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Kodzik N, Ciereszko A, Szczepkowska B, Malinowska A, Dietrich MA. Comparative proteomic analysis of the ovarian fluid and eggs of Siberian sturgeon. BMC Genomics 2024; 25:451. [PMID: 38714919 PMCID: PMC11077782 DOI: 10.1186/s12864-024-10309-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2023] [Accepted: 04/15/2024] [Indexed: 05/12/2024] Open
Abstract
BACKGROUND Sturgeon species are living fossils that exhibit unique reproductive characteristics, and elucidation of the molecular processes governing the formation and quality of sturgeon eggs is crucial. However, comprehensive data on the protein composition of sturgeon ovarian fluid (OF) and eggs and their functional significance are lacking. To address this knowledge gap, the aim of the present study was to conduct a comprehensive comparative proteomic analysis of Siberian sturgeon OF and eggs using liquid chromatography-mass spectrometry (LC-MS/MS). RESULTS A total of 617 proteins were identified in OF, and 565 proteins were identified in eggs. A total of 772 proteins showed differential abundance. Among the differentially abundant proteins, 365 were more abundant in OFs, while 407 were more abundant in eggs. We identified 339 proteins unique to OFs and 287 proteins specific to eggs, and further investigated the top 10 most abundant proteins in each. The functional annotation of the OF proteins highlighted their predominant association with immune system processes, including the complement and coagulation cascade, neutrophil and leukocyte-mediated immunity, cholesterol metabolism, and regulation of the actin cytoskeleton. Analysis of egg proteins revealed enrichment in metabolic pathways, such as oxidative phosphorylation and fatty acid metabolism, and protein ubiquitination and translation. OF-specific proteins included extracellular matrix and secretory vesicles, and eggs were enriched in proteins localized to mitochondria and ribosome components. CONCLUSIONS This study presents the first comprehensive characterization of the protein composition of sturgeon OF and eggs and elucidates their distinct functional roles. These findings advance our understanding of sturgeon reproduction, OF-egg signaling and the origin of OF proteins. The mass spectrometry proteomics data have been deposited in the ProteomeXchange Consortium with the dataset identifier PXD044168 to ensure accessibility for further research.
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Affiliation(s)
- Natalia Kodzik
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, Olsztyn, 10-748, Poland
| | - Andrzej Ciereszko
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, Olsztyn, 10-748, Poland
| | - Bożena Szczepkowska
- Department of Sturgeon Fish Breeding, Inland Fisheries Institute in Olsztyn, Pozezdrze, Pieczarki, 11-610, Poland
| | - Agata Malinowska
- Mass Spectrometry Laboratory, Institute of Biochemistry and Biophysics, Polish Academy of Sciences, Pawinskiego 5a, Warsaw, Warszawa, 02-106, Poland
| | - Mariola Aleksandra Dietrich
- Department of Gamete and Embryo Biology, Institute of Animal Reproduction and Food Research, Polish Academy of Sciences, Tuwima 10, Olsztyn, 10-748, Poland.
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Lei Q, Zhang S, Wang J, Qi C, Liu J, Cao D, Li F, Han H, Liu W, Li D, Tang C, Zhou Y. Genome-wide association studies of egg production traits by whole genome sequencing of Laiwu Black chicken. Poult Sci 2024; 103:103705. [PMID: 38598913 DOI: 10.1016/j.psj.2024.103705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Revised: 03/24/2024] [Accepted: 03/26/2024] [Indexed: 04/12/2024] Open
Abstract
Compared to high-yield commercial laying hens, Chinese indigenous chicken breeds have poor egg laying capacity due to the lack of intensive selection. However, as these breeds have not undergone systematic selection, it is possible that there is a greater abundance of genetic variations related to egg laying traits. In this study, we assessed 5 egg number (EN) traits at different stages of the egg-laying period: EN1 (from the first egg to 23 wk), EN2 (from 23 to 35 wk), EN3 (from 35 to 48 wk), EN4 (from the first egg to 35 wk), and EN5 (from the first egg to 48 wk). To investigate the molecular mechanisms underlying egg number traits in a Chinese local chicken breed, we conducted a genome-wide association study (GWAS) using data from whole-genome sequencing (WGS) of 399 Laiwu Black chickens. We obtained a total of 3.01 Tb of raw data with an average depth of 7.07 × per individual. A total of 86 genome-wide suggestive or significant single-nucleotide polymorphisms (SNP) contained within a set of 45 corresponding candidate genes were identified and found to be associated with stages EN1-EN5. The genes vitellogenin 2 (VTG2), lipase maturation factor 1 (LMF1), calcium voltage-gated channel auxiliary subunit alpha2delta 3 (CACNA2D3), poly(A) binding protein cytoplasmic 1 (PABPC1), programmed cell death 11 (PDCD11) and family with sequence similarity 213 member A (FAM213A) can be considered as the candidate genes associated with egg number traits, due to their reported association with animal reproduction traits. Noteworthy, results suggests that VTG2 and PDCD11 are not only involved in the regulation of EN3, but also in the regulation of EN5, implies that VTG2 and PDCD11 have a significant influence on egg production traits. Our study offers valuable genomic insights into the molecular genetic mechanisms that govern egg number traits in a Chinese indigenous egg-laying chicken breed. These findings have the potential to enhance the egg-laying performance of chickens.
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Affiliation(s)
- Qiuxia Lei
- Poultry Institute, Shandong Academy of Agricultural Sciences, 250100, Ji'nan, China.; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Ji'nan, China
| | - Shuer Zhang
- Shandong Animal Husbandry General Station, 250023, Ji'nan, China
| | - Jie Wang
- Poultry Institute, Shandong Academy of Agricultural Sciences, 250100, Ji'nan, China.; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Ji'nan, China
| | - Chao Qi
- Shandong Animal Husbandry General Station, 250023, Ji'nan, China
| | - Jie Liu
- Poultry Institute, Shandong Academy of Agricultural Sciences, 250100, Ji'nan, China.; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Ji'nan, China
| | - Dingguo Cao
- Poultry Institute, Shandong Academy of Agricultural Sciences, 250100, Ji'nan, China.; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Ji'nan, China
| | - Fuwei Li
- Poultry Institute, Shandong Academy of Agricultural Sciences, 250100, Ji'nan, China.; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Ji'nan, China
| | - Haixia Han
- Poultry Institute, Shandong Academy of Agricultural Sciences, 250100, Ji'nan, China.; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Ji'nan, China
| | - Wei Liu
- Poultry Institute, Shandong Academy of Agricultural Sciences, 250100, Ji'nan, China.; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Ji'nan, China
| | - Dapeng Li
- Poultry Institute, Shandong Academy of Agricultural Sciences, 250100, Ji'nan, China.; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Ji'nan, China
| | - Cunwei Tang
- Fujian Sunnzer Biological Technology Development Co. Ltd., 354100, Guang'ze, China
| | - Yan Zhou
- Poultry Institute, Shandong Academy of Agricultural Sciences, 250100, Ji'nan, China.; Poultry Breeding Engineering Technology Center of Shandong Province, 250100, Ji'nan, China..
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Huang X, Zhou W, Cao H, Zhang H, Xiang X, Yin Z. Ovarian Transcriptomic Analysis of Ninghai Indigenous Chickens at Different Egg-Laying Periods. Genes (Basel) 2022; 13:595. [PMID: 35456401 PMCID: PMC9027236 DOI: 10.3390/genes13040595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2022] [Revised: 03/17/2022] [Accepted: 03/23/2022] [Indexed: 11/25/2022] Open
Abstract
Egg production is an essential indicator of poultry fertility. The ovary is a crucial organ involved in egg production; however, little is known about the key genes and signaling pathways involved in the whole egg-laying cycle of hens. In order to explore the mechanism of egg production at different stages of the egg-laying process, ovarian tissues from four chickens were randomly selected for transcriptome analysis at each of the three ages (145 d, 204 d, and 300 d in the early, peak, and late stages of egg laying). A total of 12 gene libraries were constructed, and a total of 8433 differential genes were identified from NH145d vs. NH204d, NH145d vs. NH300d and NH300d vs. NH204d (Ninghai 145-day-old, Ninghai 204-day-old, and Ninghai 300-day-old), with 1176, 1653 and 1868 up-regulated genes, and 621, 1955 and 1160 down-regulated genes, respectively. In each of the two comparison groups, 73, 1004, and 1030 differentially expressed genes were found to be co-expressed. We analyzed the differentially expressed genes and predicted nine genes involved in egg production regulation, including LRP8, BMP6, ZP4, COL4A1, VCAN, INHBA, LOX, PTX3, and IHH, as well as several essential egg production pathways, such as regulation adhesion molecules (CAMs), calcium signaling pathways, neuroactive ligand–receptor interaction, and cytokine–cytokine receptor interaction. Transcriptional analysis of the chicken ovary during different phases of egg-lay will provide a useful molecular basis for study of the development of the egg-laying ovary.
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