always been scanty. To uncover the genetic basis of LS, the genomic sequence of Jining Gray goat groups (one famous breed for high prolificacy in China) with LS 1, 2, and 3 for firstborn was analyzed, obtaining 563.67 Gb sequence data and a total of 31,864,651 high-quality single nucleotide polymorphisms loci were identified. Particularly, the increased heterozygosity in higher LS groups, and large continuous homozygous segments associated with lower LS group had been uncovered. Through an integrated analysis of three popular methods for detecting selective sweeps (Fst, nucleotide diversity, and Tajima’s D statistic), 111 selected regions and 42 genes associated with LS were scanned genome wide. The candidate genes with highest selective signatures included KIT, KCNH7, and KMT2E in LS2 and PAK1, PRKAA1, and SMAD9 in LS3 group, respectively. Meanwhile, functional terms of programmed cell death involved in cell development and regulation of insulin receptor signaling pathway were mostly enriched with 42 candidate genes, which also included reproduction related terms of steroid metabolic process and cellular response to hormone stimulus. In conclusion, our study identified novel candidate genes involving in regulation of LS in goat, which expand our understanding of genetic fundament of reproductive ability, and the novel insights regarding to LS would be potentially applied to improve reproductive performance.

MicroRNA Expression Profile in Peripheral Blood Lymphocytes of Sheep Vaccinated with Nigeria 75/1 Peste Des Petits Ruminants Virus

Peste des petits ruminants (PPR) is one of the highly contagious transboundary viral diseases of small ruminants. Host microRNA (miRNA) expression patterns may change in response to virus infection, and it mainly works as a post-transcriptional moderator in gene expression and affects viral pathogenesis and replication. In this study, the change of miRNA expression profile in peripheral blood lymphocyte (PBMC) from sheep inoculated with PPR vaccine virus in vivo as well as primary sheep testicular (ST) cells inoculated with PPR vaccine virus in vitro were determined via deep sequencing technology. In PBMC cells, 373 and 115 differentially expressed miRNAs (DEmiRNAs) were identified 3 days and 5 days post inoculated (dpi), respectively. While, 575 DEmiRNAs were identified when comparing miRNA profiles on 5 dpi with 3 dpi. Some of the DEmiRNAs were found to change significantly via time-course during PPR vaccine virus inoculated. Similarly, in ST cells, 136 DEmiRNAs were identified at 3 dpi in comparison with mock-inoculation. A total of 12 DEmiRNAs were validated by real-time quantitative PCR (RT-qPCR). The oar-miR-150, oar-miR-370-3p and oar-miR-411b-3p were found common differentially expressed in both PPR vaccine virus-inoculated PBMC cells and ST cells. Targets prediction and functional analysis of the DEmiRNAs uncovered mainly gathering in antigen processing and presentation pathways, protein processing in endoplasmic reticulum pathways and cell adhesion molecules pathways. Our study supplies information about the DEmiRNAs in PPR vaccine virus-inoculated PBMC cells and ST cells, and provides clues for further understanding the function of miRNAs in PPR vaccine virus replication.

Research advances in reproduction for dairy goats

Considerable progress in reproduction of dairy goats has been made, with advances in reproductive technology accelerating dairy goat production since the 1980s. Reproduction in goats is described as seasonal. The onset and length of the breeding season is dependent on various factors such as breed, climate, physiological stage, male effect, breeding system, and photoperiod. The reproductive physiology of goats was investigated extensively, including hypothalamic and pituitary control of the ovary related to estrus behavior and cyclicity etc. Photoperiodic treatments coupled with the male effect allow hormone-free synchronization of ovulation, but the kidding rate is still less than for hormonal treatments. Different protocols have been developed to meet the needs and expectations of producers; dairy industries are subject to growing demands for year round production. Hormonal treatments for synchronization of estrus and ovulation in combination with artificial insemination (AI) or natural mating facilitate out-of-season breeding and the grouping of the kidding period. The AI with fresh or frozen semen has been increasingly adopted in the intensive production system, this is perhaps the most powerful tool that reproductive physiologists and geneticists have provided the dairy goat industry with for improving reproductive efficiency, genetic progress and genetic materials transportation. One of the most exciting developments in the reproduction of dairy animals is embryo transfer (ET), the so-called second generation reproductive biotechnology following AI. Multiple ovulation and ET (MOET) program in dairy goats combining with estrus synchronization (ES) and AI significantly increase annual genetic improvement by decreasing the generation interval. Based on the advances in reproduction technologies that have been utilized through experiments and investigation, this review will focus on the application of these technologies and how they can be used to promote the dairy goat research and industry development in the future.

Identification and characterization of microRNAs in the pituitary of pubescent goats

BACKGROUND

Puberty is the period during a female mammal's life when it enters estrus and ovulates for the first time; this indicates that a mammal is capable of reproduction. The onset of puberty is a complex and tightly coordinated biological event; it has been reported that microRNAs (miRNAs) are involved in regulating the initiation of puberty.

METHODS

We performed miRNA sequencing on pituitary tissue from prepubescent and pubescent goats to investigate differences in miRNA expression during the onset of puberty in female goats. The target genes of these miRNAs were evaluated by GO enrichment and KEGG pathway analysis to identify critical pathways regulated by these miRNAs during puberty in goats. Finally, we selected four known miRNA and one novel miRNAs to evaluate expression patterns in two samples via qRT-PCR to validate the RNA-seq data.

RESULTS

In this study, 476 miRNAs were detected in goat pituitary tissue; 13 of these were specifically expressed in the pituitary of prepubescent goats, and 17 were unique to the pituitary of pubescent goats. Additionally, 73 novel miRNAs were predicted in these two libraries. 20 differentially expressed miRNAs were identified in this study. KEGG pathway enrichment analysis revealed that the differentially expressed miRNA target genes were enriched in pathways related to ovary development during puberty, including the GABAergic synapse, oxytocin signaling pathway, the cAMP signaling pathway, progesterone-mediated oocyte maturation. In this study, differential miRNA expression in the pituitary tissue of prepubescent and pubescent goats were identified and characterized.

CONCLUSION

These results provide important information regarding the potential regulation of the onset of goat puberty by miRNAs, and contribute to the elucidation of miRNA regulated processes during maturation and reproduction.

An Integrated Analysis of miRNAs and Methylated Genes Encoding mRNAs and lncRNAs in Sheep Breeds with Different Fecundity

In our previous study, we investigated the regulatory relationship between lncRNAs, miRNA, and mRNAs in an effort to shed light onto the regulatory mechanisms involved in sheep fecundity. As an extension of this study, here, we aimed to identify potential regulators of sheep fecundity using a genome-wide analysis of miRNAs and the methylated genes encoding mRNAs and lncRNAs in the ovaries of Dorset sheep (low fecundity) and Small Tail Han ewes (high fecundity) with the genotype BB (Han BB) and the genotype ++ (Han ++) by performing RNA-Seq and MeDIP-Seq analyses. Methylated coding-non-coding gene co-expression networks for Han and Dorset sheep were constructed using the methylated genes encoding the differentially expressed mRNAs and lncRNAs identified in this study. In the Han BB vs. Dorset comparison, the lncRNAs TTC26 and MYH15 had the largest degree. Similarly, the lncRNA NYAP1 had the largest degree in the Han ++ vs. Dorset comparison. None of the methylated genes encoding lncRNAs were co-expressed with the methylated genes encoding mRNAs in the Han BB vs. Han ++ comparison. The methylated genes encoding lncRNAs identified here may play a vital regulatory role in sheep breeding. Our results suggest that miRNAs might play a key role in sheep prolificacy by regulating target genes related to thyroid hormone synthesis, and methylated genes encoding lncRNAs associated with tight junctions might contribute to the high breeding rate in Han sheep. These findings may contribute to a deeper understanding of sheep prolificacy.

Global transcriptome analysis identifies differentially expressed genes related to lipid metabolism in Wagyu and Holstein cattle

Fat deposition of beef cattle varies between breeds. However, the regulation mechanism is still not elucidated completely at molecular level. In the present study, we comparatively analyzed transcriptome of subcutaneous adipose tissue between Wagyu and Holstein cattle with a significant difference in fat deposition to identify key genes associated with fat metabolism and adipogenesis by high-throughput RNA-seq technology. A total of 59,149,852 and 69,947,982 high quality reads were generated, respectively. With further analysis, 662 differentially expressed genes were identified. Gene Ontology and KEGG pathway analysis revealed that many differentially expressed genes were enriched in several biological processes and pathways relevant to adipogenesis and lipid metabolism, in which PPAR and fatty acid metabolism signaling pathways with related genes such as PPARγ, PLIN2 and ELOVL6 et al. play a critical role. Protein-protein interaction network analysis showed EGR1, FOS, SERPINE1, AGT, MMP2 may have great impact on adipocyte differentiation and adipogenesis. Moreover, potential alternative splicing events and single nucleotide polymorphisms (SNPs) were also identified. In summary, we comprehensively analyzed and discussed the transcriptome of subcutaneous adipose tissue of Wagyu and Holstein cattle, which might provide a theoretical basis for better understanding molecular mechanism of fat metabolism and deposition in beef cattle.

Identification and comparative analysis of the ovarian microRNAs of prolific and non-prolific goats during the follicular phase using high-throughput sequencing

The kidding rate is one of the most important economic traits for goat production, but the genetic mechanism that is associated with ovulation rate is poorly understood. Recently, increasing evidence has suggested that microRNAs (miRNAs) influence ovarian biological processes. The present study provides the first comparison of the ovarian miRNAs of prolific Jintang black goats (JTGs) and non-prolific Tibetan goats (TBGs) during the follicular phase using RNA-Seq technology. We generated 11.19 million (M) and 11.34 M clean reads from the TBG and JTG libraries, respectively, from which a total of 389 known miRNAs were identified and 142 novel miRNAs were predicted. A total of 191 miRNAs were differentially expressed between the two breeds. Among the 10 most abundant miRNAs, miR-21-5p was defined as differentially expressed miRNA with a higher level in the JTG library than in the TBG library, but the other miRNAs were not different between the breeds. The predicted miRNA-targeted genes were further analyzed by Gene Ontology and KEGG pathway analyses. The results revealed that miR-21, miR-99a, miRNA-143, let-7f, miR-493 and miR-200b may affect follicular development. These findings will increase the current understanding of the role of ovarian miRNAs in the regulation of ovulation rate in goats.

Identification and characterization of differentially expressed miRNAs in subcutaneous adipose between Wagyu and Holstein cattle

MicroRNAs (miRNAs) are important post-transcriptional regulators involved in animal adipogenesis, however, their roles in bovine fat deposition remain poorly understood. In the present study, we conducted a comparative RNA sequencing to identify the key miRNAs involved in beef lipid accumulation by comparing the backfat small RNA samples between Wagyu (high intramuscular fat) and Holstein (moderate intramuscular fat) cattle. Fifteen miRNAs such as bta-miR-142-3p, bta-miR-379, bta-miR-196a, bta-miR-196b, bta-miR-30f and bta-miR-2887 were identified to have a higher expression level in Wagyu cattle compared with Holstein, whereas bta-miR-320a, bta-miR-874 and bta-miR-1247-3p had a lower expression level in Wagyu. Furthermore, a total of 1345 potential target genes of differentially expressed miRNAs were predicted using bioinformatics tools, in which PPARα and RXRα were known to play a critical role in adipocyte differentiation and lipid metabolism. In conclusion, the present study constructed a high-throughput RNA sequencing screen and successfully identified miRNAs such as bta-miR-874, bta-miR-320a and bta-miR-196b which may affect beef fat deposition. The present findings may provide a theoretical foundation for the utilization of beef cattle germplasm resources.