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Feng J, Zhu W, Shi H, Peng D, Zang L, Wang Y, ZhaXi L, BaiMa J, Amevor FK, Wang X, Ma X, Zhao X. Analysis of the Selection Signal of the Tibetan Black Chicken Genome Based on Whole-Genome Sequencing. Genes (Basel) 2023; 14:1672. [PMID: 37761812 PMCID: PMC10531317 DOI: 10.3390/genes14091672] [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: 07/25/2023] [Revised: 08/18/2023] [Accepted: 08/22/2023] [Indexed: 09/29/2023] Open
Abstract
BACKGROUND The Tibetan chicken has adapted well to high altitudes genetically after its long-term habitation in the plateau. In this study, we analyzed the selection signal of Tibetan black chickens (TBCs) and discovered genes associated with the characteristics of germplasm. METHODS Whole-genome sequencing (WGS) was used to identify the single-nucleotide polymorphism (SNP) markers and genetic structures in the genome of Tibetan black chickens. Further, we performed a comparative population genomics analysis between the genomic data obtained in this present study and the genomic data for five wild red jungle fowls (RJFs) accessed from the NCBI database (GenBank accession number PRJNA241474). Thereafter, the Fst and Pi selections were used to identify genes under positive selection in the Tibetan black chicken genome. RESULTS A total of 9,490,690 SNPs were identified in the Tibetan black chickens. In addition, the results from the gene ontology (GO) analysis showed that 732 genes of TBCs were enriched in a total of 210 GO terms with specific molecular functions such as regulation of cellular catabolic process, the MAPK signaling pathway, regulation of ion transport, growth, morphogenesis and lung alveolus development which may provide a better mechanism to facilitate oxygen transport and utilization in TBCs. Moreover, the results from the KEGG analysis showed that 732 genes of the TBCs were significantly enriched in the calcium signaling pathway, circadian entrainment (ADCY1, GNG7 and PER3), oxytocin signaling pathway and pathways of multiple neurodegeneration diseases. In addition, the CD86 antigen (CD86) was identified as a gene associated with the immune response in chickens. It was also revealed that genes such as TRIT1, HPCAL4, NT5C1A and HEYL were discovered under selection in Tibetan black chickens on chromosome 23. These genes may be related to the local adaptive characteristics of Tibetan black chickens, for instance, NT5C1A and HEYL may be involved in the high-altitude adaption of oxygen delivery in Tibetan black chickens. CONCLUSIONS In summary, we found that selection mainly affects the disease resistance and cold acclimatization of Tibetan black chickens. Hence, these results may provide important genetic information for the evolution and breeding of Tibetan black chickens.
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Affiliation(s)
- Jing Feng
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agricultural and Animal Husbandry Science, Lhasa 850009, China; (H.S.); (D.P.); (Y.W.); (X.M.)
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lhasa 850009, China
| | - Wei Zhu
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (W.Z.); (F.K.A.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Hairen Shi
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agricultural and Animal Husbandry Science, Lhasa 850009, China; (H.S.); (D.P.); (Y.W.); (X.M.)
- College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Da Peng
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agricultural and Animal Husbandry Science, Lhasa 850009, China; (H.S.); (D.P.); (Y.W.); (X.M.)
| | - Lei Zang
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agricultural and Animal Husbandry Science, Lhasa 850009, China; (H.S.); (D.P.); (Y.W.); (X.M.)
| | - Yan Wang
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agricultural and Animal Husbandry Science, Lhasa 850009, China; (H.S.); (D.P.); (Y.W.); (X.M.)
| | - Luobu ZhaXi
- Shannan Longzi County Agriculture and Animal Husbandry Comprehensive Service Center, Shannan 856600, China (J.B.)
| | - Jiancai BaiMa
- Shannan Longzi County Agriculture and Animal Husbandry Comprehensive Service Center, Shannan 856600, China (J.B.)
| | - Felix Kwame Amevor
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (W.Z.); (F.K.A.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
| | - Xiaoqi Wang
- Agriculture and Animal Husbandry Comprehensive Service Center of Lazi County, Shigatse 858100, China;
| | - Xueying Ma
- Institute of Animal Husbandry and Veterinary Medicine, Tibet Academy of Agricultural and Animal Husbandry Science, Lhasa 850009, China; (H.S.); (D.P.); (Y.W.); (X.M.)
| | - Xiaoling Zhao
- State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China; (W.Z.); (F.K.A.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, China
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Unver S, Yigit S, Tural E, Yigit E, Atan T. Evaluation of a circadian rhythm gene (PER3) VNTR variant in Turkish athletes. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2023; 43:173-183. [PMID: 37610137 DOI: 10.1080/15257770.2023.2248198] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/19/2022] [Revised: 08/03/2023] [Accepted: 08/08/2023] [Indexed: 08/24/2023]
Abstract
OBJECTIVE Circadian rhythmicity has been shown to contribute to the regulation of key physiological and cognitive processes related to performance. The period homolog 3 (PER3) is expressed in a circadian pattern in the suprachiasmatic nucleus. Therefore, in this study, we aimed to evaluate the role of the variable tandem repeat (VNTR) variant of the PER3 gene in athletic performance in the Turkish population. METHODS This study included 223 subjects, which consisted of 123 athletes and 100 sedentary controls. Blood samples were drawn from all subjects. DNA was extracted from whole-blood samples. The PER3 VNTR variant was genotyped using the polymerase chain reaction-restriction method (PCR). The results of the analyses were evaluated for statistical significance. RESULTS The mean ages of athletes and controls were 22 ± 2.814 and 23 ± 3.561, respectively. Endurance athletes in the group were 21.1%, and sprint athletes were 78.9%. There was no statistical significance in terms of PER3 VNTR genotype distribution or allele frequency. In the recessive model, a statistically significant association was observed when the athletes were compared with the controls according to 4/4 + 4/5 versus 5/5 genotype (p = 0.020). CONCLUSION In this case-control study, for the first time in our country, we obtained findings suggesting that the PER3 VNTR variant may affect sports performance in the Turkish population. Results need to be replicated in different ethnic and larger samples.
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Affiliation(s)
- Saban Unver
- Department of Coaching Education, Faculty of Sports Science, University of Ondokuz Mayis, Samsun, Turkey
| | - Serbulent Yigit
- Department of Genetics, Faculty of Veterinary, Ondokuz Mayıs University, Samsun, Turkey
- Department of Medical Biology, Graduate Institute, Ondokuz Mayıs University, Samsun, Turkey
| | - Ercan Tural
- Department of Physiotherapy and Rehabilitation, Faculty of Health Science, Ondokuz Mayıs University, Samsun, Turkey
| | - Ercument Yigit
- Department of Sports Management, School of Physical Education and Sports, Halic University, Istanbul, Turkey
| | - Tulin Atan
- Department of Coaching Education, Faculty of Sports Science, University of Ondokuz Mayis, Samsun, Turkey
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Chrononutrition-When We Eat Is of the Essence in Tackling Obesity. Nutrients 2022; 14:nu14235080. [PMID: 36501110 PMCID: PMC9739590 DOI: 10.3390/nu14235080] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2022] [Revised: 11/24/2022] [Accepted: 11/25/2022] [Indexed: 12/03/2022] Open
Abstract
Obesity is a chronic and relapsing public health problem with an extensive list of associated comorbidities. The worldwide prevalence of obesity has nearly tripled over the last five decades and continues to pose a serious threat to wider society and the wellbeing of future generations. The pathogenesis of obesity is complex but diet plays a key role in the onset and progression of the disease. The human diet has changed drastically across the globe, with an estimate that approximately 72% of the calories consumed today come from foods that were not part of our ancestral diets and are not compatible with our metabolism. Additionally, multiple nutrient-independent factors, e.g., cost, accessibility, behaviours, culture, education, work commitments, knowledge and societal set-up, influence our food choices and eating patterns. Much research has been focused on 'what to eat' or 'how much to eat' to reduce the obesity burden, but increasingly evidence indicates that 'when to eat' is fundamental to human metabolism. Aligning feeding patterns to the 24-h circadian clock that regulates a wide range of physiological and behavioural processes has multiple health-promoting effects with anti-obesity being a major part. This article explores the current understanding of the interactions between the body clocks, bioactive dietary components and the less appreciated role of meal timings in energy homeostasis and obesity.
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Ouyang Q, Hu S, Tang B, Hu B, Hu J, He H, Li L, Wang J. Comparative Transcriptome Analysis Provides Novel Insights into the Effect of Lipid Metabolism on Laying of Geese. Animals (Basel) 2022; 12:ani12141775. [PMID: 35883321 PMCID: PMC9311715 DOI: 10.3390/ani12141775] [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: 06/16/2022] [Revised: 07/05/2022] [Accepted: 07/07/2022] [Indexed: 11/30/2022] Open
Abstract
Simple Summary The importance of lipid metabolism in the egg production of poultry has been widely reported. Meanwhile, geese have lower egg production and unique lipid metabolism patterns compared with chicken and duck. It is of great significance to further improve egg laying performance to explore the differences of fat metabolism and the molecular mechanisms in geese with different egg laying performance. This study compared the phenotypic differences of liver and abdominal fat, as well as the transcriptome level differences of liver, abdominal fat, and ovarian stroma among high-, low-, and no-egg production groups. The results reveal that lipid metabolism regulated by the circadian rhythm of the liver may directly or indirectly affect ovarian function through the inflammation and hormone secretion of abdominal fat. Abstract The lower egg production of geese (20~60 eggs per year) compared with chicken and duck limits the development of the industry, while the yolk weight and fatty liver susceptibility of geese was higher than that of other poultry. Therefore, the relationship between lipid metabolism and the laying performance of geese remains to be explored. Phenotypically, we observed that the liver fat content of the high-, low-, and no-egg production groups decreased in turn, while the abdominal fat weight increased in turn. For transcriptional regulation, the KEGG pathways related to lipid metabolism were enriched in all pairwise comparisons of abdominal fat and liver through functional analysis. However, some KEGG pathways related to inflammation and the circadian rhythm pathway were enriched by DEGs only in abdominal fat and the liver, respectively. The DEGs in ovarian stroma among different groups enriched some KEGG pathways related to ovarian steroidogenesis and cell adhesion. Our research reveals that lipid metabolism regulated by the circadian rhythm of the liver may directly or indirectly affect ovarian function through the inflammation and hormone secretion of abdominal fat. These results offer new insights into the regulation mechanisms of goose reproductive traits.
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Li T, Liu Z, Wang Y, Zuo D, Wang S, Ju H, Wang S, Xing Y, Ling Y, Liu C, Zhang Y, Zhou H, Yin J, Cao J, Gao J. Multiplexed Visualization Method to Explore Complete Targeting Regulatory Relationships Among Circadian Genes for Insomnia Treatment. Front Neurosci 2022; 16:877802. [PMID: 35844237 PMCID: PMC9285005 DOI: 10.3389/fnins.2022.877802] [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: 02/24/2022] [Accepted: 06/01/2022] [Indexed: 11/24/2022] Open
Abstract
Understanding the complete map of melatonin synthesis, the information transfer network among circadian genes in pineal gland, promises to resolve outstanding issues in endocrine systems and improve the clinical diagnosis and treatment level of insomnia, immune disease and hysterical depression. Currently, some landmark studies have revealed some genes that regulate circadian rhythm associated with melatonin synthesis. However, these studies don't give a complete map of melatonin synthesis, as transfer information among circadian genes in pineal gland is lost. New biotechnology, integrates dynamic sequential omics and multiplexed imaging method, has been used to visualize the complete process of melatonin synthesis. It is found that there are two extremely significant information transfer processes involved in melatonin synthesis. In the first stage, as the light intensity decreased, melatonin synthesis mechanism has started, which is embodied in circadian genes, Rel, Polr2A, Mafk, and Srbf1 become active. In the second stage, circadian genes Hif1a, Bach1, Clock, E2f6, and Per2 are regulated simultaneously by four genes, Rel, Polr2A, Mafk, and Srbf1 and contribute genetic information to Aanat. The expeditious growth in this technique offer reference for an overall understanding of gene-to-gene regulatory relationship among circadian genes in pineal gland. In the study, dynamic sequential omics and the analysis process well provide the current state and future perspectives to better diagnose and cure diseases associated with melatonin synthesis disorder.
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Affiliation(s)
- Tao Li
- Inner Mongolia Key Laboratory of Bio-manufacture, College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, China
- *Correspondence: Tao Li
| | - Zhenyu Liu
- Inner Mongolia Autonomous Region Key Laboratory of Big Data Research and Application of Agriculture and Animal Husbandry, College of Computer and Information Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Yitong Wang
- Department of Neurosurgery, Beijing Hospital, Beijing, China
| | - Dongshi Zuo
- Inner Mongolia Autonomous Region Key Laboratory of Big Data Research and Application of Agriculture and Animal Husbandry, College of Computer and Information Engineering, Inner Mongolia Agricultural University, Hohhot, China
| | - Shenyuan Wang
- Inner Mongolia Key Laboratory of Bio-manufacture, College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, China
| | - Haitao Ju
- Department of Neurosurgery, Affiliated Hospital of Inner Mongolia Medical University, Hohhot, China
| | - Shichao Wang
- Clinical Genetic Laboratory, First Hospital of Hohhot, Hohhot, China
| | - Yanping Xing
- Inner Mongolia Key Laboratory of Bio-manufacture, College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, China
| | - Yu Ling
- Inner Mongolia Key Laboratory of Bio-manufacture, College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, China
| | - Chunxia Liu
- Inner Mongolia Key Laboratory of Bio-manufacture, College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, China
| | - Yanru Zhang
- Inner Mongolia Key Laboratory of Bio-manufacture, College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, China
| | - Huanmin Zhou
- Inner Mongolia Key Laboratory of Bio-manufacture, College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, China
| | - Jun Yin
- Inner Mongolia Key Laboratory of Bio-manufacture, College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, China
| | - Junwei Cao
- Inner Mongolia Key Laboratory of Bio-manufacture, College of Life Sciences, Inner Mongolia Agricultural University, Hohhot, China
- Junwei Cao
| | - Jing Gao
- Inner Mongolia Autonomous Region Key Laboratory of Big Data Research and Application of Agriculture and Animal Husbandry, College of Computer and Information Engineering, Inner Mongolia Agricultural University, Hohhot, China
- Jing Gao
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Nacar MC, Nursal AF, Kuruca N, Yigit S. A circadian rhythm gene (PER3) VNTR variant as possible risk factor in cohort of Turkish females with primary dysmenorrhea. NUCLEOSIDES, NUCLEOTIDES & NUCLEIC ACIDS 2022; 41:900-909. [PMID: 35707903 DOI: 10.1080/15257770.2022.2085743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2022] [Revised: 05/24/2022] [Accepted: 05/29/2022] [Indexed: 06/15/2023]
Abstract
Primary dysmenorrhea (PDM), which is the most prevalent problem related to the menstrual cycle in women of reproductive age, is due to sleep disorders and negative moods. Circadian rhythms, which are the immediate 24-h processes, enable an organism to adapt the suitable physiological responses to the environmental light-dark changes. Disturbed circadian rhythms are closely associated with several diseases, including sleep disorders. It has been reported that variable number tandem repeat (VNTR) variant in the coding region of circadian rhythm gene PERIOD 3 (PER3) affects sleep. Therefore, in the present study, we investigated the association between PDM and PER3 VNTR variant in Turkish females. A sample of 122 females with PDM and 150 healthy females were included in the study. Genoytyping of PER3 VNTR variant was performed on DNA by polymerase chain reaction (PCR) analysis using specific primers. We evaluated the relation between PER3 VNTR variant and PDM by calculating the odds ratios (ORs) and 95% confidence intervals (CIs). In our analyses of genotype data collected from total 272 subjects, we found that the PER3 VNTR variant was associated with development of PDM [codominant model (5/5 vs. 4/4 + 4/5): OR = 0.664; 95% CI, 0.39-1.10; p = 0.05). The three genotypes of the VNTR variant (4/4, 4/5, and 5/5) and their allelic frequencies showed nonsignificant differences between patients and control group (p > 0.05). In summary, PER3 VNTR variant may be associated with PDM in a Turkish female. However, further studies in different ethnic populations are needed to address the full role of this variant in PDM.
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Affiliation(s)
- Mehmet Can Nacar
- Department of Obstetrics and Gynecology, Adıyaman University School of Medicine, Adıyaman, Turkey
| | - Ayse Feyda Nursal
- Department of Medical Genetics, Faculty of Medicine, Hitit University, Corum, Turkey
| | - Nilufer Kuruca
- Department of Pathology, Faculty of Veterinary Medicine, Ondokuz Mayis University, Samsun, Turkey
| | - Serbulent Yigit
- Department of Genetics, Faculty of Veterinary Medicine, Ondokuz Mayis University, Samsun, Turkey
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Wan X, Zhu L, Zhao L, Peng L, Xiong J, Yang W, Yuan J, Liang F, Zhang K, Chen K. hPER3 promotes adipogenesis via hHSP90AA1-mediated inhibition of Notch1 pathway. Cell Death Dis 2021; 12:301. [PMID: 33741899 PMCID: PMC7979882 DOI: 10.1038/s41419-021-03584-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2020] [Revised: 02/26/2021] [Accepted: 03/03/2021] [Indexed: 12/17/2022]
Abstract
The period circadian regulator 3 (PER3) has been reported to play a negative role in human immortalized bone marrow-derived Scp-1 cells (iBMSCs) and patient adipose-derived stromal cells (PASCs) or a negative/positive role in mice adipogenesis. However, human PER3 (hPER3) was identified as a positive regulator of human adipose tissue-derived stromal cells (hADSCs) adipogenesis in this study. Silencing or overexpression of hPER3 in hADSCs inhibited and promoted adipogenesis in vitro. In vivo, the overexpression of hPER3 increased high-fat diet-induced inguinal white adipose tissue (iWAT) and epididymal white adipose tissue (eWAT) forms, increasing systemic glucose intolerance and insulin resistance. Molecularly, hPER3 does not interact with hPPARγ, but represses Notch1 signaling pathway to enhance adipogenesis by interacting with hHSP90AA1, which is able to combine with the promoter of hNotch1 and inactivate its expression. Thus, our study revealed hPER3 as a critical positive regulator of hADSCs adipogenesis, which was different from the other types of cells, providing a critical role of it in treating obesity.
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Affiliation(s)
- Xinxing Wan
- Department of Endocrinology, Third Xiangya Hospital, Central South University, Changsha, Hunan, 410013, China
| | - Liyong Zhu
- Department of Bariatric and Metabolic Surgery, Third Xiangya Hospital, Central South University, Changsha, Hunan, 410013, China
| | - Liling Zhao
- Department of Endocrinology, Third Xiangya Hospital, Central South University, Changsha, Hunan, 410013, China
| | - Lin Peng
- Department of Nephrology, The First Hospital of Changsha, Changsha, Hunan, 410005, China
| | - Jing Xiong
- Department of Endocrinology, Third Xiangya Hospital, Central South University, Changsha, Hunan, 410013, China
| | - Wenjun Yang
- Department of Endocrinology, Third Xiangya Hospital, Central South University, Changsha, Hunan, 410013, China
| | - Jingjing Yuan
- Department of Endocrinology, Third Xiangya Hospital, Central South University, Changsha, Hunan, 410013, China
| | - Fang Liang
- Department of Endocrinology, Third Xiangya Hospital, Central South University, Changsha, Hunan, 410013, China
| | - Keke Zhang
- Department of Endocrinology, Third Xiangya Hospital, Central South University, Changsha, Hunan, 410013, China
| | - Ke Chen
- Department of Endocrinology, Third Xiangya Hospital, Central South University, Changsha, Hunan, 410013, China.
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