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Du Y, Wei H, Li M, Wang X, Ran J, Wang J, Dong C, Zhu N. Ovary Transcriptome Profiling in Broody and Egg-laying Chahua Chickens. J Poult Sci 2024; 61:2024018. [PMID: 38854637 PMCID: PMC11156485 DOI: 10.2141/jpsa.2024018] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2024] [Accepted: 05/07/2024] [Indexed: 06/11/2024] Open
Abstract
Broodiness in egg-laying hens (EHs) leads to ovarian atrophy, resulting in reduced egg-laying performance. However, the ovarian regulatory mechanisms in broody hens (BCs) remain elusive. Therefore, ovaries were removed from 300-day-old BCs and EHs for RNA sequencing. Ovarian morphology and histological characteristics of the BC and EH groups were compared and analyzed. The EH group had significantly more hierarchical follicles (HFs) and small yellow follicles (SYFs) than that of the BC group. Although several secondary follicles (SFs) and primary follicles were observed in the ovaries of the EH group, only a few SFs were observed in the ovaries of the BC group. Subsequently, RNA-sequencing analysis was conducted to determine the ovarian expression profiles of the two groups. Transcriptome sequencing identified 259 differentially expressed genes (DEGs) between the BC and EH groups. Of the 259 DEGs, 136 were upregulated and 123 were downregulated. The DEGs were mapped to 22 gene ontology terms and 4 Kyoto Encyclopedia of Genes and Genomes pathways for ovarian tissue. The analysis showed that matrix metalloproteinases 11/13 (MMP11/MMP13) were enriched in the extracellular matrix. The extracellular matrix mediated by MMP13 is affected by follicle-stimulating hormone, prolactin, and estrogen, which are critical signaling pathways that may affect ovarian follicle development to regulate the large yellow follicle reserve process and the ovulation cycle of broody Chahua chickens. These findings indicate that understanding differences in gene expression between the ovarian tissues of BCs and EHs could serve as a valuable reference point for enhancing egg-laying performance in Chahua chickens.
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Affiliation(s)
- Yanli Du
- College of Agronomy and Life Sciences, Kunming University, Kunming 650200,
Yunnan Province, People’s Republic of China
| | - Huang Wei
- College of Agronomy and Life Sciences, Kunming University, Kunming 650200,
Yunnan Province, People’s Republic of China
| | - Meiquan Li
- College of Agronomy and Life Sciences, Kunming University, Kunming 650200,
Yunnan Province, People’s Republic of China
| | - Xiao Wang
- College of Agronomy and Life Sciences, Kunming University, Kunming 650200,
Yunnan Province, People’s Republic of China
| | - Jinshan Ran
- College of Agronomy and Life Sciences, Kunming University, Kunming 650200,
Yunnan Province, People’s Republic of China
| | - Jing Wang
- College of Agronomy and Life Sciences, Kunming University, Kunming 650200,
Yunnan Province, People’s Republic of China
| | - Cuilian Dong
- College of Agronomy and Life Sciences, Kunming University, Kunming 650200,
Yunnan Province, People’s Republic of China
| | - Na Zhu
- College of Agronomy and Life Sciences, Kunming University, Kunming 650200,
Yunnan Province, People’s Republic of China
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Tan Y, Huang Y, Xu C, Huang X, Li S, Yin Z. Long noncoding RNAs and mRNAs profiling in ovary during laying and broodiness in Taihe Black-Bone Silky Fowls (Gallus gallus Domesticus Brisson). BMC Genomics 2024; 25:357. [PMID: 38600449 PMCID: PMC11005167 DOI: 10.1186/s12864-024-10281-7] [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: 01/11/2024] [Accepted: 04/02/2024] [Indexed: 04/12/2024] Open
Abstract
BACKGROUND Broodiness significantly impacts poultry egg production, particularly notable in specific breeds such as the black-boned Silky, characterized by pronounced broodiness. An understanding of the alterations in ovarian signaling is essential for elucidating the mechanisms that influence broodiness. However, comparative research on the characteristics of long non-coding RNAs (lncRNAs) in the ovaries of broody chickens (BC) and high egg-laying chickens (GC) remains scant. In this investigation, we employed RNA sequencing to assess the ovarian transcriptomes, which include both lncRNAs and mRNAs, in eight Taihe Black-Bone Silky Fowls (TBsf), categorized into broody and high egg-laying groups. This study aims to provide a clearer understanding of the genetic underpinnings associated with broodiness and egg production. RESULTS We have identified a total of 16,444 mRNAs and 18,756 lncRNAs, of which 349 mRNAs and 651 lncRNAs exhibited significantly different expression (DE) between the BC and GC groups. Furthermore, we have identified the cis-regulated and trans-regulated target genes of differentially abundant lncRNA transcripts and have constructed an lncRNA-mRNA trans-regulated interaction network linked to ovarian follicle development. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation analyses have revealed that DE mRNAs and the target genes of DE lncRNAs are associated with pathways including neuroactive ligand-receptor interaction, CCR6 chemokine receptor binding, G-protein coupled receptor binding, cytokine-cytokine receptor interaction, and ECM-receptor interaction. CONCLUSION Our research presents a comprehensive compilation of lncRNAs and mRNAs linked to ovarian development. Additionally, it establishes a predictive interaction network involving differentially abundant lncRNAs and differentially expressed genes (DEGs) within TBsf. This significantly contributes to our understanding of the intricate interactions between lncRNAs and genes governing brooding behavior.
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Affiliation(s)
- Yuting Tan
- Zijingang Campus, Animal Science College, Zhejiang University, Hangzhou, 310058, China
| | - Yunyan Huang
- Zijingang Campus, Animal Science College, Zhejiang University, Hangzhou, 310058, China
| | - Chunhui Xu
- Zijingang Campus, Animal Science College, Zhejiang University, Hangzhou, 310058, China
| | - Xuan Huang
- Zijingang Campus, Animal Science College, Zhejiang University, Hangzhou, 310058, China
| | - Shibao Li
- Zijingang Campus, Animal Science College, Zhejiang University, Hangzhou, 310058, China
| | - Zhaozheng Yin
- Zijingang Campus, Animal Science College, Zhejiang University, Hangzhou, 310058, China.
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Song X, Li S, He S, Zheng H, Li R, Liu L, Geng T, Zhao M, Gong D. Integration of Whole-Genome Resequencing and Transcriptome Sequencing Reveals Candidate Genes in High Glossiness of Eggshell. Animals (Basel) 2024; 14:1141. [PMID: 38672292 PMCID: PMC11047648 DOI: 10.3390/ani14081141] [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: 03/04/2024] [Revised: 04/03/2024] [Accepted: 04/04/2024] [Indexed: 04/28/2024] Open
Abstract
Eggshell gloss is an important characteristic for the manifestation of eggshell appearance. However, no study has yet identified potential candidate genes for eggshell gloss between high-gloss (HG) and low-gloss (LG) chickens. The aim of this study was to perform a preliminary investigation into the formation mechanism of eggshell gloss and to identify potential genes. The eggshell gloss of 300-day-old Rhode Island Red hens was measured from three aspects. Uterine tissues of the selected HG and LG (n = 5) hens were collected for RNA-seq. Blood samples were also collected for whole-genome resequencing (WGRS). RNA-seq analysis showed that 150 differentially expressed genes (DEGs) were identified in the uterine tissues of HG and LG hens. These DEGs were mainly enriched in the calcium signaling pathway and the neuroactive ligand-receptor interaction pathway. Importantly, these two pathways were also significantly enriched in the WGRS analysis results. Further joint analysis of WGRS and RNA-seq data revealed that 5-hydroxytryptamine receptor 1F (HTR1F), zinc finger protein 536 (ZNF536), NEDD8 ubiquitin-like modifier (NEDD8), nerve growth factor (NGF) and calmodulin 1 (CALM1) are potential candidate genes for eggshell gloss. In summary, our research provides a reference for the study of eggshell gloss and lays a foundation for improving egg glossiness in layer breeding.
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Affiliation(s)
- Xiang Song
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (X.S.); (L.L.); (T.G.)
| | - Shuo Li
- Jiangsu Beinongda Agriculture and Animal Husbandry Technology Co., Ltd., Taizhou 225300, China
| | - Shixiong He
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (X.S.); (L.L.); (T.G.)
| | - Hongxiang Zheng
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (X.S.); (L.L.); (T.G.)
| | - Ruijie Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (X.S.); (L.L.); (T.G.)
| | - Long Liu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (X.S.); (L.L.); (T.G.)
| | - Tuoyu Geng
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (X.S.); (L.L.); (T.G.)
| | - Minmeng Zhao
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (X.S.); (L.L.); (T.G.)
| | - Daoqing Gong
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (X.S.); (L.L.); (T.G.)
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He Z, Ouyang Q, Chen Q, Song Y, Hu J, Hu S, He H, Li L, Liu H, Wang J. Molecular mechanisms of hypothalamic-pituitary-ovarian/thyroid axis regulating age at first egg in geese. Poult Sci 2024; 103:103478. [PMID: 38295497 PMCID: PMC10844868 DOI: 10.1016/j.psj.2024.103478] [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: 11/30/2023] [Revised: 01/10/2024] [Accepted: 01/14/2024] [Indexed: 02/02/2024] Open
Abstract
Age at first egg (AFE) has consistently garnered interest as a crucial reproductive indicator within poultry production. Previous studies have elucidated the involvement of the hypothalamic-pituitary-ovarian (HPO) and hypothalamic-pituitary-thyroid (HPT) axes in regulating poultry sexual maturity. Concurrently, there was evidence suggesting a potential co-regulatory relationship between these 2 axes. However, as of now, no comprehensive exploration of the key pathways and genes responsible for the crosstalk between the HPO and HPT axes in the regulation of AFE has been reported. In this study, we conducted a comparative analysis of morphological differences and performed transcriptomic analysis on the hypothalamus, pituitary, thyroid, and ovarian stroma between normal laying group (NG) and abnormal laying group (AG). Morphological results showed that the thyroid index difference (D-) value (thyroid index D-value=right thyroid index-left thyroid index) was significantly (P < 0.05) lower in the NG than in the AG, while the ovarian index was significantly (P < 0.01) higher in the NG than in the AG. Furthermore, between NG and AG, we identified 99, 415, 167, and 1182 differentially expressed genes (DEGs) in the hypothalamus, pituitary, thyroid, and ovarian stroma, respectively. Gene ontology (GO) analysis highlighted that DEGs from 4 tissues were predominantly enriched in the "biological processes" category. Additionally, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis revealed that 16, 14, 3, and 26 KEGG pathways were significantly enriched (P < 0.05) in the hypothalamus, pituitary, thyroid, and ovarian stroma. The MAPK signaling pathway emerged as the sole enriched pathway across all 4 tissues. Employing an integrated analysis of the protein-protein interaction (PPI) network and correlation analysis, we found GREB1 emerged as a pivotal component within the HPO axis to regulate estrogen-related signaling in the HPT axis, meanwhile, the HPT axis influenced ovarian development by regulating thyroid hormone-related signaling mainly through OPN5. Then, 10 potential candidate genes were identified, namely IGF1, JUN, ERBB4, KDR, PGF, FGFR1, GREB1, OPN5, DIO3, and THRB. These findings establish a foundation for elucidating the physiological and genetic mechanisms by which the HPO and HPT axes co-regulate goose AFE.
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Affiliation(s)
- Zhiyu He
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China
| | - Qingyuan Ouyang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China
| | - Qingliang Chen
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China
| | - Yang Song
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China
| | - Jiwei Hu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China
| | - Shenqiang Hu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China
| | - Hua He
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China
| | - Liang Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China
| | - Hehe Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China
| | - Jiwen Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China; State Key Laboratory of Swine and Poultry Breeding Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, 611130, PR China.
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5
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Huang Y, Li S, Tan Y, Xu C, Huang X, Yin Z. Identification and functional analysis of ovarian lncRNAs during different egg laying periods in Taihe Black-Bone Chickens. Front Physiol 2024; 15:1358682. [PMID: 38426211 PMCID: PMC10902129 DOI: 10.3389/fphys.2024.1358682] [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: 12/20/2023] [Accepted: 02/05/2024] [Indexed: 03/02/2024] Open
Abstract
Introduction: Long non-coding RNA (lncRNA) refers to a category of non-coding RNA molecules exceeding 200 nucleotides in length, which exerts a regulatory role in the context of ovarian development. There is a paucity of research examining the involvement of lncRNA in the regulation of ovary development in Taihe Black-Bone Chickens. In order to further investigate the egg laying regulation mechanisms of Taihe Black-Bone Chickens at different periods, transcriptome analysis was conducted on the ovarian tissues at different laying periods. Methods: This study randomly selected ovarian tissues from 12 chickens for RNA-seq. Four chickens were selected for each period, including the early laying period (102 days, Pre), the peak laying period (203 days, Peak), and the late laying period (394 days, Late). Based on our previous study of mRNA expression profiles in the same ovarian tissue, we identified three differentially expressed lncRNAs (DE lncRNAs) at different periods and searched for their cis- and trans-target genes to draw an lncRNA-mRNA network. Results and discussion: In three groups of ovarian tissues, we identified 136 DE lncRNAs, with 8 showing specific expression during the early laying period, 10 showing specific expression during the peak laying period, and 4 showing specific expression during the late laying period. The lncRNA-mRNA network revealed 16 pairs of lncRNA-target genes associated with 7 DE lncRNAs, and these 14 target genes were involved in the regulation of reproductive traits. Furthermore, these reproductive-related target genes were primarily associated with signaling pathways related to follicle and ovary development in Taihe Black-Bone Chickens, including cytokine-cytokine receptor interaction, TGF-beta signaling pathway, tyrosine metabolism, ECM-receptor interaction, focal adhesion, neuroactive ligand-receptor interaction, and cell adhesion molecules (CAMs). This study offers valuable insights for a comprehensive understanding of the influence of lncRNAs on poultry reproductive traits.
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Affiliation(s)
| | | | | | | | | | - Zhaozheng Yin
- College of Animal Science, Zhejiang University, Hangzhou, China
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6
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Chang Y, Guo R, Zeng T, Sun H, Tian Y, Han X, Cao Y, Xu L, Duan M, Lu L, Chen L. Analysis of Transcriptomic Differences in the Ovaries of High- and Low-Laying Ducks. Genes (Basel) 2024; 15:181. [PMID: 38397170 PMCID: PMC10887599 DOI: 10.3390/genes15020181] [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: 01/07/2024] [Revised: 01/21/2024] [Accepted: 01/26/2024] [Indexed: 02/25/2024] Open
Abstract
The egg-laying performance of Shan Ma ducks (Anas Platyrhynchos) is a crucial economic trait. Nevertheless, limited research has been conducted on the egg-laying performance of this species. We examined routine blood indicators and observed higher levels of metabolic and immune-related factors in the high-egg-production group compared with the low-egg-production group. Furthermore, we explored the ovarian transcriptome of both high- and low-egg-production groups of Shan Ma ducks using Illumina NovaSeq 6000 sequencing. A total of 1357 differentially expressed genes (DEGs) were identified, with 686 down-regulated and 671 up-regulated in the high-egg-production (HEP) ducks and low-egg-production (LEP) ducks. Several genes involved in the regulation of ovarian development, including neuropeptide Y (NPY), cell cycle protein-dependent kinase 1 (CDK1), and transcription factor 1 (E2F1), exhibited significant differential expressions at varying stages of egg production. Pathway functional analysis revealed that the DEGs were primarily associated with the steroid biosynthesis pathway, and the neuroactive ligand-receptor interaction pathway exhibited higher activity in the HEP group compared to the LEP group. This study offers valuable information about and novel insights into high egg production.
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Affiliation(s)
- Yuguang Chang
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Science & Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.C.); (T.Z.); (H.S.); (Y.T.); (Y.C.); (L.X.); (M.D.); (L.L.)
| | - Rongbing Guo
- College of Animal Sciences and Veterinary Medicine, Zhejiang A&F University, Hangzhou 311300, China;
| | - Tao Zeng
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Science & Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.C.); (T.Z.); (H.S.); (Y.T.); (Y.C.); (L.X.); (M.D.); (L.L.)
| | - Hanxue Sun
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Science & Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.C.); (T.Z.); (H.S.); (Y.T.); (Y.C.); (L.X.); (M.D.); (L.L.)
| | - Yong Tian
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Science & Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.C.); (T.Z.); (H.S.); (Y.T.); (Y.C.); (L.X.); (M.D.); (L.L.)
| | - Xue Han
- Institute of Animal Husbandry and Veterinary Science, Guizhou Academy of Agricultural Sciences, Guiyang 550000, China;
| | - Yongqing Cao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Science & Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.C.); (T.Z.); (H.S.); (Y.T.); (Y.C.); (L.X.); (M.D.); (L.L.)
| | - Ligen Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Science & Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.C.); (T.Z.); (H.S.); (Y.T.); (Y.C.); (L.X.); (M.D.); (L.L.)
| | - Mingcai Duan
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Science & Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.C.); (T.Z.); (H.S.); (Y.T.); (Y.C.); (L.X.); (M.D.); (L.L.)
| | - Lizhi Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Science & Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.C.); (T.Z.); (H.S.); (Y.T.); (Y.C.); (L.X.); (M.D.); (L.L.)
| | - Li Chen
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Science & Veterinary, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (Y.C.); (T.Z.); (H.S.); (Y.T.); (Y.C.); (L.X.); (M.D.); (L.L.)
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Xu W, Mu R, Gegen T, Luo J, Xiao Y, Ou S, Wu Q, Zuo Y, Chen Z, Li F. Comparative analysis of hepatic transcriptomes and metabolomes of Changshun green-shell laying hens based on different green eggshell color intensities. Poult Sci 2024; 103:103220. [PMID: 37980748 PMCID: PMC10685025 DOI: 10.1016/j.psj.2023.103220] [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: 08/07/2023] [Revised: 10/13/2023] [Accepted: 10/17/2023] [Indexed: 11/21/2023] Open
Abstract
The eggshell color of avian species is an important trait that is predominantly determined by the pigments biliverdin and protoporphyrin. Various factors affect eggshell pigment deposition and coloration; however, the underlying mechanisms remain unclear. We analyzed the hepatic transcriptomes and metabolomes of Changshun green-shell hens laying dark green and light green eggs to investigate the potential role of the liver in regulating the intensity of the green eggshell color. In total, 350 differentially expressed genes and 211 differentially altered metabolites were identified. Gene set enrichment analysis revealed that the enriched pathways and Gene Ontology (GO) terms were mainly associated with energy, immunity, and nutrient metabolism. Metabolite set enrichment analysis revealed that the enriched pathways were mainly associated with amino acid, vitamin, bile acid, and lipid metabolism. Moreover, gene-metabolite interaction network analysis revealed 1 subnetwork. Most genes and metabolites in this subnetwork were determined to be related to melanin metabolism and transport. In conclusion, our results suggest that hepatic melanin metabolism and transport are critical for eggshell coloration. Six candidate genes (CDKN2B, DDC, PYCR1, ABCG5, SLC3A1, and P2RX2) and 7 candidate metabolites (serotonin, 5-hydroxyindoleacetic acid, ornithine, acetylcholine, L-tryptophan, D-ornithine, and ADP) were suggested to play important roles in this process. Meanwhile, this study suggests that changes in hepatic energy metabolism, immune status, antioxidation activity, nutrient availability, and bile acid synthesis can impair eggshell coloration.
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Affiliation(s)
- Wenbin Xu
- College of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Duyun 558000, China; Qiannan Key Laboratory of Applied Biotechnology for Livestock and Poultry, Duyun 558000, China; College of Animal Sciences, Zhejiang University, Hangzhou 310058, China
| | - Ren Mu
- College of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Duyun 558000, China; Qiannan Key Laboratory of Applied Biotechnology for Livestock and Poultry, Duyun 558000, China.
| | - Tuya Gegen
- Qiannan Key Laboratory of Applied Biotechnology for Livestock and Poultry, Duyun 558000, China; Library, Qiannan Normal University for Nationalities, Duyun 558000, China
| | - Jiaxiang Luo
- College of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Duyun 558000, China
| | - Yang Xiao
- College of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Duyun 558000, China
| | - Shunnian Ou
- College of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Duyun 558000, China
| | - Qi Wu
- College of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Duyun 558000, China; Qiannan Key Laboratory of Applied Biotechnology for Livestock and Poultry, Duyun 558000, China
| | - Yongsong Zuo
- College of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Duyun 558000, China; Qiannan Key Laboratory of Applied Biotechnology for Livestock and Poultry, Duyun 558000, China
| | - Zhi Chen
- College of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Duyun 558000, China; Qiannan Key Laboratory of Applied Biotechnology for Livestock and Poultry, Duyun 558000, China
| | - Fangwei Li
- Guizhou Changshun Tiannong Green Shell Laying Hen Industrial Co. Ltd., Chang Shun 550700, China
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Xu W, Mu R, Gegen T, Ran T, Wu Q, Wen D, Wang F, Chen Z. Transcriptome analysis of hypothalamus and pituitary tissues reveals genetic mechanisms associated with high egg production rates in Changshun green-shell laying hens. BMC Genomics 2023; 24:792. [PMID: 38124055 PMCID: PMC10734086 DOI: 10.1186/s12864-023-09895-0] [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: 08/03/2023] [Accepted: 12/12/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND Changshun green-shell laying hens are unique to the Guizhou Province, China, and have high egg quality but relatively low yield. Egg production traits are regulated by the hypothalamus-pituitary-ovary axis. However, the underlying mechanism remains unclear. Thus, we conducted RNA sequencing of hypothalamic and pituitary tissues from low- and high-yielding Changshun green-shell laying hens to identify critical pathways and candidate genes involved in controlling the egg production rate. RESULTS More than 39 million clean reads per sample were obtained, and more than 82% were mapped to the Gallus gallus genome. Further analysis identified 1,817 and 1,171 differentially expressed genes (DEGs) in the hypothalamus and pituitary, respectively. Nineteen DEGs were upregulated in both the hypothalamus and pituitary of high-yielding chickens. The functions of these DEGs were mainly associated with ion transport or signal transduction. Gene set enrichment analysis revealed that the pathways enriched in the hypothalamus were mainly associated with gonadotropin-releasing hormone (GnRH) secretion, neurotransmitter release, and circadian rhythms. The pathways enriched in the pituitary were mainly associated with GnRH secretion, energy metabolism, and signal transduction. Five and four DEGs in the hypothalamus and pituitary, respectively, were selected randomly for qRT-PCR analysis. The expression trends determined via qRT-PCR were consistent with the RNA-seq results. CONCLUSIONS The current study identified 19 DEGs upregulated in both the hypothalamus and pituitary gland, which could provide an important reference for further studies on the molecular mechanisms underlying egg production in Changshun green-shell laying hens. In addition, enrichment analysis showed that GnRH secretion and signal transduction, especially neurotransmitter release, play crucial roles in the regulation of egg production.
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Affiliation(s)
- Wenbin Xu
- College of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Jianjiang Road 5, Duyun, 558000, China
- Qiannan Key Laboratory of Applied Biotechnology for Livestock and Poultry, Duyun, 558000, China
- College of Animal Sciences, Zhejiang University, Hangzhou, 310058, China
| | - Ren Mu
- College of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Jianjiang Road 5, Duyun, 558000, China.
- Qiannan Key Laboratory of Applied Biotechnology for Livestock and Poultry, Duyun, 558000, China.
| | - Tuya Gegen
- Qiannan Key Laboratory of Applied Biotechnology for Livestock and Poultry, Duyun, 558000, China
- Library, Qiannan Normal University for Nationalities, Duyun, 558000, China
| | - Tiantian Ran
- College of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Jianjiang Road 5, Duyun, 558000, China
| | - Qi Wu
- College of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Jianjiang Road 5, Duyun, 558000, China
- Qiannan Key Laboratory of Applied Biotechnology for Livestock and Poultry, Duyun, 558000, China
| | - Di Wen
- College of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Jianjiang Road 5, Duyun, 558000, China
| | - Fen Wang
- College of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Jianjiang Road 5, Duyun, 558000, China
| | - Zhi Chen
- College of Biological Science and Agriculture, Qiannan Normal University for Nationalities, Jianjiang Road 5, Duyun, 558000, China.
- Qiannan Key Laboratory of Applied Biotechnology for Livestock and Poultry, Duyun, 558000, China.
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9
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Xiang X, Huang X, Wang J, Zhang H, Zhou W, Xu C, Huang Y, Tan Y, Yin Z. Transcriptomic and metabolomic analyses of the ovaries of Taihe black-bone silky fowls at the peak egg-laying and nesting period. Front Genet 2023; 14:1222087. [PMID: 37876591 PMCID: PMC10591096 DOI: 10.3389/fgene.2023.1222087] [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: 05/13/2023] [Accepted: 09/25/2023] [Indexed: 10/26/2023] Open
Abstract
The poor reproductive performance of most local Chinese chickens limits the economic benefits and output of related enterprises. As an excellent local breed in China, Taihe black-bone silky fowl is in urgent need of our development and utilization. In this study, we performed transcriptomic and metabolomic analyses of the ovaries of Taihe black-bone silky fowls at the peak egg-laying period (PP) and nesting period (NP) to reveal the molecular mechanisms affecting reproductive performance. In the transcriptome, we identified five key differentially expressed genes (DEGs) that may affect the reproductive performance of Taihe black-bone silky fowl: BCHE, CCL5, SMOC1, CYTL1, and SCIN, as well as three important pathways: the extracellular region, Neuroactive ligand-receptor interaction and Cytokine-cytokine receptor interaction. In the metabolome, we predicted three important ovarian significantly differential metabolites (SDMs): LPC 20:4, Bisphenol A, and Cortisol. By integration analysis of transcriptome and metabolome, we identified three important metabolite-gene pairs: "LPC 20:4-BCHE", "Bisphenol A-SMOC1", and "Cortisol- SCIN". In summary, this study contributes to a deeper understanding of the regulatory mechanism of egg production in Taihe black-bone silky fowl and provides a scientific basis for improving the reproductive performance of Chinese local chickens.
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Affiliation(s)
- Xin Xiang
- Animal Science College, Zhejiang University, Hangzhou, China
| | - Xuan Huang
- Animal Science College, Zhejiang University, Hangzhou, China
| | | | - Haiyang Zhang
- Animal Science College, Zhejiang University, Hangzhou, China
| | - Wei Zhou
- Animal Science College, Zhejiang University, Hangzhou, China
| | - Chunhui Xu
- Animal Science College, Zhejiang University, Hangzhou, China
| | - Yunyan Huang
- Animal Science College, Zhejiang University, Hangzhou, China
| | - Yuting Tan
- Animal Science College, Zhejiang University, Hangzhou, China
| | - Zhaozheng Yin
- Animal Science College, Zhejiang University, Hangzhou, China
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10
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Cai D, Wang Z, Zhou Z, Lin D, Ju X, Nie Q. Integration of transcriptome sequencing and whole genome resequencing reveal candidate genes in egg production of upright and pendulous-comb chickens. Poult Sci 2023; 102:102504. [PMID: 36739803 PMCID: PMC9932115 DOI: 10.1016/j.psj.2023.102504] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2022] [Revised: 12/30/2022] [Accepted: 01/10/2023] [Indexed: 01/18/2023] Open
Abstract
Egg production performance plays an important role in the poultry industry across the world. Previous studies have shown a great difference in egg production performance between pendulous-comb (PC) and upright-comb (UC) chickens. However, there are no reports to identify potential candidate genes for egg production in PC and UC chickens. In the present study, 1,606 laying chickens were raised, and the egg laid by individual chicken was collected for 100 d. Moreover, the expression level of estrogen and progesterone hormones was measured at the start-laying and peak-laying periods of hens. Besides, 4 PC and 4 UC chickens were selected at 217 d of age to perform transcriptome sequencing (RNA-seq) and whole genome resequencing (WGS) to screen the potential candidate genes of egg production. The results showed that PC chicken demonstrated better egg production performance (P < 0.05) and higher estrogen and progesterone hormone expression levels than UC chicken (P < 0.05). RNA-seq analysis showed that 341 upregulated and 1,036 downregulated differentially expressed genes (DEGs) were identified in the ovary tissues of PC and UC chickens. These DEGs were mainly enriched in protein-related, lipid-related, and nucleic acids-related biological processes including ribosome, peptide biosynthetic process, lipid transport terms, and catalytic activity acting on RNA which can significantly affect egg production in chicken. The enrichment results of WGS analysis were consistent with RNA-seq. Further, joint analysis of WGS and RNA-seq data was utilized to screen 30 genes and CAMK1D, CLSTN2, MAST2, PIK3C2G, TBC1D1, STK3, ADGRB3, and PPARGC1A were identified as potential candidate genes for egg production in PC and UC chickens. In summary, our study provides a wealth of information for a better understanding of the genetic and molecular mechanism for the future breeding of PC and UC chickens for egg production.
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Affiliation(s)
- Danfeng Cai
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China
| | - Zhijun Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China,College of Animal Science and Technology, Zhejiang Agriculture and Forestry University, Lin'an 311300, China
| | - Zhen Zhou
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China
| | - Duo Lin
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China
| | - Xing Ju
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China,Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China
| | - Qinghua Nie
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Lingnan Guangdong Laboratory of Agriculture, College of Animal Science, South China Agricultural University, Guangzhou 510642, Guangdong, China; Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding, and Key Laboratory of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture, Guangzhou 510642, Guangdong, China.
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11
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Wang Y, Wang Y, Wang L, Wei B, Lv X, Huang Y, Zhang H, Chen W. Dietary supplementation with Clostridium butyricum and its ferment substance improves the egg quality and ovarian function in laying hens from 50 to 58 weeks of age. Anim Sci J 2023; 94:e13877. [PMID: 37818858 DOI: 10.1111/asj.13877] [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: 04/04/2023] [Revised: 07/19/2023] [Accepted: 08/01/2023] [Indexed: 10/13/2023]
Abstract
The current study was conducted to explore the effects of dietary Clostridium butyricum (C. butyricum) and fermented calcium (Ca) butyrate produced by C. butyricum on the performance and egg quality of post-peak laying. A total of 384 50-week-old hens were fed a basal diet, the basal diet with 300 mg/kg of fermented Ca butyrate or 1 × 109 CFU/kg C. butyricum for 8 weeks. Hens received a C. butyricum exhibited higher yolk properties, albumen height, and Haugh unit. A diet with fermented Ca butyrate or C. butyricum increased the egg mass and the pre-grade yellow follicle number. RNA-sequencing (RNA-seq) data showed that these observations were associated with cytokine-cytokine receptor interaction and intestinal immune status. Accordingly, when compared with the basal diet group, Ca butyrate and C. butyricum addition decreased serum pro-inflammatory cytokine levels and increased the concentration of immunoglobulin A, along with improved intestinal barrier. In addition, dietary C. butyricum inclusion induced a higher abundance of Ruminococcaceae and Lachnospiraceae at the family level. In summary, dietary fermented Ca butyrate or C. butyricum supplementation improved egg quality and ovarian function, which might be related to the enhanced intestinal barrier and immunity in post-peak laying hens.
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Affiliation(s)
- Yongshuai Wang
- College of Animal Science and Technology, Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture, Henan Agricultural University, Zhengzhou, China
| | - Yilu Wang
- College of Animal Science and Technology, Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture, Henan Agricultural University, Zhengzhou, China
| | - Leilei Wang
- College of Animal Science and Technology, Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture, Henan Agricultural University, Zhengzhou, China
| | - Bin Wei
- College of Animal Science and Technology, Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture, Henan Agricultural University, Zhengzhou, China
| | - Xiangyun Lv
- Charoen Pokphand Group Co., Ltd., Zhumadian, Henan, China
| | - Yanqun Huang
- College of Animal Science and Technology, Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture, Henan Agricultural University, Zhengzhou, China
| | - Huaiyong Zhang
- College of Animal Science and Technology, Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture, Henan Agricultural University, Zhengzhou, China
- Laboratory for Animal Nutrition and Animal Product Quality, Department of Animal Sciences and Aquatic Ecology, Ghent University, Ghent, Belgium
| | - Wen Chen
- College of Animal Science and Technology, Key Laboratory of Animal Biochemistry and Nutrition, Ministry of Agriculture, Henan Agricultural University, Zhengzhou, China
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12
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Bhavana K, Foote DJ, Srikanth K, Balakrishnan CN, Prabhu VR, Sankaralingam S, Singha HS, Gopalakrishnan A, Nagarajan M. Comparative transcriptome analysis of Indian domestic duck reveals candidate genes associated with egg production. Sci Rep 2022; 12:10943. [PMID: 35768515 PMCID: PMC9243076 DOI: 10.1038/s41598-022-15099-5] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2022] [Accepted: 06/17/2022] [Indexed: 12/12/2022] Open
Abstract
Egg production is an important economic trait and a key indicator of reproductive performance in ducks. Egg production is regulated by several factors including genes. However the genes involved in egg production in duck remain unclear. In this study, we compared the ovarian transcriptome of high egg laying (HEL) and low egg laying (LEL) ducks using RNA-Seq to identify the genes involved in egg production. The HEL ducks laid on average 433 eggs while the LEL ducks laid 221 eggs over 93 weeks. A total of 489 genes were found to be significantly differentially expressed out of which 310 and 179 genes were up and downregulated, respectively, in the HEL group. Thirty-eight differentially expressed genes (DEGs), including LHX9, GRIA1, DBH, SYCP2L, HSD17B2, PAR6, CAPRIN2, STC2, and RAB27B were found to be potentially related to egg production and folliculogenesis. Gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis suggested that DEGs were enriched for functions related to glutamate receptor activity, serine-type endopeptidase activity, immune function, progesterone mediated oocyte maturation and MAPK signaling. Protein-protein interaction network analysis (PPI) showed strong interaction between 32 DEGs in two distinct clusters. Together, these findings suggest a mix of genetic and immunological factors affect egg production, and highlights candidate genes and pathways, that provides an understanding of the molecular mechanisms regulating egg production in ducks and in birds more broadly.
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Affiliation(s)
- Karippadakam Bhavana
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | - Dustin J Foote
- Department of Biology, East Carolina University, Greenville, NC, 27858, USA
| | - Krishnamoorthy Srikanth
- Department of Animal Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, NY, 14853, USA
| | | | - Vandana R Prabhu
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India.,ICAR-Central Marine Fisheries Research Institute, Ernakulam North PO, Kochi, Kerala, 682 018, India
| | - Shanmugam Sankaralingam
- Department of Poultry Science, College of Veterinary and Animal Sciences, Mannuthy, Thrissur, Kerala, 680 651, India
| | - Hijam Surachandra Singha
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India
| | | | - Muniyandi Nagarajan
- Department of Genomic Science, School of Biological Sciences, Central University of Kerala, Kasaragod, Kerala, 671316, India.
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13
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Comparative transcriptomics in the hypothalamic-pituitary-gonad axis of mammals and poultry. Genomics 2022; 114:110396. [DOI: 10.1016/j.ygeno.2022.110396] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 05/25/2022] [Accepted: 06/01/2022] [Indexed: 11/22/2022]
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14
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Wu H, Li H, Hou Y, Huang L, Hu J, Lu Y, Liu X. Differences in egg yolk precursor formation of Guangxi Ma chickens with dissimilar laying rate at the same or various ages. Theriogenology 2022; 184:13-25. [DOI: 10.1016/j.theriogenology.2022.02.020] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2021] [Revised: 02/15/2022] [Accepted: 02/21/2022] [Indexed: 12/13/2022]
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