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Ghafouri F, Sadeghi M, Bahrami A, Naserkheil M, Dehghanian Reyhan V, Javanmard A, Miraei-Ashtiani SR, Ghahremani S, Barkema HW, Abdollahi-Arpanahi R, Kastelic JP. Construction of a circRNA- lincRNA-lncRNA-miRNA-mRNA ceRNA regulatory network identifies genes and pathways linked to goat fertility. Front Genet 2023; 14:1195480. [PMID: 37547465 PMCID: PMC10400778 DOI: 10.3389/fgene.2023.1195480] [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: 03/28/2023] [Accepted: 07/03/2023] [Indexed: 08/08/2023] Open
Abstract
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.
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Affiliation(s)
- Farzad Ghafouri
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Mostafa Sadeghi
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Abolfazl Bahrami
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
- Biomedical Center for Systems Biology Science Munich, Ludwig-Maximilians-University, Munich, Germany
| | - Masoumeh Naserkheil
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
- Animal Breeding and Genetics Division, National Institute of Animal Science, Cheonan-si, Republic of Korea
| | - Vahid Dehghanian Reyhan
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Arash Javanmard
- Department of Animal Sciences, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| | - Seyed Reza Miraei-Ashtiani
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - Soheila Ghahremani
- Department of Animal Science, Faculty of Agriculture, University of Tarbiat Modares, Tehran, Iran
| | - Herman W. Barkema
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
| | - Rostam Abdollahi-Arpanahi
- Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran, Karaj, Iran
| | - John P. Kastelic
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB, Canada
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Naicy T, Venkatachalapathy RT, Aravindakshan TV, Raghavan KC, Mini M, Shyama K. Relative abundance of tissue mRNA and association of the single nucleotide polymorphism of the goat NGF gene with prolificacy. Anim Reprod Sci 2016; 173:42-8. [PMID: 27576174 DOI: 10.1016/j.anireprosci.2016.08.009] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2016] [Revised: 08/19/2016] [Accepted: 08/25/2016] [Indexed: 10/21/2022]
Abstract
Nerve Growth Factor (NGF) promotes the development of pre-antral ovarian follicles through ovarian innervations and regulation of ovarian response to gonadotropins. The present study was conducted to study the tissue gene expression profile, to characterize the genetic variants, find associations of the NGF gene with prolificacy in the prolific Malabari and less prolific Attappady Black goats because NGF has an important role in reproduction by augmenting ovarian folliculogenesis. Relative abundance of NGF mRNA was greatest in reproductive tissues signifying its role in reproduction. The PCR-SSCP analysis of a 251bp fragment of Exon 3 of the NGF gene from the 277 goats revealed four diplotypes (EE, EF, FF and EG) with respective frequencies of 0.76, 0.22, 0.01 and 0.01. Sequencing of the representative samples revealed one synonymous and one novel non synonymous mutations (g.705G>A and g.715C>T). Statistical analysis indicated that the SNP g.705G>A was associated with litter size in Attappady Black goats (P<0.05) and a PCR-RFLP was designed using the restriction enzyme, BpiI, for rapid screening of the SNP. The results of the present study suggest that the NGF gene is a primary candidate gene affecting prolificacy in goats and may be used for Marker Assisted Selection (MAS) in goats, especially in lowly prolific Attappady Black goats.
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Affiliation(s)
- Thomas Naicy
- Department of Animal Breeding, Genetics and Biostatistics, College of Veterinary and Animal Sciences, Mannuthy, Thrissur-680651, Kerala, India.
| | - R Thirupathy Venkatachalapathy
- Centre for Advanced Studies in Animal Genetics and Breeding, College of Veterinary and Animal Sciences, Mannuthy, Thrissur-680651, Kerala, India
| | - T V Aravindakshan
- Centre for Advanced Studies in Animal Genetics and Breeding, College of Veterinary and Animal Sciences, Mannuthy, Thrissur-680651, Kerala, India
| | - K C Raghavan
- Centre for Advanced Studies in Animal Genetics and Breeding, College of Veterinary and Animal Sciences, Mannuthy, Thrissur-680651, Kerala, India
| | - M Mini
- Department of Veterinary Microbiology, College of Veterinary and Animal Sciences, Mannuthy, Thrissur-680651, Kerala, India
| | - K Shyama
- Department of Animal Nutrition, College of Veterinary and Animal Sciences, Mannuthy, Thrissur-680651, Kerala, India
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Naicy T, Venkatachalapathy RT, Aravindakshan TV, Radhika G, Raghavan KC, Mini M, Shyama K. Nerve Growth Factor gene ovarian expression, polymorphism identification, and association with litter size in goats. Theriogenology 2016; 86:2172-2178.e3. [PMID: 27544869 DOI: 10.1016/j.theriogenology.2016.07.011] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Revised: 07/12/2016] [Accepted: 07/12/2016] [Indexed: 12/11/2022]
Abstract
The Nerve Growth Factor (NGF) plays an important role in reproduction by augmenting folliculogenesis. In this study, the coding regions of caprine NGF gene were analyzed to detect single-nucleotide polymorphisms (SNPs), their association with litter size, and the relative ovarian expression of NGF gene in the two indigenous goat breeds of South India viz., the prolific Malabari and less-prolific Attappady Black. The sequence analysis of the third exon containing the entire open reading frame of NGF gene was observed to be of 808 bp with one nonsynonymous mutation at 217th position. Later, polymerase chain reaction (PCR) was performed to amplify a region of 188 bp covering the region carrying the detected mutation. The genomic DNAs from the goats under study (n = 277) were subjected to PCR and single strand conformation polymorphism (SSCP). On analysis, four diplotypes viz., AA, AB, AC, and AD were observed with respective frequencies of 0.50, 0.22, 0.27, and 0.01. Sequencing of the representative samples revealed an additional synonymous mutation, i.e., g.291C>A. Statistical analysis indicated that NGF diplotypes and the SNP g.217G>A were associated with litter size in goats (P < 0.05). Relative expression of NGF gene was significantly higher in the ovaries of goats with history of multiple than single births (P < 0.05). The results of the present study suggest the significant effect of the NGF gene on litter size in goats and identified SNPs would benefit the selection of prolific animals in future marker-assisted breeding programs. The two novel PCR-restriction fragment length polymorphisms designed, based on the detected SNPs, would help in the rapid screening of large number of animals in a breeding population for identifying individual animals with desired genetic characteristics.
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Affiliation(s)
- T Naicy
- Department of Animal Breeding, Genetics and Biostatistics, College of Veterinary and Animal Sciences, Thrissur, Kerala, India.
| | - R T Venkatachalapathy
- Centre for Advanced Studies in Animal Genetics and Breeding, College of Veterinary and Animal Sciences, Thrissur, Kerala, India
| | - T V Aravindakshan
- Centre for Advanced Studies in Animal Genetics and Breeding, College of Veterinary and Animal Sciences, Thrissur, Kerala, India
| | - G Radhika
- Department of Animal Breeding, Genetics and Biostatistics, College of Veterinary and Animal Sciences, Thrissur, Kerala, India
| | - K C Raghavan
- Centre for Advanced Studies in Animal Genetics and Breeding, College of Veterinary and Animal Sciences, Thrissur, Kerala, India
| | - M Mini
- Department of Veterinary Microbiology, College of Veterinary and Animal Sciences, Thrissur, Kerala, India
| | - K Shyama
- Department of Animal Nutrition, College of Veterinary and Animal Sciences, Thrissur, Kerala, India
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Hou JX, An XP, Han P, Peng JY, Cao BY. Two missense mutations in exon 9 of caprinePRLRgene were associated with litter size. Anim Genet 2014; 46:87-90. [DOI: 10.1111/age.12223] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 08/05/2014] [Indexed: 12/15/2022]
Affiliation(s)
- J. X. Hou
- College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi 712100 China
| | - X. P. An
- College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi 712100 China
| | - P. Han
- College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi 712100 China
| | - J. Y. Peng
- College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi 712100 China
| | - B. Y. Cao
- College of Animal Science and Technology; Northwest A&F University; Yangling Shaanxi 712100 China
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