Hypothalamic Transcriptome Analysis Reveals the Crucial MicroRNAs and mRNAs Affecting Litter Size in Goats

The hypothalamus was the coordination center of the endocrine system, which played an important role in goat reproduction. However, the molecular mechanism of hypothalamus regulating litter size in goats was still poorly understood. This study aims to investigate the key functional genes associated with prolificacy by hypothalamus transcriptome analysis of goats. In this research, an integrated analysis of microRNAs (miRNAs)-mRNA was conducted using the hypothalamic tissue of Yunshang black goats in the follicular stage. A total of 72,220 transcripts were detected in RNA-seq. Besides, 1,836 differentially expressed genes (DEGs) were identified between high fecundity goats at the follicular phase (FP-HY) and low fecundity goats at the follicular phase (FP-LY). DEGs were significantly enriched in 71 Gene Ontology (GO) terms and 8 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. The transcriptome data suggested that DEGs such as BMPR1B, FGFR1, IGF1 and CREB1 are directly or indirectly involved in many processes like hypothalamic gonadal hormone secretion. The miRNA-seq identified 1,837 miRNAs, of which 28 differentially expressed miRNAs (DEMs). These DEMs may affect the nerve cells survival of goat hypothalamic regulating the function of target genes and further affect the hormone secretion activities related to reproduction. They were enriched in prolactin signaling pathway, Jak-STAT signaling pathway and GnRH signaling pathway, as well as various metabolic pathways. Integrated analysis of DEMs and DEGs showed that 87 DEGs were potential target genes of 28 DEMs. After constructing a miRNA-mRNA pathway network, we identified several mRNA-miRNAs pairs by functional enrichment analysis, which was involved in hypothalamic nerve apoptosis. For example, NTRK3 was co-regulated by Novel-1187 and Novel-566, as well as another target PPP1R13L regulated by Novel-566. These results indicated that these key genes and miRNAs may play an important role in the development of goat hypothalamus and represent candidate targets for further research. This study provides a basis for further explanation of the basic molecular mechanism of hypothalamus, but also provides a new idea for a comprehensive understanding of prolificacy characteristics in Yunshang black goats.

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

Scientific Reports ◽

10.1038/s41598-021-01817-y ◽

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

10.21203/rs.3.rs-67727/v1 ◽

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.

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Transcriptome Profile Analysis Reveals an Estrogen Induced LncRNA Associated with Lipid Metabolism and Carcass Traits in Chickens (Gallus Gallus)

Cellular Physiology and Biochemistry ◽

10.1159/000494785 ◽

2018 ◽

Vol 50 (5) ◽

pp. 1638-1658 ◽

Cited By ~ 6

Author(s):

Hong Li ◽

Zhenzhen Gu ◽

Liyu Yang ◽

Yadong Tian ◽

Xiangtao Kang ◽

...

Keyword(s):

Lipid Metabolism ◽

Target Genes ◽

Laying Hens ◽

Functional Enrichment ◽

Differentially Expressed ◽

Integrated Analysis ◽

Chicken Carcass ◽

Triglyceride Content

Background/Aims: Accumulating evidences have demonstrated that long noncoding RNAs (lncRNA) play important roles in hepatic lipid metabolism in mammals. However, no systematic screening of the potential lncRNAs in the livers of laying hens has been performed, and few studies have been reported concerning the effects of the lncRNAs on lipid metabolism in the livers of chickens during egg-laying period. The purpose of this study was to compare the difference in lncRNA expression in the livers of pre-laying and peak-laying hens at the age of 20 and 30 weeks old by transcriptome sequencing and to investigate the interaction networks among lncRNAs, mRNAs and miRNAs. Moreover, the regulatory mechanism and biological function of lncLTR, a significantly differentially expressed lncRNA in the liver between pre- and peak-laying hens, was explored in vitro and in vivo. Methods: Bioinformatics analyses were conducted to identify the differentially expressed (DE) lncRNAs between the two groups of hens. The target genes of the DE lncRNA were predicated for further functional enrichment. An integrated analysis was performed among the DE lncRNA datasets, DE mRNAs and DE miRNA datasets obtained from the same samples to predict the interaction relationship. In addition, in vivo and in vitro trials were carried out to determine the expression regulation of lncLTR, and polymorphism association analysis was conducted to detect the biological role of ncLTR. Results: A total of 124 DE lncRNAs with a P-value ≤ 0.05 were identified. Among them, 44 lncRNAs including 30 known and 14 novel lncRNAs were significant differentially expressed (SDE) with FDR ≤ 0.05. Thirty-two lncRNAs were upregulated and 12 were downregulated in peak-laying group compared with pre-laying group. The functional enrichment results revealed that target genes of some lncRNAs are involved in the lipid metabolism process. Integrated analysis suggested that some of the genes involved in lipid metabolism might be regulated by both the lncRNA and the miRNA. In addition, an upregulated lncRNA, designated lncLTR, was demonstrated to be induced by estrogen via ERβ signaling. The c242. G>A SNP in lncLTR was significantly associated with chicken carcass weight, evisceration weight, semi-evisceration weight, head weight, double-wing weight, claw weight traits, and blood biochemical index, especially for the blood triglyceride content. Conclusion: A series of lncRNAs associated with lipid metabolism in the livers of chickens were identified by transcriptome sequencing and functional analysis, providing a valuable data resource for further studies on chicken hepatic metabolism activities. LncLTR was regulated by estrogen via ERβ signaling and associated with chicken carcass trait and blood triglyceride content.

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Integrated Analysis of lncRNA and mRNA Reveals Novel Insights into Wool Bending in Zhongwei Goat

Animals ◽

10.3390/ani11113326 ◽

2021 ◽

Vol 11 (11) ◽

pp. 3326

Author(s):

Xiaobo Li ◽

Zhanfa Liu ◽

Shaohui Ye ◽

Yue Liu ◽

Qian Chen ◽

...

Keyword(s):

Signaling Pathway ◽

Target Genes ◽

Economic Value ◽

Enrichment Analysis ◽

Functional Enrichment Analysis ◽

Hair Follicles ◽

Functional Enrichment ◽

Integrated Analysis ◽

Rna Seq ◽

Camp Signaling Pathway

Chinese Zhongwei goat is a rare and precious fur breed as its lamb fur is a well-known fur product. Wool bending of lamb fur of the Zhongwei goat is its most striking feature. However, the curvature of the wool decreases gradually with growth, which significantly affects its quality and economic value. The mechanism regulating the phenotypic changes of hair bending is still unclear. In the present study, the skin tissues of Zhongwei goats at 45 days (curving wool) and 108 days (slight-curving wool) after birth were taken as the research objects, and the expression profiling of long non-coding RNAs (lncRNAs) and mRNAs were analyzed based on the Ribo Zero RNA sequencing (RNA-seq) method. In total, 46,013 mRNAs and 13,549 lncRNAs were identified, of which 352 were differentially expressed mRNAs and 60 were. lncRNAs. Functional enrichment analysis of the target genes of lncRNAs were mainly enriched in PI3K-Akt, Arachidonic acid metabolic, cAMP, Wnt, and other signaling pathways. The qRT-PCR results of eight selected lncRNAs and target genes were consistent with the sequencing result, which indicated our data were reliable. Through the analysis of the weighted gene co-expression network, 13 co-expression modules were identified. The turquoise module contained a large number of differential expressed lncRNAs, which were mainly enriched in the PI3K-Akt signaling pathway and cAMP signaling pathway. The predicted LOC102172600 and LOC102191729 might affect the development of hair follicles and the curvature of wool by regulating the target genes. Our study provides novel insights into the potential roles of lncRNAs in the regulation of wool bending. In addition, the study offers a theoretical basis for further study of goat wool growth, so as to be a guidance and reference for breeding and improvement in the future.

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Analysis of potential regulatory LncRNAs and CircRNAs in the oxidative myofiber and glycolytic myofiber of chickens

Scientific Reports ◽

10.1038/s41598-021-00176-y ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Xiaojun Ju ◽

Yifan Liu ◽

Yanju Shan ◽

Gaige Ji ◽

Ming Zhang ◽

...

Keyword(s):

Cell Differentiation ◽

Signaling Pathway ◽

Muscle Cell ◽

Regulatory Mechanism ◽

Functional Enrichment ◽

Differentially Expressed ◽

Myoblast Differentiation ◽

Integrated Analysis ◽

Muscle Cell Differentiation ◽

Myofiber Type

AbstractSART and PMM are mainly composed of oxidative myofibers and glycolytic myofibers, respectively, and myofiber types profoundly influence postnatal muscle growth and meat quality. SART and PMM are composed of lncRNAs and circRNAs that participate in myofiber type regulation. To elucidate the regulatory mechanism of myofiber type, lncRNA and circRNA sequencing was used to systematically compare the transcriptomes of the SART and PMM of Chinese female Qingyuan partridge chickens at their marketing age. The luminance value (L*), redness value (a*), average diameter, cross-sectional area, and density difference between the PMM and SART were significant (p < 0.05). ATPase staining results showed that PMMs were all darkly stained and belonged to the glycolytic type, and the proportion of oxidative myofibers in SART was 81.7%. A total of 5 420 lncRNAs were identified, of which 365 were differentially expressed in the SART compared with the PMM (p < 0.05). The cis-regulatory analysis identified target genes that were enriched for specific GO terms and KEGG pathways (p < 0.05), including striated muscle cell differentiation, regulation of cell proliferation, regulation of muscle cell differentiation, myoblast differentiation, regulation of myoblast differentiation, and MAPK signaling pathway. Pathways and coexpression network analyses suggested that XR_003077811.1, XR_003072304.1, XR_001465942.2, XR_001465741.2, XR_001470487.1, XR_003077673.1 and XR_003074785.1 played important roles in regulating oxidative myofibers by TBX3, QKI, MYBPC1, CALM2, and PPARGC1A expression. A total of 10 487 circRNAs were identified, of which 305 circRNAs were differentially expressed in the SART compared with the PMM (p < 0.05). Functional enrichment analysis showed that differentially expressed circRNAs were involved in host gene expression and were enriched in the AMPK, calcium signaling pathway, FoxO signaling pathway, p53 signaling pathway, and cellular senescence. Novel_circ_004282 and novel_circ_002121 played important roles in regulating oxidative myofibers by PPP3CA and NFATC1 expression. Using lncRNA-miRNA/circRNA-miRNA integrated analysis, we identified many candidate interaction networks that might affect muscle fiber performance. Important lncRNA-miRNA-mRNA networks, such as lncRNA-XR_003074785.1/miR-193-3p/PPARGC1A, regulate oxidative myofibers. This study reveals that lncXR_003077811.1, lncXR_003072304.1, lncXR_001465942.2, lncXR_001465741.2, lncXR_001470487.1, lncXR_003077673.1, XR_003074785.1, novel_circ_004282 and novel_circ_002121 might regulate oxidative myofibers. The lncRNA-XR_003074785.1/miR-193-3p/PPARGC1A pathway might regulate oxidative myofibers. All these findings provide rich resources for further in-depth research on the regulatory mechanism of lncRNAs and circRNAs in myofibers.

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Integrated Analysis of circRNA-miRNA-mRNA Regulatory Networks in the Intestine of Sebastes schlegelii Following Edwardsiella tarda Challenge

Frontiers in Immunology ◽

10.3389/fimmu.2020.618687 ◽

2021 ◽

Vol 11 ◽

Author(s):

Min Cao ◽

Xu Yan ◽

Baofeng Su ◽

Ning Yang ◽

Qiang Fu ◽

...

Keyword(s):

Signaling Pathways ◽

Signaling Pathway ◽

Regulatory Networks ◽

Target Genes ◽

Differentially Expressed ◽

Edwardsiella Tarda ◽

Circular Rnas ◽

Integrated Analysis ◽

Apoptosis Pathway ◽

Sebastes Schlegelii

Sebastes schlegelii, an important aquaculture species, has been widely cultured in East Asian countries. With the increase in the cultivation scale, various diseases have become major threats to the industry. Evidence has shown that non-coding RNAs (ncRNAs) have remarkable functions in the interactions between pathogens and their hosts. However, little is known about the mechanisms of circular RNAs (circRNAs) and coding RNAs in the process of preventing pathogen infection in the intestine in teleosts. In this study, we aimed to uncover the global landscape of mRNAs, circRNAs, and microRNAs (miRNAs) in response to Edwardsiella tarda infection at different time points (0, 2, 6, 12, and 24 h) and to construct regulatory networks for exploring the immune regulatory mechanism in the intestine of S. schlegelii. In total, 1,794 mRNAs, 87 circRNAs, and 79 miRNAs were differentially expressed. The differentially expressed RNAs were quantitatively validated using qRT-PCR. Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analysis showed that most of the differentially expressed mRNA genes and the target genes of ncRNAs were related to immune signaling pathways, such as the NF-κB signal pathway, pathogen recognition receptors related to signaling pathways (Toll-like receptors and Nod-like receptors), and the chemokine signaling pathway. Based on these differentially expressed genes, 624 circRNA-miRNA pairs and 2,694 miRNA-mRNA pairs were predicted using the miRanda software. Integrated analyses generated 25 circRNA-miRNA-mRNA interaction networks. In a novel_circ_0004195/novel-530/IκB interaction network, novel_530 was upregulated, while its two targets, novel_circ_0004195 and IκB, were downregulated after E. tarda infection. In addition, two circRNA-miRNA-mRNA networks related to apoptosis (novel_circ_0003210/novel_152/apoptosis-stimulating of p53 protein 1) and interleukin (novel_circ_0001907/novel_127/interleukin-1 receptor type 2) were also identified in our study. We thus speculated that the downstream NF-κB signaling pathway, p53 signaling pathway, and apoptosis pathway might play vital roles in the immune response in the intestine of S. schlegelii. This study revealed a landscape of RNAs in the intestine of S. schlegelii during E. tarda infection and provided clues for further study on the immune mechanisms and signaling networks based on the circRNA-miRNA-mRNA axis in S. schlegelii.

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Transcriptome Analysis Reveals that Long Noncoding RNAs Contribute to Development Differences of Medium-sized Ovarian Follicle between Meishan and Duroc Sows

10.21203/rs.3.rs-53459/v1 ◽

2020 ◽

Author(s):

Mengxun Li ◽

Yi Liu ◽

Lipeng Ma ◽

Zhichao Zhao ◽

Su Xie ◽

...

Keyword(s):

Litter Size ◽

Target Genes ◽

Ovarian Follicle ◽

Hormone Secretion ◽

Follicular Development ◽

Signalling Pathway ◽

Differentially Expressed ◽

Protein Coding ◽

Reading Frame ◽

In Cis

Abstract Background: Ovulation rate is an extremely important factor of litter size in sows. It differs greatly among pig breeds of different genetic backgrounds. Long non-coding RNAs (lncRNAs) can regulate follicle development, granulosa cell(GC) growth and hormone secretion, which in turn affects sow litter size.Results: In our research, we identified 3554 lncRNAs and 25491 mRNAs in M2 follicle from Meishan and Duroc pigs. lncRNAs sequence and open reading frame(ORF) length is shorter than mRNAs, and it has fewer exons, lower abundance and conserved than protein-coding RNAs. Furthermore, 201 lncRNAs were differentially expressed in breeds, and quantitative trait loci (QTL) analysis of differential expression (DE) lncRNAs were performed. 127 DE lncRNAs are located in 119 reproduction trait-related loci. In addition, the lncRNAs potential target genes (PTGs) in cis or trans were predicted. Gene ontology(GO) and KEGG pathway analysis revealed that some PTGs were include some follicular development and hormone secretion-related biological processes or pathways, such as regulation of progesterone biosynthetic process, oestrogen metabolic process and ovarian steroidogenesis and PI3K-Akt signalling pathway. Furthermore，We also screened 19 differentially expressed lncRNAs of PI3K-Akt signalling pathway as candidates. Conclusions: This study provided a new significance on the roles of lncRNAs in follicular growth and development and porcine reproduction.

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Integrated analysis of lncRNAs and mRNAs reveals key trans-target genes associated with ETEC-F4ac adhesion phenotype in porcine small intestine epithelial cells

BMC Genomics ◽

10.1186/s12864-020-07192-8 ◽

2020 ◽

Vol 21 (1) ◽

Author(s):

Serafino M. A. Augustino ◽

Qinglei Xu ◽

Xueqin Liu ◽

Siyuan Mi ◽

Liangyu Shi ◽

...

Keyword(s):

Small Intestine ◽

Epithelial Cells ◽

Signaling Pathway ◽

Focal Adhesion ◽

Target Genes ◽

Adherens Junction ◽

Interaction Network ◽

Differentially Expressed ◽

Integrated Analysis ◽

Large White

Abstract Background Long non-coding RNAs (lncRNAs) play crucial roles in gene regulation at the transcriptional and post-transcriptional levels. LncRNAs are belonging to a large class of transcripts with ≥200 nt in length which do not code for proteins, have been widely investigated in various physiological and pathological contexts by high-throughput sequencing techniques and bioinformatics analysis. However, little is known about the regulatory mechanisms by which lncRNAs regulate genes that are associated with Enterotoxigenic Escherichia coli F4 fimbriae (ETEC-F4ac) adhesion phenotype in small intestine epithelial cells of Large White piglets. To address this, we used RNA sequencing to profile lncRNAs and mRNAs of small intestine epithelial cells in Large White piglets differing in their ETEC-F4 adhesion phenotypes and ITGB5 genotypes. Eight male piglets were used in this study and were divided into two groups on the basis of their adhesion phenotype and ITGB5 genotypes, a candidate gene for F4ac receptor. Non-adhesive group (n = 4) with CC genotype and adhesive group (n = 4) with TT genotype. Results In total, 78 differentially expressed lncRNAs (DE-lncRNA) and 223 differentially expressed mRNAs (log2 |FC| > 1, P < 0.05) were identified in the comparison of non-adhesive vs. adhesive small intestine epithelial cells. Furthermore, cis- and trans-regulatory target genes of DE-lncRNAs were identified, then interaction networks of lncRNAs and their cis- and trans-target differentially expressed genes (DEGs) were constructed separately. A total of 194 cis-targets were involved in the lncRNAs-cis genes interaction network and 61 trans-targets, were involved in lncRNA-trans gene interaction network that we constructed. We determined that cis-target genes were involved in alcoholism, systemic lupus erythematosus, viral carcinogenesis and malaria. Whereas trans-target DEGs were engaged in three important pathways related to the ETEC-F4 adhesion phenotype namely cGMP-PKG signaling pathway, focal adhesion, and adherens junction. The trans-target DEGs which directly involved in these pathways are KCNMB1 in cGMP-PKG signaling pathway, GRB2 in focal adhesion pathway and ACTN4 in focal adhesion and adherens junction pathways. Conclusion The findings of the current study provides an insight into biological functions and epigenetic regulatory mechanism of lncRNAs on porcine small intestine epithelial cells adhesion to ETEC-F4-ac and piglets’ diarrhea susceptibility/resistance.

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A combined microRNA and transcriptome analysis illuminates the resistance response of rice against brown planthopper

10.21203/rs.2.17550/v2 ◽

2020 ◽

Author(s):

Jiaoyan Tan ◽

Yan Wu ◽

Jianping Guo ◽

Huimin Li ◽

Lili Zhu ◽

...

Keyword(s):

Mrna Expression ◽

Transcriptome Analysis ◽

Molecular Mechanisms ◽

Target Genes ◽

Expression Profiles ◽

Brown Planthopper ◽

Differentially Expressed ◽

Integrated Analysis ◽

Resistance Response

Abstract Background : The brown planthopper (BPH, Nilaparvata lugens Stål) is a kind of phloem-feeding pest that adversely affects rice yield. Recently, the BPH-resistance gene, BPH6 , was cloned and applied in rice breeding to effectively control BPH. However, the molecular mechanisms underlying BPH6 are poorly understood. Results: Here, an integrated miRNA and mRNA expression profiling analysis was performed on BPH6 -transgenic (BPH6G) and Nipponbare (wild type, WT) plants after BPH infestation, and a total of 217 differentially expressed miRNAs (DEMs) and 7,874 differentially expressed mRNAs (DEGs) were identified. 29 miRNAs, including members of miR160, miR166 and miR169 family were opposite expressed during early or late feeding stages between the two varieties, whilst 9 miRNAs were specifically expressed in BPH6G plants, suggesting involvement of these miRNAs in BPH6 -mediated resistance to BPH. In the transcriptome analysis, 949 DEGs were opposite expressed during early or late feeding stages of the two genotypes, which were enriched in metabolic processes, cellular development, cell wall organization, cellular component movement and hormone transport, and certain primary and secondary metabolite synthesis. 24 genes were further selected as candidates for BPH resistance. Integrated analysis of the DEMs and DEGs showed that 34 miRNAs corresponding to 42 target genes were candidate miRNA-mRNA pairs for BPH resistance, 18 pairs were verified by qRT-PCR, and two pairs were confirmed by in vivo analysis. Conclusions: For the first time, we reported integrated small RNA and transcriptome sequencing to illustrate resistance mechanisms against BPH in rice. Our results provide a valuable resource to ascertain changes in BPH-induced miRNA and mRNA expression profiles and enable to comprehend plant-insect interactions and find a way for efficient insect control.

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Comprehensive Analysis of miRNAs and Target mRNAs between Immature and Mature Testis Tissue in Chinese Red Steppes Cattle

Animals ◽

10.3390/ani11113024 ◽

2021 ◽

Vol 11 (11) ◽

pp. 3024

Author(s):

Xibi Fang ◽

Lihong Qin ◽

Haibin Yu ◽

Ping Jiang ◽

Lixin Xia ◽

...

Keyword(s):

Signaling Pathway ◽

Molecular Mechanisms ◽

Target Genes ◽

Gonad Development ◽

Male Reproduction ◽

Differentially Expressed ◽

Integrated Analysis ◽

Adult Cattle ◽

Expression Levels ◽

Regulated Gene Expression

This study aims to screen potential regulators and regulate fecundity networks between microRNAs (miRNAs) and target genes. The bovine testes of immature and mature Chinese Red Steppes were performed by genome-wide analysis of mRNAs and miRNAs. Compared with testicular tissues of newborns, 6051 upregulated genes and 7104 downregulated genes in adult cattle were identified as differentially expressed genes (DEGs). The DEGs were significantly enriched in 808 GO terms (p < 0.05) including male gonad development, male genitalia development, spermatogenesis, and sperm motility. Moreover, DEGs were also significantly enriched in 105 KEGG pathways (p < 0.05), including cGMP-PKG signaling pathway and calcium signaling pathway. To explore the expression of miRNA-regulated gene expression, 896 differentially expressed target genes negatively regulated with the expression levels of 31 differentially expressed miRNAs (DERs) were predicted and analyzed, and a network-integrated analysis was constructed. Furthermore, real-time PCR was performed to verify the expression levels of DEGs and DERs. Our results identified novel candidate DEGs and DERs correlated with male reproduction and intricate regulating networks between miRNAs and genes, which will be valuable for future genetic and epigenetic studies of sperm development and maturity, as well as providing valuable insights into the molecular mechanisms of male fertility and spermatogenesis in cattle.

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