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Chen H, Wu Y, Zhu Y, Luo K, Zheng S, Tang H, Xuan R, Huang Y, Li J, Xiong R, Fang X, Wang L, Gong Y, Miao J, Zhou J, Tan H, Wang Y, Wu L, Ouyang J, Huang M, Yan X. Deciphering the Genetic Landscape: Insights Into the Genomic Signatures of Changle Goose. Evol Appl 2024; 17:e13768. [PMID: 39175938 PMCID: PMC11340016 DOI: 10.1111/eva.13768] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2024] [Revised: 07/25/2024] [Accepted: 07/29/2024] [Indexed: 08/24/2024] Open
Abstract
The Changle goose (CLG), a Chinese indigenous breed, is celebrated for its adaptability, rapid growth, and premium meat quality. Despite its agricultural value, the exploration of its genomic attributes has been scant. Our study entailed whole-genome resequencing of 303 geese across CLG and five other Chinese breeds, revealing distinct genetic diversity metrics. We discovered significant migration events from Xingguo gray goose to CLG and minor gene flow between them. We identified genomic regions through selective sweep analysis, correlating with CLG's unique traits. An elevated inbreeding coefficient in CLG, alongside reduced heterozygosity and rare single nucleotide polymorphisms (RSNPs), suggests a narrowed genetic diversity. Genomic regions related to reproduction, meat quality, and growth were identified, with the GATA3 gene showing strong selection signals for meat quality. A non-synonymous mutation in the Sloc2a1 gene, which is associated with reproductive traits in the CLG, exhibited significant differences in allelic frequency. The roles of CD82, CDH8, and PRKAB1 in growth and development, alongside FABP4, FAF1, ESR1, and AKAP12 in reproduction, were highlighted. Additionally, Cdkal1 and Mfsd14a may influence meat quality. This comprehensive genetic analysis underpins the unique genetic makeup of CLG, providing a basis for its conservation and informed breeding strategies.
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Affiliation(s)
- Hao Chen
- College of Life SciencesJiangxi Science and Technology Normal UniversityNanchangChina
| | - Yan Wu
- College of Life SciencesJiangxi Science and Technology Normal UniversityNanchangChina
| | - Yihao Zhu
- College of Life SciencesJiangxi Science and Technology Normal UniversityNanchangChina
| | - Keyi Luo
- College of Life SciencesJiangxi Science and Technology Normal UniversityNanchangChina
| | - Sumei Zheng
- College of Life SciencesJiangxi Science and Technology Normal UniversityNanchangChina
| | - Hongbo Tang
- College of Life SciencesJiangxi Science and Technology Normal UniversityNanchangChina
| | - Rui Xuan
- College of Life SciencesJiangxi Science and Technology Normal UniversityNanchangChina
| | - Yuxuan Huang
- College of Life SciencesJiangxi Science and Technology Normal UniversityNanchangChina
| | - Jiawei Li
- College of Life SciencesJiangxi Science and Technology Normal UniversityNanchangChina
| | - Rui Xiong
- College of Life SciencesJiangxi Science and Technology Normal UniversityNanchangChina
| | - Xinyan Fang
- College of Life SciencesJiangxi Science and Technology Normal UniversityNanchangChina
| | - Lei Wang
- College of Life SciencesJiangxi Science and Technology Normal UniversityNanchangChina
| | - Yujie Gong
- College of Life SciencesJiangxi Science and Technology Normal UniversityNanchangChina
| | - Junjie Miao
- College of Life SciencesJiangxi Science and Technology Normal UniversityNanchangChina
| | - Jing Zhou
- College of Life SciencesJiangxi Science and Technology Normal UniversityNanchangChina
| | - Hongli Tan
- College of Life SciencesJiangxi Science and Technology Normal UniversityNanchangChina
| | - Yanan Wang
- College of Life SciencesJiangxi Science and Technology Normal UniversityNanchangChina
| | - Liping Wu
- College of Life SciencesJiangxi Science and Technology Normal UniversityNanchangChina
| | - Jing Ouyang
- College of Life SciencesJiangxi Science and Technology Normal UniversityNanchangChina
| | - Min Huang
- College of Animal Sciences & TechnologyZhejiang A&F UniversityHangzhouChina
| | - Xueming Yan
- College of Life SciencesJiangxi Science and Technology Normal UniversityNanchangChina
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Mantri M, Zhang HH, Spanos E, Ren YA, De Vlaminck I. A spatiotemporal molecular atlas of the ovulating mouse ovary. Proc Natl Acad Sci U S A 2024; 121:e2317418121. [PMID: 38252830 PMCID: PMC10835069 DOI: 10.1073/pnas.2317418121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2023] [Accepted: 12/18/2023] [Indexed: 01/24/2024] Open
Abstract
Ovulation is essential for reproductive success, yet the underlying cellular and molecular mechanisms are far from clear. Here, we applied high-resolution spatiotemporal transcriptomics to map out cell type- and ovulation stage-specific molecular programs as function of time during follicle maturation and ovulation in mice. Our analysis revealed dynamic molecular transitions within granulosa cell types that occur in tight coordination with mesenchymal cell proliferation. We identified molecular markers for the emerging cumulus cell fate during the preantral-to-antral transition. We describe transcriptional programs that respond rapidly to ovulation stimulation and those associated with follicle rupture, highlighting the prominent roles of apoptotic and metabolic pathways during the final stages of follicle maturation. We further report stage-specific oocyte-cumulus cell interactions and diverging molecular differentiation in follicles approaching ovulation. Collectively, this study provides insights into the cellular and molecular processes that regulate mouse ovarian follicle maturation and ovulation with important implications for advancing therapeutic strategies in reproductive medicine.
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Affiliation(s)
- Madhav Mantri
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY14850
| | | | - Emmanuel Spanos
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY14850
| | - Yi A. Ren
- Department of Animal Science, Cornell University, Ithaca, NY14850
| | - Iwijn De Vlaminck
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY14850
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Mantri M, Zhang HH, Spanos E, Ren YA, Vlaminck ID. A Spatiotemporal Molecular Atlas of the Ovulating Mouse Ovary. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2023:2023.08.21.554210. [PMID: 37662215 PMCID: PMC10473623 DOI: 10.1101/2023.08.21.554210] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/05/2023]
Abstract
Ovulation is essential for reproductive success, yet the underlying cellular and molecular mechanisms are far from clear. Here, we applied high-resolution spatiotemporal transcriptomics to map out cell-type- and ovulation-stage-specific molecular programs as function of time during follicle maturation and ovulation in mice. Our analysis revealed dynamic molecular transitions within granulosa cell types that occur in tight coordination with mesenchymal cell proliferation. We identified new molecular markers for the emerging cumulus cell fate during the preantral-to-antral transition. We describe transcriptional programs that respond rapidly to ovulation stimulation and those associated with follicle rupture, highlighting the prominent roles of apoptotic and metabolic pathways during the final stages of follicle maturation. We further report stage-specific oocyte-cumulus cell interactions and diverging molecular differentiation in follicles approaching ovulation. Collectively, this study provides insights into the cellular and molecular processes that regulate mouse ovarian follicle maturation and ovulation with important implications for advancing therapeutic strategies in reproductive medicine.
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Affiliation(s)
- Madhav Mantri
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York
| | | | - Emmanuel Spanos
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York
| | - Yi A Ren
- Department of Animal Science, Cornell University, Ithaca, New York
| | - Iwijn De Vlaminck
- Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, New York
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Ning Z, Deng X, Li L, Feng J, Du X, Amevor FK, Tian Y, Li L, Rao Y, Yi Z, Du X, Cui Z, Zhao X. miR-128-3p regulates chicken granulosa cell function via 14-3-3β/FoxO and PPAR-γ/LPL signaling pathways. Int J Biol Macromol 2023; 241:124654. [PMID: 37119902 DOI: 10.1016/j.ijbiomac.2023.124654] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2023] [Revised: 04/23/2023] [Accepted: 04/24/2023] [Indexed: 05/01/2023]
Abstract
MicroRNAs (miRNAs) are class of 22 nt short RNA sequences which inhibit protein translation through binding to the 3'UTR of its target genes. The continuous ovulatory property of chicken follicle makes it a perfect model for studying granulosa cell (GC) functions. In this study, we found that large number of miRNAs including miR-128-3p, were differentially expressed in the GCs of F1 and F5 follicles of chicken. Subsequently, the results revealed that miR-128-3p inhibited proliferation, the formation of lipid droplets, and hormone secretion in chicken primary GCs through directly targeting YWHAB and PPAR-γ genes. To determine the effects of 14-3-3β (encoded by YWHAB) protein on GCs functions, we overexpressed or inhibited the expression of YWHAB, and the results showed that YWHAB inhibited the function of FoxO proteins. Collectively, we found that miR-128-3p was highly expressed in the chicken F1 follicles compared to the F5 follicles. In addition, the results indicated that miR-128-3p promoted GC apoptosis through 14-3-3β/FoxO pathway via repressing YWHAB, and inhibited lipid synthesis by impeding the PPAR-γ/LPL pathway, as well as reduced the secretion of progesterone and estrogen. Taken together, the results showed that miR-128-3p plays a regulatory role in chicken granulosa cell function via 14-3-3β/FoxO and PPAR-γ/LPL signaling pathways.
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Affiliation(s)
- Zifan Ning
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, PR China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, PR China
| | - Xun Deng
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, PR China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, PR China
| | - Liang Li
- Institute of Animal Husbandry and Veterinary Medicine, Guizhou Provincial Academy of Agricultural Sciences, Guiyang, PR China
| | - Jing Feng
- Institute of Animal Husbandry and Veterinary Medicine, College of Agriculture and Animal Husbandry of Tibet Autonomous Region, Lhasa, PR China
| | - Xiaxia Du
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, PR China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, PR China
| | - Felix Kwame Amevor
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, PR China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, PR China
| | - Yaofu Tian
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, PR China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, PR China
| | - Lingxiang Li
- Bazhong Academy of Agriculture and Forestry Sciences, Bazhong, PR China
| | - Yong Rao
- Bazhong Academy of Agriculture and Forestry Sciences, Bazhong, PR China
| | - Zhixin Yi
- Bazhong Academy of Agriculture and Forestry Sciences, Bazhong, PR China
| | - Xiaohui Du
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, PR China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, PR China
| | - Zhifu Cui
- College of Animal Science and Technology, Southwest University, Chongqing, PR China.
| | - Xiaoling Zhao
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, PR China; Key Laboratory of Livestock and Poultry Multi-omics, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology (Institute of Animal Genetics and Breeding), Sichuan Agricultural University, PR China.
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Nimisha K, Srikanth K, Velayutham D, Nandan D, Sankaralingam S, Nagarajan M. Comparative liver transcriptome analysis of duck reveals potential genes associated with egg production. Mol Biol Rep 2022; 49:5963-5972. [PMID: 35476172 DOI: 10.1007/s11033-022-07380-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2021] [Revised: 01/30/2022] [Accepted: 03/16/2022] [Indexed: 01/21/2023]
Abstract
BACKGROUND Molecular studies on egg production in ducks were mostly focused on brain and ovaries as they are directly involved in egg production. Liver plays a vital role in cellular lipid metabolism. It also plays a decisive role in reproductive organ development, including yolk generation in laying ducks at sexual maturity. However, the precise molecular mechanism involved in the liver-blood-ovary axis in ducks remains elusive. METHODS AND RESULTS In this study, we analysed the liver transcriptome of laying (LA), immature (IM) and broody (BR) ducks using RNA sequencing to understand the role of genes expressed in the liver. The comparative transcriptome analysis revealed 82 DEGs between LA and IM ducks, 47 DEGs between LA and BR ducks and 51 DEGs between IM and BR ducks. GO analysis of DEGs, showed that DEGs were mainly involved in cellular anatomical entity, intracellular, metabolic process, and binding. Furthermore, pathway analysis indicated the important role of Wnt signaling pathway in egg formation and embryo development. Our study showed several candidate genes including vitellogenin-1, vitellogenin-2, riboflavin binding protein, G protein subunit gamma 4, and fatty acid binding protein 3 that are potentially related to egg production in ducks. CONCLUSIONS The study provides valuable information on the genes responsible for egg production and thus, pave the way for further investigation on the molecular mechanisms of egg production in duck.
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Affiliation(s)
- Koodali Nimisha
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, 671316, Kasaragod, Kerala, India
| | - Krishnamoorthy Srikanth
- Department of Animal Science, College of Agriculture and Life Sciences, Cornell University, 14853, Ithaca, NY, United States
| | | | - Dharam Nandan
- AgriGenome Labs Pvt. Ltd, 682042, Kochi, Kerala, India
| | - Shanmugam Sankaralingam
- Department of Poultry Science, College of Veterinary and Animal Sciences, 680 651, Mannuthy, Thrissur, Kerala, India
| | - Muniyandi Nagarajan
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, 671316, Kasaragod, Kerala, India.
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He H, Li D, Tian Y, Wei Q, Amevor FK, Sun C, Yu C, Yang C, Du H, Jiang X, Ma M, Cui C, Zhang Z, Tian K, Zhang Y, Zhu Q, Yin H. miRNA sequencing analysis of healthy and atretic follicles of chickens revealed that miR-30a-5p inhibits granulosa cell death via targeting Beclin1. J Anim Sci Biotechnol 2022; 13:55. [PMID: 35410457 PMCID: PMC9003977 DOI: 10.1186/s40104-022-00697-0] [Citation(s) in RCA: 33] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 02/21/2022] [Indexed: 01/15/2023] Open
Abstract
Background The egg production performance of chickens is affected by many factors, including genetics, nutrition and environmental conditions. These factors all play a role in egg production by affecting the development of follicles. MicroRNAs (miRNAs) are important non-coding RNAs that regulate biological processes by targeting genes or other non-coding RNAs after transcription. In the animal reproduction process, miRNA is known to affect the development and atresia of follicles by regulating apoptosis and autophagy of granulosa cells (GCs). Results In this study, we identified potential miRNAs in the atretic follicles of broody chickens and unatretic follicles of healthy chickens. We identified gga-miR-30a-5p in 50 differentially expressed miRNAs and found that gga-miR-30a-5p played a regulatory role in the development of chicken follicles. The function of miR-30a-5p was explored through the transfection test of miR-30a-5p inhibitor and miR-30a-5p mimics. In the study, we used qPCR, western blot and flow cytometry to detect granulosa cell apoptosis, autophagy and steroid hormone synthesis. Confocal microscopy and transmission electron microscopy are used for the observation of autophagolysosomes. The levels of estradiol (E2), progesterone (P4), malondialdehyde (MDA) and superoxide dismutase (SOD) were detected by ELISA. The results showed that miR-30a-5p showed a negative effect on autophagy and apoptosis of granulosa cells, and also contributed in steroid hormones and reactive oxygen species (ROS) production. In addition, the results obtained from the biosynthesis and dual luciferase experiments showed that Beclin1 was the target gene of miR-30a-5p. The rescue experiment conducted further confirmed that Beclin1 belongs to the miR-30a-5p regulatory pathway. Conclusions In summary, after deep miRNA sequencing on healthy and atretic follicles, the results indicated that miR-30a-5p inhibits granulosa cell death by inhibiting Beclin1. Supplementary Information The online version contains supplementary material available at 10.1186/s40104-022-00697-0.
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Affiliation(s)
- Haorong He
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Dongmei Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yongtong Tian
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Qinyao Wei
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Felix Kwame Amevor
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Congjiao Sun
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Chunlin Yu
- Animal Breeding and Genetics key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, China
| | - Chaowu Yang
- Animal Breeding and Genetics key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, China
| | - Huarui Du
- Animal Breeding and Genetics key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, China
| | - Xiaosong Jiang
- Animal Breeding and Genetics key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, 610066, China
| | - Menggen Ma
- College of Resources, Sichuan Agricultural University, Chengdu, 611130, China
| | - Can Cui
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Zhichao Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Kai Tian
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yao Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Qing Zhu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
| | - Huadong Yin
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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