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Zhao Y, Zhang L, Wang L, Zhang J, Shen W, Ma Y, Ding C, Wu G. Identification and Analysis of Genes Related to Testicular Size in 14-Day-Old Piglets. Animals (Basel) 2024; 14:172. [PMID: 38200903 PMCID: PMC10778417 DOI: 10.3390/ani14010172] [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: 11/06/2023] [Revised: 12/27/2023] [Accepted: 12/29/2023] [Indexed: 01/12/2024] Open
Abstract
The RNA-Seq technology was used to screen the key genes that affect the early development of the testes of Duroc × Landrace × Yorkshire piglets, to determine the regulatory pathway and provide reference for subsequent reproductive performance research, breeding, and other production practices. This study selected 14-day-old Duroc × Landrace × Yorkshire piglets as the trial animals. Testes from piglets with similar weights and no pathological changes were divided into small testis (ST) and large testis (LT) groups, and the RNA-Seq screening of differentially expressed genes (DEGs) was performed to find candidate genes and regulatory pathways related to early testicular development. The results show that 570 DEGs were found in the ST and LT groups, with 281 upregulated and 289 downregulated. The DEGs were mainly enriched on 47 gene ontology (GO) functional items. The Kyoto encyclopedia of genes and genotypes (KEGG) enrichment analysis found that there were 44 significantly enriched KEGG signal pathways, and the regulation of testicular development mainly focused on the arachidonic acid metabolism, Wnt signaling pathway and GnRH secretion pathways. The PTGES, SFRP1, SPP1, PLA2G4E, KCNJ5, PTGS2, and HCN1 genes were found to be as closely related to the testicular development of these Duroc × Landrace × Yorkshire piglets, and the differential gene expression was consistent with the real-time quantitative reverse transcription PCR (real-time qRT-PCR) validation results. This study was validated by high-throughput sequencing analysis and real-time qRT-PCR, and showed that the PTGES, SFRP1, SPP1, PLA2G4E, KCNJ5, PTGS2, and HCN1 genes may be involved in the regulation of germ cell development, spermatogenesis and semen traits. These should be further studied as candidate genes for early testicular development and reproductive trait regulation in boars.
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Affiliation(s)
- Yunjiao Zhao
- Plateau Livestock Genetic Resources Protection and Innovative Utilization Key Laboratory of Qinghai Province, Qinghai Academy of Animal and Veterinary Medicine, Qinghai University, Xining 810016, China; (Y.Z.); (L.W.); (J.Z.); (W.S.); (Y.M.); (C.D.)
| | - Liangzhi Zhang
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Northwest Institute of Plateau Biology, Xining 810008, China;
| | - Lei Wang
- Plateau Livestock Genetic Resources Protection and Innovative Utilization Key Laboratory of Qinghai Province, Qinghai Academy of Animal and Veterinary Medicine, Qinghai University, Xining 810016, China; (Y.Z.); (L.W.); (J.Z.); (W.S.); (Y.M.); (C.D.)
| | - Jianbo Zhang
- Plateau Livestock Genetic Resources Protection and Innovative Utilization Key Laboratory of Qinghai Province, Qinghai Academy of Animal and Veterinary Medicine, Qinghai University, Xining 810016, China; (Y.Z.); (L.W.); (J.Z.); (W.S.); (Y.M.); (C.D.)
| | - Wenjuan Shen
- Plateau Livestock Genetic Resources Protection and Innovative Utilization Key Laboratory of Qinghai Province, Qinghai Academy of Animal and Veterinary Medicine, Qinghai University, Xining 810016, China; (Y.Z.); (L.W.); (J.Z.); (W.S.); (Y.M.); (C.D.)
| | - Yuhong Ma
- Plateau Livestock Genetic Resources Protection and Innovative Utilization Key Laboratory of Qinghai Province, Qinghai Academy of Animal and Veterinary Medicine, Qinghai University, Xining 810016, China; (Y.Z.); (L.W.); (J.Z.); (W.S.); (Y.M.); (C.D.)
| | - Chengxiang Ding
- Plateau Livestock Genetic Resources Protection and Innovative Utilization Key Laboratory of Qinghai Province, Qinghai Academy of Animal and Veterinary Medicine, Qinghai University, Xining 810016, China; (Y.Z.); (L.W.); (J.Z.); (W.S.); (Y.M.); (C.D.)
| | - Guofang Wu
- Plateau Livestock Genetic Resources Protection and Innovative Utilization Key Laboratory of Qinghai Province, Qinghai Academy of Animal and Veterinary Medicine, Qinghai University, Xining 810016, China; (Y.Z.); (L.W.); (J.Z.); (W.S.); (Y.M.); (C.D.)
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Xu H, Zhang S, Duan Q, Lou M, Ling Y. Comprehensive analyses of 435 goat transcriptomes provides insight into male reproduction. Int J Biol Macromol 2024; 255:127942. [PMID: 37979751 DOI: 10.1016/j.ijbiomac.2023.127942] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2023] [Revised: 09/25/2023] [Accepted: 11/01/2023] [Indexed: 11/20/2023]
Abstract
A systematic analysis of genes related to reproduction is crucial for obtaining a comprehensive understanding of the molecular mechanisms that underlie male reproductive traits in mammals. Here, we utilized 435 goat transcriptome datasets to unveil the testicular tissue-specific genes (TSGs), allele-specific expression (ASE) genes and their uncharacterized transcriptional features related to male goat reproduction. Results showed a total of 1790 TSGs were identified in goat testis, which was the most among all tissues. GO enrichment analyses suggested that testicular TSGs were mainly involved in spermatogenesis, multicellular organism development, spermatid development, and flagellated sperm motility. Subsequently, a total of 95 highly conserved TSGs (HCTSGs), 508 middle conserved TSGs (MCTSGs) and 42 no conserved TSGs (NCTSGs) were identified in goat testis. GO enrichment analyses suggested that the HCTSGs and MCTSGs has a more important association with male reproduction than NCTSGs. Additionally, we identified 644 ASE genes, including 88 tissue-specific ASE (TS-ASE) genes (e.g., FSIP2, TDRD9). GO enrichment analyses indicated that both ASE genes and TS-ASE genes were associated with goat male reproduction. Overall, this study revealed an extensive gene set involved in the regulation of male goat reproduction and their dynamic transcription patterns. Data reported here provide valuable insights for a further improvement of the economic benefits of goats as well as future treatments for male infertility.
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Affiliation(s)
- Han Xu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Sihuan Zhang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Qin Duan
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Mengyu Lou
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, Anhui, China
| | - Yinghui Ling
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, Anhui, China; Anhui Province Key Laboratory of Local Livestock and Poultry Genetic Resource Conservation and Bio-Breeding, Anhui Agricultural University, Hefei 230036, Anhui, China.
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Wang P, Zhang X, Huo H, Li W, Liu Z, Wang L, Li L, Sun YH, Huo J. Transcriptomic analysis of testis and epididymis tissues from Banna mini-pig inbred line boars with single-molecule long-read sequencing†. Biol Reprod 2023; 108:465-478. [PMID: 36477198 DOI: 10.1093/biolre/ioac216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Revised: 05/04/2022] [Accepted: 11/30/2022] [Indexed: 12/14/2022] Open
Abstract
In mammals, testis and epididymis are critical components of the male reproductive system for androgen production, spermatogenesis, sperm transportation, as well as sperm maturation. Here, we report single-molecule real-time sequencing data from the testis and epididymis of the Banna mini-pig inbred line (BMI), a promising laboratory animal for medical research. We obtained high-quality full-length transcriptomes and identified 9879 isoforms and 8761 isoforms in the BMI testis and epididymis, respectively. Most of the isoforms we identified have novel exon structures that will greatly improve the annotation of testis- and epididymis-expressed genes in pigs. We also found that 3055 genes (over 50%) were shared between BMI testis and epididymis, indicating widespread expression profiles of genes related to reproduction. We characterized extensive alternative splicing events in BMI testis and epididymis and showed that 96 testis-expressed genes and 79 epididymis-expressed genes have more than six isoforms, revealing the complexity of alternative splicing. We accurately defined the transcribed isoforms in BMI testis and epididymis by combining Pacific Biotechnology Isoform-sequencing (PacBio Iso-Seq) and Illumina RNA Sequencing (RNA-seq) techniques. The refined annotation of some key genes governing male reproduction will facilitate further understanding of the molecular mechanisms underlying BMI male sterility. In addition, the high-confident identification of 548 and 669 long noncoding RNAs (lncRNAs) in these two tissues has established a candidate gene set for future functional investigations. Overall, our study provides new insights into the role of the testis and epididymis during BMI reproduction, paving the path for further studies on BMI male infertility.
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Affiliation(s)
- Pei Wang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Xia Zhang
- College of Life Science, Lyuliang University, Lvliang, China
| | - Hailong Huo
- Yunnan Vocational and Technical college of Agriculture, Kunming, China
| | - Weizhen Li
- College of Veterinary Medicine, Yunnan Agricultural University, Kunming, China
| | - Zhipeng Liu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Lina Wang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Luogang Li
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Yu H Sun
- Department of Biology, University of Rochester, Rochester, NY, USA
| | - Jinlong Huo
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
- Department of Biology, University of Rochester, Rochester, NY, USA
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Zhang S, Xu H, Jiang E, Akhatayeva Z, Jiang F, Song E, Pan C, Chen H, Lan X. Screening of Bovine Tissue-Specific Expressed Genes and Identification of Genetic Variation Within an Adipose Tissue-Specific lncRNA Gene. Front Vet Sci 2022; 9:887520. [PMID: 35647086 PMCID: PMC9130833 DOI: 10.3389/fvets.2022.887520] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2022] [Accepted: 04/19/2022] [Indexed: 12/13/2022] Open
Abstract
Global classification of bovine genes is important for studies of biology and tissue-specific gene editing. Herein, we classified the tissue-specific expressed genes and uncovered an important variation in the promoter region of an adipose tissue-specific lncRNA gene. Statistical analysis demonstrated that the number of genes specifically expressed in the brain was the highest, while it was lowest in the adipose tissues. A total of 1,575 genes were found to be significantly higher expressed in adipose tissues. Bioinformatic analysis and qRT-PCR were used to uncover the expression profiles of the 23 adipose tissue-specific and highly expressed genes in 8 tissues. The results showed that most of the 23 genes have higher expression level in adipose tissue. Besides, we detected a 12 bp insertion/deletion (indel) variation (rs720343880) in the promoter region of an adipose tissue-specific lncRNA gene (LOC100847835). The different genotypes of this variation were associated with carcass traits of cattle. Therefore, the outcomes of the present study can be used as a starting point to explore the development of cattle organs and tissues, as well as to improve the quality of cattle products.
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Affiliation(s)
- Sihuan Zhang
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Han Xu
- School of Medicine, Sun Yat-sen University, Guangzhou, China
| | - Enhui Jiang
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Zhanerke Akhatayeva
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Fugui Jiang
- Institute of Animal Science and Veterinary, Shandong Academy of Agriculture Science, Jinan, China
| | - Enliang Song
- Institute of Animal Science and Veterinary, Shandong Academy of Agriculture Science, Jinan, China
| | - Chuanying Pan
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Xianyang, China
- *Correspondence: Xianyong Lan
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Comparative transcriptomic analysis reveals the gonadal development-related gene response to environmental temperature in Mauremys mutica. COMPARATIVE BIOCHEMISTRY AND PHYSIOLOGY D-GENOMICS & PROTEOMICS 2021; 40:100925. [PMID: 34689019 DOI: 10.1016/j.cbd.2021.100925] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2021] [Revised: 10/11/2021] [Accepted: 10/14/2021] [Indexed: 01/15/2023]
Abstract
The Asian yellow pond turtle (Mauremys mutica) displays temperature-dependent sex determination (TSD), in which incubation temperature during embryonic development determines the sexual fate of the individual. However, the mechanism of the sex determination/differentiation of Mauremys mutica remains a mystery. Here, we first analyzed the temperature-specific gonadal transcriptomes of Mauremys mutica prior to gonad formation and gonads during the thermosensitive period. We uncovered a list of candidates that respond to temperature stimuli enriched in several categories, such as heat shock protein family members dnajb6a, dnaja4, hspa8 and hsp90aa1, temperature sensor genes mmp17 and mmp28, and putative novel temperature-responsive genes tmco6, gria3 and eif3f. Notably, striking differences were identified in the expression profiles of genes underlying sexual development, such as tex15, insr, igf1r, cirbp, esr1, dmrt2 and Serpinh1. Moreover, we analyzed the similarity and divergence of the timecourse of gene expression among Mauremys mutica and two other reported TSD turtles (Trachemys scripta and Chrysemys picta). The shared genes revealed the common gonad-specific regulatory mechanisms existing in these three TSD turtles that initiate their sexual development. Therefore, our findings could provide basic data to elucidate the mechanisms of sex determination/differentiation of M. mutica, even contributing to further understanding of these mechanisms in other TSD turtles.
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Robic A, Cerutti C, Kühn C, Faraut T. Comparative Analysis of the Circular Transcriptome in Muscle, Liver, and Testis in Three Livestock Species. Front Genet 2021; 12:665153. [PMID: 34040640 PMCID: PMC8141914 DOI: 10.3389/fgene.2021.665153] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 04/07/2021] [Indexed: 12/13/2022] Open
Abstract
Circular RNAs have been observed in a large number of species and tissues and are now recognized as a clear component of the transcriptome. Our study takes advantage of functional datasets produced within the FAANG consortium to investigate the pervasiveness of circular RNA transcription in farm animals. We describe here the circular transcriptional landscape in pig, sheep and bovine testicular, muscular and liver tissues using total 66 RNA-seq datasets. After an exhaustive detection of circular RNAs, we propose an annotation of exonic, intronic and sub-exonic circRNAs and comparative analyses of circRNA content to evaluate the variability between individuals, tissues and species. Despite technical bias due to the various origins of the datasets, we were able to characterize some features (i) (ruminant) liver contains more exonic circRNAs than muscle (ii) in testis, the number of exonic circRNAs seems associated with the sexual maturity of the animal. (iii) a particular class of circRNAs, sub-exonic circRNAs, are produced by a large variety of multi-exonic genes (protein-coding genes, long non-coding RNAs and pseudogenes) and mono-exonic genes (protein-coding genes from mitochondrial genome and small non-coding genes). Moreover, for multi-exonic genes there seems to be a relationship between the sub-exonic circRNAs transcription level and the linear transcription level. Finally, sub-exonic circRNAs produced by mono-exonic genes (mitochondrial protein-coding genes, ribozyme, and sno) exhibit a particular behavior. Caution has to be taken regarding the interpretation of the unannotated circRNA proportion in a given tissue/species: clusters of circRNAs without annotation were characterized in genomic regions with annotation and/or assembly problems of the respective animal genomes. This study highlights the importance of improving genome annotation to better consider candidate circRNAs and to better understand the circular transcriptome. Furthermore, it emphasizes the need for considering the relative “weight” of circRNAs/parent genes for comparative analyses of several circular transcriptomes. Although there are points of agreement in the circular transcriptome of the same tissue in two species, it will be not possible to do without the characterization of it in both species.
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Affiliation(s)
- Annie Robic
- INRAE, ENVT, GenPhySE, Université de Toulouse, Castanet-Tolosan, France
| | - Chloé Cerutti
- INRAE, ENVT, GenPhySE, Université de Toulouse, Castanet-Tolosan, France
| | - Christa Kühn
- Institute Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany.,Faculty of Agricultural and Environmental Sciences, University of Rostock, Rostock, Germany
| | - Thomas Faraut
- INRAE, ENVT, GenPhySE, Université de Toulouse, Castanet-Tolosan, France
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Fraser L, Paukszto Ł, Mańkowska A, Brym P, Gilun P, Jastrzębski JP, Pareek CS, Kumar D, Pierzchała M. Regulatory Potential of Long Non-Coding RNAs (lncRNAs) in Boar Spermatozoa with Good and Poor Freezability. Life (Basel) 2020; 10:life10110300. [PMID: 33233438 PMCID: PMC7700223 DOI: 10.3390/life10110300] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 11/14/2020] [Accepted: 11/19/2020] [Indexed: 12/14/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are suggested to play an important role in the sperm biological processes. We performed de novo transcriptome assembly to characterize lncRNAs in spermatozoa, and to investigate the role of the potential target genes of the differentially expressed lncRNAs (DElncRNAs) in sperm freezability. We detected approximately 4007 DElncRNAs, which were differentially expressed in spermatozoa from boars classified as having good and poor semen freezability (GSF and PSF, respectively). Most of the DElncRNAs were upregulated in boars of the PSF group and appeared to significantly affect the sperm's response to the cryopreservation conditions. Furthermore, we predicted that the potential target genes were regulated by DElncRNAs in cis or trans. It was found that DElncRNAs of both freezability groups had potential cis- and trans-regulatory effects on different protein-coding genes, such as COX7A2L, TXNDC8 and SOX-7. Gene Ontology (GO) enrichment revealed that the DElncRNA target genes are associated with numerous biological processes, including signal transduction, response to stress, cell death (apoptosis), motility and embryo development. Significant differences in the de novo assembled transcriptome expression profiles of the DElncRNAs between the freezability groups were confirmed by quantitative real-time PCR analysis. This study reveals the potential effects of protein-coding genes of DElncRNAs on sperm functions, which could contribute to further research on their relevance in semen freezability.
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Affiliation(s)
- Leyland Fraser
- Department of Animal Biochemistry and Biotechnology, Faculty of Animal Bioengineering, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland;
- Correspondence:
| | - Łukasz Paukszto
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland; (Ł.P.); (J.P.J.)
| | - Anna Mańkowska
- Department of Animal Biochemistry and Biotechnology, Faculty of Animal Bioengineering, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland;
| | - Paweł Brym
- Department of Animal Genetics, Faculty of Animal Bioengineering, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland;
| | - Przemysław Gilun
- Department of Local Physiological Regulations, Institute of Animal Reproduction and Food Research of the Polish Academy of Sciences, Bydgoska 7, 10-243 Olsztyn, Poland;
| | - Jan P. Jastrzębski
- Department of Plant Physiology, Genetics and Biotechnology, Faculty of Biology and Biotechnology, University of Warmia and Mazury in Olsztyn, 10-719 Olsztyn, Poland; (Ł.P.); (J.P.J.)
| | - Chandra S. Pareek
- Institute of Veterinary Medicine, Faculty of Biological and Veterinary Sciences, Nicolaus Copernicus, University, 87-100 Toruń, Poland;
| | - Dibyendu Kumar
- Waksman Institute of Microbiology, Rutgers, The State University of New Jersey, Piscataway, NJ 08554, USA;
| | - Mariusz Pierzchała
- Institute of Genetics and Animal Breeding, Polish Academy of Sciences, Jastrzębiec, 05-552 Magdalenka, Poland;
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