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Yin Y, Zhang J, Li X, Duan M, Zhao M, Zhang F, Chamba Y, Shang P. Application of RNA-Seq Technology for Screening Reproduction-Related Differentially Expressed Genes in Tibetan and Yorkshire Pig Ovarian Tissue. Vet Sci 2024; 11:283. [PMID: 39057967 PMCID: PMC11281381 DOI: 10.3390/vetsci11070283] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2024] [Revised: 06/13/2024] [Accepted: 06/17/2024] [Indexed: 07/28/2024] Open
Abstract
The purpose of this study was to explore and verify genes that regulate the reproductive traits of Tibetan pigs at the mRNA level. The ovarian tissues of Tibetan pigs (TPs) and Yorkshire pigs (YPs) were selected as research objects, and cDNA libraries of the ovarian tissue transcripts of Tibetan pigs and Yorkshire pigs were successfully constructed by the RNA-Seq technique. A total of 651 differentially expressed genes (DEGs) were screened, including 414 up-regulated genes and 237 down-regulated genes. Through GO and KEGG enrichment analysis, it was found that these differentially expressed genes were significantly enriched in cell process, reproductive process, reproduction, cell proliferation, binding, and catalytic activity, as well as oxidative phosphorylation, endocrine resistance, thyroid hormone, Notch, and other signal transduction pathways. Genes significantly enriched in pathways closely related to reproductive regulation were analyzed and selected, and the AR, CYP11A1, CYP17A1, INHBA, ARRB2, EGFR, ETS1, HSD17B1, IGF1R, MIF, SCARB1, and SMAD4 genes were identified as important candidate genes. Twelve differentially expressed genes related to reproduction were verified by RT-qPCR. The results showed that the expression of the AR, CYP17A1, EGFR, ETS1, IGF1R, and SMAD4 genes was significantly higher in Tibetan pigs than in Yorkshire pigs, while the expression of the CYP11A1, INHBA, ARRB2, HSD17B, MIF, and SCARB1 genes in Tibetan pigs was significantly lower than in Yorkshire pigs. The purpose of this study is to provide a theoretical basis for exploring the molecular mechanism of reproductive trait effect genes and the application of molecular breeding in Tibetan pigs.
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Affiliation(s)
- Yikai Yin
- College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi 860000, China; (Y.Y.); (J.Z.); (X.L.); (M.D.); (M.Z.); (F.Z.)
- The Provincial and Ministerial Co-Founded Collaborative Innovation Center for R&D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Linzhi 860000, China
- Key Laboratory for the Genetic Improvement and Reproduction Technology of the Tibetan Swine, Linzhi 860000, China
| | - Jian Zhang
- College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi 860000, China; (Y.Y.); (J.Z.); (X.L.); (M.D.); (M.Z.); (F.Z.)
- The Provincial and Ministerial Co-Founded Collaborative Innovation Center for R&D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Linzhi 860000, China
- Key Laboratory for the Genetic Improvement and Reproduction Technology of the Tibetan Swine, Linzhi 860000, China
| | - Xindi Li
- College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi 860000, China; (Y.Y.); (J.Z.); (X.L.); (M.D.); (M.Z.); (F.Z.)
- The Provincial and Ministerial Co-Founded Collaborative Innovation Center for R&D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Linzhi 860000, China
- Key Laboratory for the Genetic Improvement and Reproduction Technology of the Tibetan Swine, Linzhi 860000, China
| | - Mengqi Duan
- College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi 860000, China; (Y.Y.); (J.Z.); (X.L.); (M.D.); (M.Z.); (F.Z.)
- The Provincial and Ministerial Co-Founded Collaborative Innovation Center for R&D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Linzhi 860000, China
- Key Laboratory for the Genetic Improvement and Reproduction Technology of the Tibetan Swine, Linzhi 860000, China
| | - Mingxuan Zhao
- College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi 860000, China; (Y.Y.); (J.Z.); (X.L.); (M.D.); (M.Z.); (F.Z.)
- The Provincial and Ministerial Co-Founded Collaborative Innovation Center for R&D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Linzhi 860000, China
- Key Laboratory for the Genetic Improvement and Reproduction Technology of the Tibetan Swine, Linzhi 860000, China
| | - Feifan Zhang
- College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi 860000, China; (Y.Y.); (J.Z.); (X.L.); (M.D.); (M.Z.); (F.Z.)
- The Provincial and Ministerial Co-Founded Collaborative Innovation Center for R&D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Linzhi 860000, China
- Key Laboratory for the Genetic Improvement and Reproduction Technology of the Tibetan Swine, Linzhi 860000, China
| | - Yangzom Chamba
- College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi 860000, China; (Y.Y.); (J.Z.); (X.L.); (M.D.); (M.Z.); (F.Z.)
- The Provincial and Ministerial Co-Founded Collaborative Innovation Center for R&D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Linzhi 860000, China
- Key Laboratory for the Genetic Improvement and Reproduction Technology of the Tibetan Swine, Linzhi 860000, China
| | - Peng Shang
- College of Animal Science, Tibet Agriculture and Animal Husbandry College, Linzhi 860000, China; (Y.Y.); (J.Z.); (X.L.); (M.D.); (M.Z.); (F.Z.)
- The Provincial and Ministerial Co-Founded Collaborative Innovation Center for R&D in Tibet Characteristic Agricultural and Animal Husbandry Resources, Linzhi 860000, China
- Key Laboratory for the Genetic Improvement and Reproduction Technology of the Tibetan Swine, Linzhi 860000, China
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Liu M, Chen J, Zhang C, Liu S, Chao X, Yang H, Muhammad A, Zhou B, Ao W, Schinckel AP. Deciphering Estrus Expression in Gilts: The Role of Alternative Polyadenylation and LincRNAs in Reproductive Transcriptomics. Animals (Basel) 2024; 14:791. [PMID: 38473176 DOI: 10.3390/ani14050791] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2024] [Revised: 02/29/2024] [Accepted: 03/01/2024] [Indexed: 03/14/2024] Open
Abstract
The fertility rate and litter size of female pigs are critically affected by the expression of estrus. The objective of this study was to elucidate the regulatory mechanisms of estrus expression by analyzing the differential expression of genes and long intergenic non-coding RNAs (lincRNA), as well as the utilization of alternative polyadenylation (APA) sites, in the vulva and vagina during the estrus and diestrus stages of Large White and indigenous Chinese Mi gilts. Our study revealed that the number of differentially expressed genes (DEG) in the vulva was less than that in the vagina, and the DEGs in the vulva were enriched in pathways such as "neural" pathways and steroid hormone responses, including the "Calcium signaling pathway" and "Oxytocin signaling pathway". The DEGs in the vagina were enriched in the "Metabolic pathways" and "VEGF signaling pathway". Furthermore, 27 and 21 differentially expressed lincRNAs (DEL), whose target genes were enriched in the "Endocrine resistance" pathway, were identified in the vulva and vagina, respectively. Additionally, we observed that 63 and 618 transcripts of the 3'-untranslated region (3'-UTR) were lengthened during estrus in the vulva and vagina, respectively. Interestingly, the genes undergoing APA events in the vulva exhibited species-specific enrichment in neural or steroid-related pathways, whereas those in the vagina were enriched in apoptosis or autophagy-related pathways. Further bioinformatic analysis of these lengthened 3'-UTRs revealed the presence of multiple miRNAs binding sites and cytoplasmic polyadenylation element (CPE) regulatory aspects. In particular, we identified more than 10 CPEs in the validated lengthened 3'-UTRs of the NFIX, PCNX4, CEP162 and ABHD2 genes using RT-qPCR. These findings demonstrated the involvement of APA and lincRNAs in the regulation of estrus expression in female pigs, providing new insights into the molecular mechanisms underlying estrus expression in pigs.
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Affiliation(s)
- Mingzheng Liu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Jiahao Chen
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Chunlei Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Shuhan Liu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Xiaohuan Chao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Huan Yang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Asim Muhammad
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Bo Zhou
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China
| | - Weiping Ao
- College of Animal Science and Technology, Tarim University, Alar 843300, China
| | - Allan P Schinckel
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907-2054, USA
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Xiang X, Huang X, Wang J, Zhang H, Zhou W, Xu C, Huang Y, Tan Y, Yin Z. Transcriptomic and metabolomic analyses of the ovaries of Taihe black-bone silky fowls at the peak egg-laying and nesting period. Front Genet 2023; 14:1222087. [PMID: 37876591 PMCID: PMC10591096 DOI: 10.3389/fgene.2023.1222087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2023] [Accepted: 09/25/2023] [Indexed: 10/26/2023] Open
Abstract
The poor reproductive performance of most local Chinese chickens limits the economic benefits and output of related enterprises. As an excellent local breed in China, Taihe black-bone silky fowl is in urgent need of our development and utilization. In this study, we performed transcriptomic and metabolomic analyses of the ovaries of Taihe black-bone silky fowls at the peak egg-laying period (PP) and nesting period (NP) to reveal the molecular mechanisms affecting reproductive performance. In the transcriptome, we identified five key differentially expressed genes (DEGs) that may affect the reproductive performance of Taihe black-bone silky fowl: BCHE, CCL5, SMOC1, CYTL1, and SCIN, as well as three important pathways: the extracellular region, Neuroactive ligand-receptor interaction and Cytokine-cytokine receptor interaction. In the metabolome, we predicted three important ovarian significantly differential metabolites (SDMs): LPC 20:4, Bisphenol A, and Cortisol. By integration analysis of transcriptome and metabolome, we identified three important metabolite-gene pairs: "LPC 20:4-BCHE", "Bisphenol A-SMOC1", and "Cortisol- SCIN". In summary, this study contributes to a deeper understanding of the regulatory mechanism of egg production in Taihe black-bone silky fowl and provides a scientific basis for improving the reproductive performance of Chinese local chickens.
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Affiliation(s)
- Xin Xiang
- Animal Science College, Zhejiang University, Hangzhou, China
| | - Xuan Huang
- Animal Science College, Zhejiang University, Hangzhou, China
| | | | - Haiyang Zhang
- Animal Science College, Zhejiang University, Hangzhou, China
| | - Wei Zhou
- Animal Science College, Zhejiang University, Hangzhou, China
| | - Chunhui Xu
- Animal Science College, Zhejiang University, Hangzhou, China
| | - Yunyan Huang
- Animal Science College, Zhejiang University, Hangzhou, China
| | - Yuting Tan
- Animal Science College, Zhejiang University, Hangzhou, China
| | - Zhaozheng Yin
- Animal Science College, Zhejiang University, Hangzhou, China
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Kulus J, Kranc W, Kulus M, Dzięgiel P, Bukowska D, Mozdziak P, Kempisty B, Antosik P. Expression of genes regulating cell division in porcine follicular granulosa cells. Cell Div 2023; 18:12. [PMID: 37550786 PMCID: PMC10408085 DOI: 10.1186/s13008-023-00094-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 07/27/2023] [Indexed: 08/09/2023] Open
Abstract
BACKGROUND Cell cycle regulation influences the proliferation of granulosa cells and affects many processes related to ovarian folliclular growth and ovulation. Abnormal regulation of the cell cycle can lead to many diseases within the ovary. The aim of this study was to describe the expression profile of genes within granulosa cells, which are related to the formation of the cytoskeleton, organization of cell organelles inside the cell, and regulation of cell division. Established in vitro primary cultures from porcine ovarian follicle granulosa cells were maintained for 48, 96, 144 h and evaluated via microarray expression analysis. RESULTS Analyzed genes were assigned to 12 gene ontology groups "actin cytoskeleton organization", "actin filament organization", "actin filament-based process", "cell-matrix adhesion", "cell-substrate adhesion", "chromosome segregation", "chromosome separation", "cytoskeleton organization", "DNA integrity checkpoint", "DNA replication initiation", "organelle fision", "organelle organization". Among the genes with significantly changed expression, those whose role in processes within the ovary are selected for consideration. Genes with increased expression include (ITGA11, CNN1, CCl2, TPM2, ACTN1, VCAM-1, COL3A1, GSN, FRMD6, PLK2). Genes with reduced expression inlcude (KIF14, TACC3, ESPL1, CDC45, TTK, CDC20, CDK1, FBXO5, NEK2-NIMA, CCNE2). For the results obtained by microarray expressions, quantitative validation by RT-qPCR was performed. CONCLUSIONS The results indicated expression profile of genes, which can be considered as new molecular markers of cellular processes involved in signaling, cell structure organization. The expression profile of selected genes brings new insight into regulation of physiological processes in porcine follicular granulosa cells during primary in vitro culture.
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Affiliation(s)
- Jakub Kulus
- Department of Diagnostics and Clinical Sciences, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, Torun, Poland
| | - Wiesława Kranc
- Department of Anatomy, Poznan University of Medical Sciences, Poznan, Poland
| | - Magdalena Kulus
- Department of Veterinary Surgery, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, Torun, Poland
| | - Piotr Dzięgiel
- Division of Histology and Embryology, Department of Human Morphology and Embryology, Wroclaw Medical University, Wroclaw, Poland
- Department of Physiotherapy, Wroclaw University School of Physical Education, Wroclaw, Poland
| | - Dorota Bukowska
- Department of Diagnostics and Clinical Sciences, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, Torun, Poland
| | - Paul Mozdziak
- Physiology Graduate Faculty, College of Agriculture and Life Sciences, North Carolina State University, Raleigh, NC, 27695, USA
| | - Bartosz Kempisty
- Department of Veterinary Surgery, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, Torun, Poland.
- Physiology Graduate Faculty, College of Agriculture and Life Sciences, North Carolina State University, Raleigh, NC, 27695, USA.
- Division of Anatomy, Department of Human Morphology and Embryology, Wroclaw Medical University, Wroclaw, Poland.
- Center of Assisted Reproduction, Department of Obstetrics and Gynecology, University Hospital and Masaryk University, Brno, Czech Republic.
| | - Paweł Antosik
- Department of Veterinary Surgery, Institute of Veterinary Medicine, Nicolaus Copernicus University in Torun, Torun, Poland
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Zhu Y, Ye J, Qin P, Yan X, Gong X, Li X, Liu Y, Li Y, Yu T, Zhang Y, Ling Y, Wang J, Cao H, Fang F. Analysis of serum reproductive hormones and ovarian genes in pubertal female goats. J Ovarian Res 2023; 16:69. [PMID: 37024956 PMCID: PMC10080748 DOI: 10.1186/s13048-023-01150-0] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2022] [Accepted: 03/29/2023] [Indexed: 04/08/2023] Open
Abstract
BACKGROUND Age at puberty is an important factor affecting goat fertility, with endocrine and genetic factors playing a crucial role in the onset of puberty. To better understand the relationship between endocrine and genetic factors and mechanisms underlying puberty onset in goats, reproductive hormone levels were analyzed by ELISA and ultraperformance liquid chromatography-multiple reaction monitoring-multistage/mass spectrometry and RNA sequencing was performed to analyze ovarian genes. RESULTS Serum follicle stimulating hormone, luteinizing hormone, estradiol, 11-deoxycortisol, 11-deoxycorticosterone, corticosterone, cortisone, and cortisol levels were found to be higher but progesterone were lower in pubertal goats as compared to those in prepubertal goats (P < 0.05). A total of 18,139 genes were identified in cDNA libraries, and 75 differentially expressed genes (DEGs) were identified (|log2 fold change|≥ 1, P ≤ 0.05), of which 32 were significantly up- and 43 were down-regulated in pubertal goats. Gene ontology enrichment analyses indicated that DEGs were mainly involved in "metabolic process," "signaling," "reproduction," and "growth." Further, DEGs were significantly enriched in 91 Kyoto Encyclopedia of Genes and Genomes pathways, including estrogen signaling pathway, steroid hormone biosynthesis, and cAMP signaling pathway. Bioinformatics analysis showed that PRLR and THBS1 were highly expressed in pubertal ovaries, and ZP3, ZP4, and ASTL showed low expression, suggesting their involvement in follicular development and lutealization. CONCLUSIONS To summarize, serum hormone changes and ovarian DEGs expression were investigated in our study. Further studies are warranted to comprehensively explore the functions of DEGs in goat puberty.
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Affiliation(s)
- Yanyun Zhu
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Jing Ye
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Ping Qin
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Xu Yan
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Xinbao Gong
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Xiaoqian Li
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Ya Liu
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Yunsheng Li
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China
| | - Tong Yu
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Yunhai Zhang
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Yinghui Ling
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Juhua Wang
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China
| | - Hongguo Cao
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, China
| | - Fugui Fang
- Department of Animal Veterinary Science, College of Animal Science and Technology, Anhui Agricultural University, 130 Changjiang West Road, Hefei, Anhui, 230036, China.
- Anhui Province Key Laboratory of Local Livestock and Poultry, Genetical Resource Conservation and Breeding, College of Animal Science and Technology, Anhui Agricultural University, Hefei, Anhui, 230036, China.
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Selection of suitable reference gene for gene expression studies of porcine ovaries under different conditions in quantitative reverse transcription polymerase chain reaction assay. JOURNAL OF ANIMAL REPRODUCTION AND BIOTECHNOLOGY 2022. [DOI: 10.12750/jarb.37.2.96] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/08/2022] Open
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Liu M, Xu Q, Zhao J, Guo Y, Zhang C, Chao X, Cheng M, Schinckel AP, Zhou B. Comprehensive Transcriptome Analysis of Follicles from Two Stages of the Estrus Cycle of Two Breeds Reveals the Roles of Long Intergenic Non-Coding RNAs in Gilts. BIOLOGY 2022; 11:biology11050716. [PMID: 35625443 PMCID: PMC9138455 DOI: 10.3390/biology11050716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/30/2022] [Revised: 04/28/2022] [Accepted: 05/05/2022] [Indexed: 11/21/2022]
Abstract
Simple Summary This study provides new perspectives about the roles of lincRNAs in the estrus expression of gilts, which is correlated with ovarian steroid hormone and follicular development. Follicular tissues from two stages of the estrus cycle of Large White and Mi gilts were used for RNA-seq. Some genes and lincRNAs related to estrus expression in pigs were discovered. PPI and ceRNA networks related to the estrus expression were constructed. These results suggest that the estrus expression may be affected by lincRNAs and their target genes. Abstract Visible and long-lasting estrus expression of gilts and sows effectively sends a mating signal. To reveal the roles of Long Intergenic Non-coding RNAs (lincRNAs) in estrus expression, RNA-seq was used to investigate the lincRNAs expression of follicular tissues from Large White gilts at diestrus (LD) and estrus (LE), and Chinese Mi gilts at diestrus (MD) and estrus (ME). Seventy-three differentially expressed lincRNAs (DELs) were found in all comparisons (LE vs. ME, LD vs. LE, and MD vs. ME comparisons). Eleven lincRNAs were differentially expressed in both LD vs. LE and MD vs. ME comparisons. Fifteen DELs were mapped onto the pig corpus luteum number Quantitative Trait Loci (QTL) fragments. A protein–protein interaction (PPI) network that involved estrus expression using 20 DEGs was then constructed. Interestingly, three predicted target DEGs (PTGs) (CYP19A1 of MSTRG.10910, CDK1 of MSTRG.10910 and MSTRG.23984, SCARB1 of MSTRG.1559) were observed in the PPI network. A competitive endogenous RNA (ceRNA) network including three lincRNAs, five miRNAs, and five genes was constructed. Our study provides new insight into the lincRNAs associated with estrus expression and follicular development in gilts.
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Affiliation(s)
- Mingzheng Liu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.L.); (Q.X.); (J.Z.); (Y.G.); (C.Z.); (X.C.); (M.C.)
| | - Qinglei Xu
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.L.); (Q.X.); (J.Z.); (Y.G.); (C.Z.); (X.C.); (M.C.)
| | - Jing Zhao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.L.); (Q.X.); (J.Z.); (Y.G.); (C.Z.); (X.C.); (M.C.)
| | - Yanli Guo
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.L.); (Q.X.); (J.Z.); (Y.G.); (C.Z.); (X.C.); (M.C.)
| | - Chunlei Zhang
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.L.); (Q.X.); (J.Z.); (Y.G.); (C.Z.); (X.C.); (M.C.)
| | - Xiaohuan Chao
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.L.); (Q.X.); (J.Z.); (Y.G.); (C.Z.); (X.C.); (M.C.)
| | - Meng Cheng
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.L.); (Q.X.); (J.Z.); (Y.G.); (C.Z.); (X.C.); (M.C.)
| | - Allan P. Schinckel
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907-2054, USA;
| | - Bo Zhou
- College of Animal Science and Technology, Nanjing Agricultural University, Nanjing 210095, China; (M.L.); (Q.X.); (J.Z.); (Y.G.); (C.Z.); (X.C.); (M.C.)
- Correspondence:
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Park Y, Park YB, Lim SW, Lim B, Kim JM. Time Series Ovarian Transcriptome Analyses of the Porcine Estrous Cycle Reveals Gene Expression Changes during Steroid Metabolism and Corpus Luteum Development. Animals (Basel) 2022; 12:ani12030376. [PMID: 35158699 PMCID: PMC8833361 DOI: 10.3390/ani12030376] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 02/01/2022] [Accepted: 02/02/2022] [Indexed: 12/13/2022] Open
Abstract
Simple Summary The estrous cycle, which is divided into follicular and luteal phases based on ovulation, is influenced by reproductive hormones which affect reproduction and cause changes in the reproductive system of the pig. As the main reproductive organ, the ovary is involved in ovulation and changes in the corpus luteum. We aimed to identify dynamic changes in gene expression through differentially expressed gene profiling and to provide a comprehensive understanding of the molecular mechanisms that occur in the pig ovary during the estrous cycle. The transcriptome analysis revealed that the dynamic change in gene expression was more activated in the luteal phase than in the follicular phase. Functional analysis revealed that the metestrus and diestrus periods are important in preparation for pregnancy or the next estrous cycle after ovulation. Abstract The porcine estrous cycle is influenced by reproductive hormones, which affect porcine reproduction and result in physiological changes in the reproductive organs. The ovary is involved in ovulation, luteinization, corpus luteum development, and luteolysis. Here, we aimed to provide a comprehensive understanding of the gene expression patterns in porcine ovarian transcriptomes during the estrous cycle through differentially expressed genes profiling and description of molecular mechanisms. The transcriptomes of porcine ovary were obtained during the estrous cycle at three-day intervals from day 0 to day 18 using RNA-seq. At seven time points of the estrous cycle, 4414 DEG were identified; these were classified into three clusters according to their expression patterns. During the late metestrus and diestrus periods, the expression in cluster 1 increased rapidly, and steroid biosynthesis was significant in the pathway. Cluster 2 gene expression patterns represented the cytokine–cytokine receptor interaction in significant pathways. In cluster 3, the hedgehog signaling pathway was selected as the significant pathway. Our study exhibited dynamic gene expression changes with these three different patterns of cluster 1, 2, and 3. The results helped identify the functions and related significant genes especially during the late metestrus and diestrus periods in the estrous cycle.
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Molecular assessment and transcriptome profiling of wild fish populations of Oryzias mekongensis and O. songkhramensis (Adrianichthyidae: Beloniformes) from Thailand. PLoS One 2020; 15:e0242382. [PMID: 33211755 PMCID: PMC7676673 DOI: 10.1371/journal.pone.0242382] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2020] [Accepted: 11/01/2020] [Indexed: 11/19/2022] Open
Abstract
Among the fish of the genus Oryzias, two species are frequently used as model animals in biological research. In Thailand, Oryzias mekongensis is usually found in natural freshwater near the Mekong Basin in the northeast region, while O. songkhramensis inhabits the Songkhram Basin. For differential morphological identification, the coloured bands on the dorsal and ventral margins of the caudal fin are used to distinguish O. mekongensis from O. songkhramensis. However, these characteristics are insufficient to justify species differentiation, and little molecular evidence is available to supplement them. This study aimed to investigate the molecular population and transcriptome profiles of adult O. mekongensis and O. songkhramensis. In the molecular tree based on cytochrome b sequences, O. mekongensis exhibited four clades that were clearly distinguished from O. songkhramensis. Clade 1 of the O. mekongensis population was close to the Mekong River and lived in the eastern portion of the upper northeast region. Clade 2 was far from the Mekong River and inhabited the middle region of the Songkhram River. Clade 3 was positioned to the west of the Songkhram River, and clade 4 was to the south of the Songkhram River Basin. After RNA sequencing using an Illumina HiSeq 2500 platform, the gene category annotations hardly differentiated the species and were discussed in the text. Based on the present findings, population dispersal of these Oryzias species might be associated with geographic variations of the upper northeast region. Molecular genetics and transcriptome profiling might advance our understanding of the evolution of teleost fish.
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Identification of Ovarian Circular RNAs and Differential Expression Analysis between MeiShan and Large White Pigs. Animals (Basel) 2020; 10:ani10071114. [PMID: 32610571 PMCID: PMC7401585 DOI: 10.3390/ani10071114] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Revised: 06/22/2020] [Accepted: 06/26/2020] [Indexed: 12/16/2022] Open
Abstract
MeiShan and Large White pigs differ in their female fecundity. However, the mechanisms behind the gene expression and regulation that cause these differences remain unclear. In this study, we profiled circRNAs and identified 5,879 circRNAs from the ovaries of MeiShan and Large White pigs. Eighty-five circRNAs were differentially expressed between the two pig breeds. Of these, 37 were up-regulated and 48 were down-regulated in MeiShan pigs. Gene ontology enrichment analysis suggested that the differentially expressed circRNA were involved in the hormone-mediated signaling pathway. We verified that circSCIN and its parent gene, scinderin (SCIN), were differentially expressed by reverse transcription and quantitative PCR (RT-qPCR). Luciferase assays demonstrated that circSCIN can target and sponge miR-133 and miR-148a/b. The identification of differentially expressed circRNAs (DECs) and their regulatory functions increased our understanding of the differences in reproductive efficiency between MeiShan and Large White pigs.
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Srikanth K, Park W, Lim D, Lee KT, Jang GW, Choi BH, Ka H, Park JE, Kim JM. Serial gene co-expression network approach to mine biological meanings from integrated transcriptomes of the porcine endometrium during estrous cycle. Funct Integr Genomics 2019; 20:117-131. [PMID: 31396752 DOI: 10.1007/s10142-019-00703-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2018] [Revised: 07/03/2019] [Accepted: 07/22/2019] [Indexed: 01/22/2023]
Abstract
The estrous cycle is a complex process regulated by several hormones. To understand the dynamic changes in gene expression that takes place in the swine endometrium during the estrous cycle relative to the day of estrus onset, we performed RNA-sequencing analysis on days 0, 3, 6, 9, 12, 15, and 18, resulting in the identification of 4495 differentially expressed genes (DEGs; Q ≤ 0.05 and |log2FC| ≥ 1) at various phases in the estrous cycle. These DEGs were integrated into multiple gene co-expression networks based on different fold changes and correlation coefficient (R2) thresholds and a suitable network, which included 899 genes (|log2FC| ≥ 2 and R2 ≥ 0.99), was identified for downstream analyses based on the biological relevance of the Gene Ontology (GO) terms enriched. The genes in this network were partitioned into 6 clusters based on the expression pattern. Several GO terms including cell cycle, apoptosis, hormone signaling, and lipid biosynthetic process were found to be enriched. Furthermore, we found 15 significant KEGG pathways, including cell adhesion molecules, cytokine-cytokine receptor signaling, steroid biosynthesis, and estrogen signaling pathways. We identified several genes and GO terms to be stage-specific. Moreover, the identified genes and pathways extend our understanding of porcine endometrial regulation during estrous cycle and will serve as a good resource for future studies.
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Affiliation(s)
- Krishnamoorthy Srikanth
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea
| | - WonCheoul Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea
| | - Dajeong Lim
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea
| | - Kyung Tai Lee
- Animal Genetics and Breeding Division, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea
| | - Gul Won Jang
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea
| | - Bong Hwan Choi
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea
| | - Hakhyun Ka
- Division of Biological Science and Technology, Yonsei University, Wonju, 26493, Republic of Korea.
| | - Jong-Eun Park
- Animal Genomics and Bioinformatics Division, National Institute of Animal Science, RDA, Wanju, 55365, Republic of Korea.
| | - Jun-Mo Kim
- Department of Animal Science and Technology, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea.
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