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Ji G, Zhang M, Ju X, Liu Y, Shan Y, Tu Y, Zou J, Shu J, Li H, Zhao W. Dynamic Transcriptome Profile Analysis of Mechanisms Related to Melanin Deposition in Chicken Muscle Development. Animals (Basel) 2024; 14:2702. [PMID: 39335292 PMCID: PMC11428610 DOI: 10.3390/ani14182702] [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: 07/31/2024] [Revised: 09/10/2024] [Accepted: 09/11/2024] [Indexed: 09/30/2024] Open
Abstract
The pectoral muscle is an important component of skeletal muscle. The blackness of pectoral muscles can directly affect the economic value of black-boned chickens. Although the genes associated with melanogenesis in mammals and birds have been thoroughly investigated, only little is known about the key genes involved in muscle hyperpigmentation during embryonic development. Here, we analyzed melanin deposition patterns in the pectoral muscle of Yugan black-boned chickens and compared differentially expressed genes (DEGs) between the muscles of Wenchang (non-black-boned chickens) and Yugan black-boned chickens on embryonic days 9, 13, 17, and 21. Melanin pigments were found to gradually accumulate in the muscle fibers over time. Using RNA-seq, there were 40, 97, 169, and 94 genes were identified as DEGs, respectively, between Yugan black-boned chicken muscles and Wenchang chickens at embryonic day 9, 13, 17, and 21 stages (fold change ≥2.0, false discovery rate (FDR) < 0.05). Thirteen DEGs, such as MSTRG.720, EDNRB2, TYRP1, and DCT, were commonly identified among the time points observed. These DEGs were mainly involved in pigmentation, melanin biosynthetic and metabolic processes, and secondary metabolite biosynthetic processes. Pathway analysis of the DEGs revealed that they were mainly associated with melanogenesis and tyrosine metabolism. Moreover, weighted gene co-expression network analysis (WGCNA) was used to detect core modules and central genes related to melanogenesis in the muscles of black-boned chickens. A total of 24 modules were identified. Correlation analysis indicated that one of them (the orange module) was positively correlated with muscle pigmentation traits (r > 0.8 and p < 0.001). Correlations between gene expression and L* values of the breast muscle were investigated in Yugan and Taihe black-boned chickens after hatching. The results confirmed that EDNRB2, GPNMB, TRPM1, TYR, and DCT expression levels were significantly associated with L* values (p < 0.01) in black-boned chickens (p < 0.05). Our results suggest that EDNRB2, GPNMB, TRPM1, TYR, and DCT are the essential genes regulating melanin deposition in the breast muscle of black-boned chickens. MSTRG.720 is a potential candidate gene involved in melanin deposition in the breast muscles of Yugan black-boned chickens.
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Affiliation(s)
- Gaige Ji
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Jiangsu Institute of Poultry Science, Yangzhou 225125, China
| | - Ming Zhang
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Jiangsu Institute of Poultry Science, Yangzhou 225125, China
| | - Xiaojun Ju
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Jiangsu Institute of Poultry Science, Yangzhou 225125, China
| | - Yifan Liu
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Jiangsu Institute of Poultry Science, Yangzhou 225125, China
| | - Yanju Shan
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Jiangsu Institute of Poultry Science, Yangzhou 225125, China
| | - Yunjie Tu
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Jiangsu Institute of Poultry Science, Yangzhou 225125, China
| | - Jianmin Zou
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Jiangsu Institute of Poultry Science, Yangzhou 225125, China
| | - Jingting Shu
- Key Laboratory for Poultry Genetics and Breeding of Jiangsu Province, Jiangsu Institute of Poultry Science, Yangzhou 225125, China
| | - Hua Li
- School of Life Science and Engineering, Foshan University, Foshan 528231, China
| | - Weidong Zhao
- Taihe Fengsheng Agricultural and Livestock Co., Ltd., Ji’an 343732, China
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Li R, Li D, Xu S, Zhang P, Zhang Z, He F, Li W, Sun G, Jiang R, Li Z, Tian Y, Liu X, Kang X. Whole-transcriptome sequencing reveals a melanin-related ceRNA regulatory network in the breast muscle of Xichuan black-bone chicken. Poult Sci 2024; 103:103539. [PMID: 38382189 PMCID: PMC10900940 DOI: 10.1016/j.psj.2024.103539] [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: 11/28/2023] [Revised: 01/31/2024] [Accepted: 02/05/2024] [Indexed: 02/23/2024] Open
Abstract
The economic losses incurred due to reduced muscle pigmentation highlight the crucial role of melanin-based coloration in the meat of black-bone chickens. Melanogenesis in the breast muscle of black-bone chickens is currently poorly understood in terms of molecular mechanisms. This study employed whole-transcriptome sequencing to analyze black and white breast muscle samples from black-bone chickens, leading to the identification of 367 differentially expressed (DE) mRNAs, 48 DElncRNAs, 104 DEcircRNAs, and 112 DEmiRNAs involved in melanin deposition. Based on these findings, a competitive endogenous RNA (ceRNA) network was developed to better understand the complex mechanisms of melanin deposition. Furthermore, our analysis revealed key DEmRNAs (TYR, DCT, EDNRB, MLPH and OCA2) regulated by DEmiRNAs (gga-miR-140-5p, gga-miR-1682, gga-miR-3529, gga-miR-499-3p, novel-m0012-3p, gga-miR-200b-5p, gga-miR-203a, gga-miR-6651-5p, gga-miR-7455-3p, gga-miR-31-5p, miR-140-x, miR-455-x, novel-m0065-3p, gga-miR-29b-1-5p, miR-455-y, novel-m0085-3p, and gga-miR-196-1-3p). These DEmiRNAs competitively interacted with DElncRNAs including MSTRG.2609.2, MSTRG.4185.1, LOC112530666, LOC112533366, LOC771030, LOC107054724, LOC121107411, LOC100859072, LOC101750037, LOC121108550, LOC121109224, LOC121110876, and LOC101749016, as well as DEcircRNAs, such as novel_circ_000158, novel_circ_000623, novel_001518, and novel_circ_003596. The findings from this study provide insight into the mechanisms that regulate lncRNA, circRNA, miRNA, and mRNA expression in chicken melanin deposition.
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Affiliation(s)
- Ruiting Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, 450046, China
| | - DongHua Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, 450046, China.
| | - Shuohui Xu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, 450046, China
| | - Pengwei Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, 450046, China
| | - Zhiyuan Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, 450046, China
| | - Fumin He
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, 450046, China
| | - Wenting Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, 450046, China; The Shennong Laboratory, Zhengzhou, 450046, China
| | - Guirong Sun
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, 450046, China; The Shennong Laboratory, Zhengzhou, 450046, China
| | - Ruirui Jiang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, 450046, China
| | - Zhuanjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, 450046, China
| | - Yadong Tian
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, 450046, China
| | - Xiaojun Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, 450046, China
| | - Xiangtao Kang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, 450046, China; Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou, 450046, China; The Shennong Laboratory, Zhengzhou, 450046, China
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Pan R, Hua T, Ding Y, Bai H, Jiang Y, Wang Z, Hu M, Chen G, Wu X, Chang G. Study on changing disciplinarian of beak colors in ducks and the regulation network based on transcriptome sequencing. Poult Sci 2024; 103:103266. [PMID: 38039827 PMCID: PMC10698678 DOI: 10.1016/j.psj.2023.103266] [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: 09/26/2023] [Accepted: 11/03/2023] [Indexed: 12/03/2023] Open
Abstract
Beak color in ducks is a primary characteristic of local breeds and genetic resources. Among them, black beaks, a rare packaging trait of high-quality duck products, have attracted much attention. In this study, Runzhou White Created ducks (black beak) and white-feathered Putian black ducks (yellow beak) were used to construct the F2 generation resource population to study the changing discipline of beak color combined with the beak color statistics of gray-beaked ducklings of Runzhou White Created ducks. Subsequently, transcriptome sequencing was performed to identify genetic markers related to beak color. To explore the rules of beak color change and its regulatory network, trends, and trend analysis and weighted gene co-expression network analysis(WGCNA)were performed. The screening results were verified by real-time quantitative polymerase chain reaction. A large difference was observed between the beak colors of birds from the F1 generation at 0 and 42 d of age. The F2 generation results show that nearly half of the black-beaked ducklings become green-beaked; the proportion of black spots for gray- and patterned-beaked ducklings increases with age, with most becoming green-beaked. Moreover, the beak color darkened from the first day, and the gray color value decreased significantly from the second day. Transcriptome sequencing indicated that TYR was differentially expressed between black and yellow beaks at 4 to 6 wk of age, and trend and WGCNA analyses showed that EDNRB signaling pathway genes and MITF were highly expressed in the first week, and TYR, TYRP1, and DCT were highly expressed at 4 to 6 wk of age. Therefore, there is melanin synthesis and deposition after hatching for gray- and patterned-beaked ducklings, while the yellow pigment might be deposited in the epidermis of beaks for black-beaked ducklings. The EDNRB signaling pathway is probably involved in early melanosome maturation and melanin formation in duck beaks, and genes such as TYR can maintain the black-beak phenotype.
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Affiliation(s)
- Rui Pan
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Tian Hua
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Yifan Ding
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Hao Bai
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Yong Jiang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Zhixiu Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Min Hu
- Zhenjiang Tiancheng Agricultural Science and Technology Co., Ltd., Zhenjiang 212000, China
| | - Guohong Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Xinsheng Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
| | - Guobin Chang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China.
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Zhang W, Jin M, Lu Z, Li T, Wang H, Yuan Z, Wei C. Whole Genome Resequencing Reveals Selection Signals Related to Wool Color in Sheep. Animals (Basel) 2023; 13:3265. [PMID: 37893989 PMCID: PMC10603731 DOI: 10.3390/ani13203265] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/22/2023] [Revised: 10/10/2023] [Accepted: 10/17/2023] [Indexed: 10/29/2023] Open
Abstract
Wool color is controlled by a variety of genes. Although the gene regulation of some wool colors has been studied in relative depth, there may still be unknown genetic variants and control genes for some colors or different breeds of wool that need to be identified and recognized by whole genome resequencing. Therefore, we used whole genome resequencing data to compare and analyze sheep populations of different breeds by population differentiation index and nucleotide diversity ratios (Fst and θπ ratio) as well as extended haplotype purity between populations (XP-EHH) to reveal selection signals related to wool coloration in sheep. Screening in the non-white wool color group (G1 vs. G2) yielded 365 candidate genes, among which PDE4B, GMDS, GATA1, RCOR1, MAPK4, SLC36A1, and PPP3CA were associated with the formation of non-white wool; an enrichment analysis of the candidate genes yielded 21 significant GO terms and 49 significant KEGG pathways (p < 0.05), among which 17 GO terms and 21 KEGG pathways were associated with the formation of non-white wool. Screening in the white wool color group (G2 vs. G1) yielded 214 candidate genes, including ABCD4, VSX2, ITCH, NNT, POLA1, IGF1R, HOXA10, and DAO, which were associated with the formation of white wool; an enrichment analysis of the candidate genes revealed 9 significant GO-enriched pathways and 19 significant KEGG pathways (p < 0.05), including 5 GO terms and 12 KEGG pathways associated with the formation of white wool. In addition to furthering our understanding of wool color genetics, this research is important for breeding purposes.
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Affiliation(s)
- Wentao Zhang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (W.Z.); (M.J.); (T.L.); (H.W.)
| | - Meilin Jin
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (W.Z.); (M.J.); (T.L.); (H.W.)
| | - Zengkui Lu
- Key Laboratory of Animal Genetics and Breeding on Tibetan Plateau, Ministry of Agriculture and Rural Affairs, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China;
| | - Taotao Li
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (W.Z.); (M.J.); (T.L.); (H.W.)
| | - Huihua Wang
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (W.Z.); (M.J.); (T.L.); (H.W.)
| | - Zehu Yuan
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education of China, Yangzhou University, Yangzhou 225009, China;
| | - Caihong Wei
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (W.Z.); (M.J.); (T.L.); (H.W.)
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Pan R, Hua T, Guo Q, Bai H, Jiang Y, Wang Z, Bi Y, Chen G, Wu X, Chang G. Identification of SNPs in MITF associated with beak color of duck. Front Genet 2023; 14:1161396. [PMID: 37671042 PMCID: PMC10475569 DOI: 10.3389/fgene.2023.1161396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Accepted: 07/27/2023] [Indexed: 09/07/2023] Open
Abstract
Introduction: Beak color-a pigment-related trait-is an important feature of duck breeds. Recently, little research has addressed genetic mechanism of the beak colors in poultry, whereas the process and the regulation factors of melanin deposition have been well described. Methods: To investigate the genetic mechanism of beak colors, we conducted an integrated analysis of genomic selection signatures to identify a candidate site associated with beak color. For this, we used black-billed (Yiyang I meat duck synthetic line H1, H2, H3&HF) and yellow-billed ducks (Cherry Valley ducks and white feather Putian black duck). Quantitative real-time PCR and genotyping approaches were used to verify the function of the candidate site. Results: We identified 3,895 windows containing 509 genes. After GO and KEGG enrichment analysis, nine genes were selected. Ultimately, MITF was selected by comparing the genomic differentiation (FST). After loci information selection, 41 extreme significantly different loci were selected, which are all located in intron regions of MITF and are in almost complete linkage disequilibrium. Subsequently, the site ASM874695v1:10:g.17814522T > A in MITF was selected as the marker site. Furthermore, we found that MITF expression is significantly higher in black-beaked ducks than in yellow-beaked ducks of the F2 generation (p < 0.01). After genotyping, most yellow-billed individuals are found with homozygous variant; at the same time, there are no birds with homozygous variant in black-billed populations, while the birds with homozygous and heterozygous variant share the same proportion. Conclusion: MITF plays a very critical role in the melanogenesis and melanin deposition of duck beaks, which can effectively affect the beak color. The MITF site, ASM874695v1:10:g.17814522T > A could be selected as a marker site for the duck beak color phenotype.
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Affiliation(s)
- Rui Pan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Tian Hua
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Qixin Guo
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Hao Bai
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yong Jiang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Zhixiu Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Yulin Bi
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Guohong Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Xinsheng Wu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
| | - Guobin Chang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou, China
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Li R, Wang Y, Liu Y, Li D, Tian Y, Liu X, Kang X, Li Z. Effects of SLC45A2 and GPNMB on Melanin Deposition Based on Transcriptome Sequencing in Chicken Feather Follicles. Animals (Basel) 2023; 13:2608. [PMID: 37627399 PMCID: PMC10451703 DOI: 10.3390/ani13162608] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2023] [Revised: 08/04/2023] [Accepted: 08/10/2023] [Indexed: 08/27/2023] Open
Abstract
As an essential genetic and economic trait, chicken feather color has long been an important research topic. To further understand the mechanism of melanin deposition associated with coloration in chicken feathers, we selected feather follicle tissues from the neck and wings of chickens with differently colored feathers (yellow, sub-Columbian, and silver) for transcriptome analysis. We focused on genes that were expressed in both the wings and neck and were expressed with the same trends in breeds with two different plumage colors, specifically, SLC45A2, GPNMB, MLPH, TYR, KIT, WNT11, and FZD1. GO and KEGG enrichment analyses showed the DEGs were enriched in melanin-related pathways, such as tyrosine metabolic pathway and melanogenesis, and PPI analysis highlighted the genes SLC45A2 and GPNMB as associated with melanin deposition. Verification experiments in chicken melanocytes demonstrated that these two genes promote melanocyte melanin deposition. These data enrich our knowledge of the mechanisms that regulate chicken feather color.
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Affiliation(s)
- Ruiting Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (R.L.); (Y.W.); (Y.L.); (D.L.)
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
| | - Yanxing Wang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (R.L.); (Y.W.); (Y.L.); (D.L.)
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
| | - Yihan Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (R.L.); (Y.W.); (Y.L.); (D.L.)
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
| | - Donghua Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (R.L.); (Y.W.); (Y.L.); (D.L.)
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
| | - Yadong Tian
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (R.L.); (Y.W.); (Y.L.); (D.L.)
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
| | - Xiaojun Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (R.L.); (Y.W.); (Y.L.); (D.L.)
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
| | - Xiangtao Kang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (R.L.); (Y.W.); (Y.L.); (D.L.)
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
- The Shennong Laboratory, Zhengzhou 450000, China
| | - Zhuanjian Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China; (R.L.); (Y.W.); (Y.L.); (D.L.)
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Zhengzhou 450046, China
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Arora R, Sharma R, Ahlawat S, Chhabra P, Kumar A, Kaur M, Vijh RK, Lal SB, Mishra DC, Farooqi MS, Srivastava S. Transcriptomics reveals key genes responsible for functional diversity in pectoralis major muscles of native black Kadaknath and broiler chicken. 3 Biotech 2023; 13:253. [PMID: 37396468 PMCID: PMC10310660 DOI: 10.1007/s13205-023-03682-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 06/21/2023] [Indexed: 07/04/2023] Open
Abstract
RNA sequencing-based expression profiles from pectoralis major muscles of black meat (Kadaknath) and white meat (broiler) chicken were compared to identify differentially expressed genes. A total of 156 genes with log2 fold change ≥ ± 2.0 showed higher expression in Kadaknath and 68 genes were expressed at a lower level in comparison to broiler. Significantly enriched biological functions of up-regulated genes in Kadaknath were skeletal muscle cell differentiation, regulation of response to reactive oxygen, positive regulation of fat cell differentiation and melanosome. Significant ontology terms up-regulated in broiler included DNA replication origin binding, G-protein coupled receptor signaling pathway and chemokine activity. Highly inter-connected differentially expressed genes in Kadaknath (ATFs, C/EPDs) were observed to be important regulators of cellular adaptive functions, while in broiler, the hub genes were involved in cell cycle progression and DNA replication. The study is an attempt to get an insight into the transcript diversity of pectoralis major muscles of Kadaknath and broiler chicken. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-023-03682-0.
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Affiliation(s)
- Reena Arora
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
- Animal Biotechnology Division, G T Road By-Pass, P O Box 129, Karnal, Haryana 132001 India
| | - Rekha Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Sonika Ahlawat
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Pooja Chhabra
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Ashish Kumar
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | - Mandeep Kaur
- ICAR-National Bureau of Animal Genetic Resources, Karnal, India
| | | | - Shashi Bhushan Lal
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | | | - Md. Samir Farooqi
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Sudhir Srivastava
- ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
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Zi X, Ge X, Zhu Y, Liu Y, Sun D, Li Z, Liu M, You Z, Wang B, Kang J, Dou T, Ge C, Wang K. Transcriptome Profile Analysis Identifies Candidate Genes for the Melanin Pigmentation of Skin in Tengchong Snow Chickens. Vet Sci 2023; 10:vetsci10050341. [PMID: 37235424 DOI: 10.3390/vetsci10050341] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2023] [Revised: 05/05/2023] [Accepted: 05/08/2023] [Indexed: 05/28/2023] Open
Abstract
Tengchong Snow chickens are one of the most precious, black-boned chickens in Yunnan province and usually produce black meat. However, we found a small number of white meat traits in the chicken population during feeding. In order to determine the pattern of melanin deposition and the molecular mechanism of formation in the Tengchong Snow chicken, we measured the luminance value (L value) and melanin content in the skin of black meat chickens (Bc) and white meat chickens (Wc) using a color colorimeter, ELISA kit, and enzyme marker. The results showed that the L value of skin tissues in black meat chickens was significantly lower than that of white meat chickens, and the L value of skin tissues gradually increased with an increase in age. The melanin content of skin tissues in black meat chickens was higher than that of white meat chickens, and melanin content in the skin tissues gradually decreased with an increase in age, but this difference was not significant (p > 0.05); the L value of skin tissues in black meat chickens was negatively correlated with melanin content, and the correlation coefficient was mostly above -0.6. In addition, based on the phenotypic results, we chose to perform the comparative transcriptome profiling of skin tissues at 90 days of age. We screened a total of 44 differential genes, of which 32 were upregulated and 12 were downregulated. These DEGs were mainly involved in melanogenesis, tyrosine metabolism and RNA transport. We identified TYR, DCT, and EDNRB2 as possible master effector genes for skin pigmentation in Tengchong Snow black meat chickens through DEGs analysis. Finally, we measured the mRNA of TYR, DCT, MC1R, EDNRB2, GPR143, MITF, and TYRP1 genes through a quantitative real-time polymerase chain reaction (qPCR) and found that the mRNA of all the above seven genes decreased with increasing age. In conclusion, our study initially constructed an evaluation system for the black-boned traits of Tengchong Snow chickens and found key candidate genes regulating melanin deposition, which could provide an important theoretical basis for the selection and breeding of black-boned chickens.
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Affiliation(s)
- Xiannian Zi
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Xuehai Ge
- Shenzhen Hualong Sunda Information Technology Co., Ltd., Shenzhen 518000, China
| | - Yixuan Zhu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Yong Liu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Dawei Sun
- Yunnan Animal Science and Veterinary Institute, Kunming 650224, China
| | - Zijian Li
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Mengqian Liu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Zhengrong You
- Zhaotong Animal Husbandry and Veterinary Technology Extension Station, Zhaotong 657000, China
| | - Bo Wang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Jiajia Kang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Tengfei Dou
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Changrong Ge
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Kun Wang
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
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9
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Yu S, Wang G, Liao J, Shen X, Chen J. Integrated analysis of long non-coding RNAs and mRNA expression profiles identified potential interactions regulating melanogenesis in chicken skin. Br Poult Sci 2023; 64:19-25. [PMID: 35979716 DOI: 10.1080/00071668.2022.2113506] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
Abstract
1. Long non-coding RNAs (lncRNAs) play important roles in various physiological functions. However, the mechanisms underlying the regulation of lncRNAs in melanogenesis remain unclear. To determine the molecular mechanisms involved in skin melanogenesis, the present study depicted the expression profiles of lncRNAs and messenger RNAs (mRNAs) in black- (B group) and white- (W group) skinned chickens using RNA sequencing.2. In total, 373 differentially expressed lncRNAs (DELs; 203 up-regulated and 170 down-regulated) and 253 differentially expressed genes (DEGs; 152 up-regulated and 101 down-regulated) were identified between the B and W groups. A total of eight known melanogenesis-related genes were identified (KIT, TYRP1, DCT (TYRP2), SLC45A2, OCA2, EDNRB2, TRPM1 and RAB38).3. Functional annotation of the co-expressed DEGs and DELs was performed using Gene Ontology (GO) and Kyoto Encyclopaedia of Genes and Genomes (KEGG) pathway analyses. The co-expressed DEGs were mainly involved in melanogenesis and the co-expressed genes of 117 and 108 DELs were significantly enriched in the melanogenesis and tyrosine metabolism pathways, respectively.4. The DEL-DEG interaction network revealed that three lncRNAs (XR_003072387.1, XR_003075112.1, and XR_003077033.1) and DCT genes may have key roles in regulating melanogenesis in chicken skin. This data provides the groundwork for studying the lncRNA regulatory mechanisms of skin melanogenesis and suggested a new perspective on the modulation of melanogenesis in chicken skin based on a lncRNA-mRNA causal regulatory network.
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Affiliation(s)
- S Yu
- Engineering Research Center of Sichuan Province Higher School of Local Chicken Breeds Industrialization in Southern Sichuan, College of Life Science, Leshan Normal University, Leshan, Shizhong, China
| | - G Wang
- Engineering Research Center of Sichuan Province Higher School of Local Chicken Breeds Industrialization in Southern Sichuan, College of Life Science, Leshan Normal University, Leshan, Shizhong, China
| | - J Liao
- Engineering Research Center of Sichuan Province Higher School of Local Chicken Breeds Industrialization in Southern Sichuan, College of Life Science, Leshan Normal University, Leshan, Shizhong, China
| | - X Shen
- Engineering Research Center of Sichuan Province Higher School of Local Chicken Breeds Industrialization in Southern Sichuan, College of Life Science, Leshan Normal University, Leshan, Shizhong, China
| | - J Chen
- Engineering Research Center of Sichuan Province Higher School of Local Chicken Breeds Industrialization in Southern Sichuan, College of Life Science, Leshan Normal University, Leshan, Shizhong, China
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10
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Zhang P, Cao Y, Fu Y, Zhu H, Xu S, Zhang Y, Li W, Sun G, Jiang R, Han R, Li H, Li G, Tian Y, Liu X, Kang X, Li D. Revealing the Regulatory Mechanism of lncRNA-LMEP on Melanin Deposition Based on High-Throughput Sequencing in Xichuan Chicken Skin. Genes (Basel) 2022; 13:2143. [PMID: 36421818 PMCID: PMC9690664 DOI: 10.3390/genes13112143] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2022] [Revised: 11/09/2022] [Accepted: 11/12/2022] [Indexed: 08/27/2023] Open
Abstract
The therapeutic, medicinal, and nourishing properties of black-bone chickens are highly regarded by consumers in China. However, some birds may have yellow skin (YS) or light skin rather than black skin (BS), which causes economic losses every year. Long noncoding RNAs (lncRNAs) are widely present in living organisms, and they perform various biological functions. Many genes associated with BS pigmentation have been discovered, but the lncRNAs involved and their detailed mechanisms have remained untested. We detected 56 differentially expressed lncRNAs from the RNA-seq of dorsal skin (BS versus YS) and found that TCONS_00054154 plays a vital role in melanogenesis by the combined analysis of lncRNAs and mRNAs. We found that the full length of the TCONS_00054154 sequence was 3093 bp by RACE PCR, and we named it LMEP. Moreover, a subcellular localization analysis identified that LMEP is mainly present in the cytoplasm. After the overexpression and the interference with LMEP, the tyrosinase content significantly increased and decreased, respectively (p < 0.05). In summary, we identified the important lncRNAs of chicken skin pigmentation and initially determined the effect of LMEP on melanin deposition.
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Affiliation(s)
- Pengwei Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Yanfang Cao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Yawei Fu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Huiyuan Zhu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Shuohui Xu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
| | - Yanhua Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou 450046, China
| | - Wenting Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou 450046, China
| | - Guirong Sun
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou 450046, China
| | - Ruirui Jiang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou 450046, China
| | - Ruili Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou 450046, China
| | - Hong Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou 450046, China
| | - Guoxi Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou 450046, China
| | - Yadong Tian
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou 450046, China
| | - Xiaojun Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou 450046, China
| | - Xiangtao Kang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou 450046, China
| | - Donghua Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou 450046, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Zhengzhou 450046, China
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11
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Zhang J, Geng X, Zhang Y, Zhao X, Zhang P, Sun G, Li W, Li D, Han R, Li G, Tian Y, Liu X, Kang X, Jiang R. Interaction Between Cecal Metabolites and Liver Lipid Metabolism Pathways During Induced Molting in Laying Hens. Front Physiol 2022; 13:862721. [PMID: 35677092 PMCID: PMC9169092 DOI: 10.3389/fphys.2022.862721] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2022] [Accepted: 03/23/2022] [Indexed: 11/23/2022] Open
Abstract
Moult is a normal physiological phenomenon in poultry. Induced molting (IM) is the most widely used and economical molting technique. By inducing moult, the laying hens can grow new feathers during the next laying cycle and improve laying performance. However, the lack of energy supply has a huge impact on both the liver and intestines and acts on the intestines and liver through the “gut-liver axis”. More importantly, lipid metabolism in the liver is closely related to the laying performance of laying hens. Therefore, in this study, cecal metabolites and liver transcriptome data during IM of laying hens at the late stage of laying (stop feeding method) were analyzed together to reveal the regulatory mechanism of “gut-liver axis” affecting the laying performance of laying hens from the perspective of lipid metabolism. Transcriptome analysis revealed that 4,796 genes were obtained, among which 2,784 genes had significant differences (p < 0.05). Forty-nine genes were associated with lipid metabolism, and five core genes (AGPAT2, SGPL1, SPTLC1, PISD, and CYP51A1) were identified by WGCNA. Most of these differential genes are enriched in steroid biosynthesis, cholesterol metabolism, drug metabolism—cytochrome P450, synthesis and degradation of ketone bodies, PPAR signaling pathway, and bile secretion. A total of 96 differential metabolites were obtained by correlating them with metabolome data. Induced moult affects laying performance by regulating genes related to lipid metabolism, and the cecal metabolites associated with these genes are likely to regulate the expression of these genes through the “enterohepatic circulation”. This experiment enriched the theoretical basis of induced moult and provided the basis for prolonging the feeding cycle of laying hens.
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Affiliation(s)
- Jun Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China
| | - Xiaoqing Geng
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China
| | - Yihui Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China
| | - Xinlong Zhao
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China
| | - Pengwei Zhang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China
| | - Guirong Sun
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China
| | - Wenting Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China
| | - Donghua Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China
| | - Ruili Han
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China
| | - Guoxi Li
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China
| | - Yadong Tian
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China
| | - Xiaojun Liu
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China
| | - Xiangtao Kang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China
| | - Ruirui Jiang
- College of Animal Science and Technology, Henan Agricultural University, Zhengzhou, China
- Henan Innovative Engineering Research Center of Poultry Germplasm Resource, Henan Agricultural University, Zhengzhou, China
- *Correspondence: Ruirui Jiang,
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12
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Dou T, Yan S, Liu L, Wang K, Jian Z, Xu Z, Zhao J, Wang Q, Sun S, Talpur MZ, Duan X, Gu D, He Y, Du Y, Abdulwahid AM, Li Q, Rong H, Cao W, Su Z, Zhao G, Liu R, Zhao S, Huang Y, Te Pas MFW, Ge C, Jia J. Integrative analysis of transcriptomics and metabolomics to reveal the melanogenesis pathway of muscle and related meat characters in Wuliangshan black-boned chickens. BMC Genomics 2022; 23:173. [PMID: 35236293 PMCID: PMC8892760 DOI: 10.1186/s12864-022-08388-w] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/14/2021] [Accepted: 02/03/2022] [Indexed: 12/02/2022] Open
Abstract
Background Melanin is an important antioxidant in food and has been used in medicine and cosmetology. Chicken meat with high melanin content from black-boned chickens have been considered a high nutritious food with potential medicinal properties. The molecular mechanism of melanogenesis of skeletal muscle in black-boned chickens remain poorly understood. This study investigated the biological gene-metabolite associations regulating the muscle melanogenesis pathways in Wuliangshan black-boned chickens with two normal boned chicken breeds as control. Results We identified 25 differentially expressed genes and 11 transcription factors in the melanogenesis pathways. High levels of the meat flavor compounds inosine monophosphate, hypoxanthine, lysophospholipid, hydroxyoctadecadienoic acid, and nicotinamide mononucleotide were found in Wuliangshan black-boned chickens. Conclusion Integrative analysis of transcriptomics and metabolomics revealed the dual physiological functions of the PDZK1 gene, involved in pigmentation and/or melanogenesis and regulating the phospholipid signaling processes in muscle of black boned chickens. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08388-w.
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Affiliation(s)
- Tengfei Dou
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Shixiong Yan
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Lixian Liu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China.,Yunnan Vocational and Technical College of Agriculture, Kunming, 650031, Yunnan Province, People's Republic of China
| | - Kun Wang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Zonghui Jian
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Zhiqiang Xu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China.,College of Food Science, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Jingying Zhao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Qiuting Wang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Shuai Sun
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Mir Zulqarnain Talpur
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Xiaohua Duan
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China.,Yunnan University of Traditional Chinese Medical, Kunming, 650500, Yunnan Province, People's Republic of China
| | - Dahai Gu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China.,College of Food Science, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Yang He
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Yanli Du
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Alsoufi Mohammed Abdulwahid
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Qihua Li
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Hua Rong
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Weina Cao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Zhengchang Su
- Department of Bioinformatics and Genomics, College of Computing and Informatics, the University of North Carolina at Charlotte, Charlotte, NC, 28223, USA
| | - Guiping Zhao
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Ranran Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, People's Republic of China
| | - Sumei Zhao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Ying Huang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China
| | - Marinus F W Te Pas
- Wageningen Livestock Research, Wageningen UR, Wageningen, 238050, The Netherlands. .,Visiting Professor Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China.
| | - Changrong Ge
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China.
| | - Junjing Jia
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan Province, People's Republic of China.
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13
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Jian H, Zu P, Rao Y, Li W, Mou T, Lin J, Zhang F. Comparative analysis of melanin deposition between Chishui silky fowl and Taihe silky fowl. JOURNAL OF APPLIED ANIMAL RESEARCH 2021. [DOI: 10.1080/09712119.2021.1981911] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- Huafeng Jian
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, The Ministry of Education, Guizhou University, Guiyang, People’s Republic of China
- Guizhou Province Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science, Guizhou University, Guiyang, People’s Republic of China
- Research Institute of Poultry, Guizhou University, Guiyang, People’s Republic of China
- Guizhou University Science and Research Poultry Farm, Guiyang, People’s Republic of China
| | - Panyu Zu
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, The Ministry of Education, Guizhou University, Guiyang, People’s Republic of China
- Guizhou Province Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science, Guizhou University, Guiyang, People’s Republic of China
- Research Institute of Poultry, Guizhou University, Guiyang, People’s Republic of China
- Guizhou University Science and Research Poultry Farm, Guiyang, People’s Republic of China
| | - Yongchao Rao
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, The Ministry of Education, Guizhou University, Guiyang, People’s Republic of China
- Guizhou Province Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science, Guizhou University, Guiyang, People’s Republic of China
- Research Institute of Poultry, Guizhou University, Guiyang, People’s Republic of China
- Guizhou University Science and Research Poultry Farm, Guiyang, People’s Republic of China
| | - Wei Li
- Guizhou Province Management Station of Livestock Genetic Resources, Guiyang, People’s Republic of China
| | - Tenghui Mou
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, The Ministry of Education, Guizhou University, Guiyang, People’s Republic of China
- Guizhou Province Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science, Guizhou University, Guiyang, People’s Republic of China
- Research Institute of Poultry, Guizhou University, Guiyang, People’s Republic of China
- Guizhou University Science and Research Poultry Farm, Guiyang, People’s Republic of China
| | - Jiadong Lin
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, The Ministry of Education, Guizhou University, Guiyang, People’s Republic of China
- Guizhou Province Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science, Guizhou University, Guiyang, People’s Republic of China
- Research Institute of Poultry, Guizhou University, Guiyang, People’s Republic of China
- Guizhou University Science and Research Poultry Farm, Guiyang, People’s Republic of China
| | - Fuping Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction in the Plateau Mountainous Region, The Ministry of Education, Guizhou University, Guiyang, People’s Republic of China
- Guizhou Province Key Laboratory of Animal Genetics, Breeding and Reproduction, College of Animal Science, Guizhou University, Guiyang, People’s Republic of China
- Research Institute of Poultry, Guizhou University, Guiyang, People’s Republic of China
- Guizhou University Science and Research Poultry Farm, Guiyang, People’s Republic of China
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14
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Kubota S, Promkhun K, Sinpru P, Suwanvichanee C, Molee W, Molee A. RNA Profiles of the Korat Chicken Breast Muscle with Increased Carnosine Content Produced through Dietary Supplementation with β-Alanine or L-Histidine. Animals (Basel) 2021; 11:ani11092596. [PMID: 34573562 PMCID: PMC8464878 DOI: 10.3390/ani11092596] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Revised: 08/28/2021] [Accepted: 08/31/2021] [Indexed: 12/24/2022] Open
Abstract
Simple Summary Carnosine is a bioactive food component with several potential health benefits for humans due to its physiological functions. Dietary supplementation with β-alanine or L-histidine can increase the carnosine content of skeletal muscles in chickens. Dietary supplementation with β-alanine or L-histidine has produced a slow-growing chicken variety with high carnosine content in the breast meat; however, the supplementation with L-histidine alone softens the meat toughness, which may affect consumers’ willingness to buy the meat. Gene expression is a key factor that influences meat quality. Understanding the molecular mechanisms that affect carnosine content and meat toughness would allow the production of more value-added slow-growing chickens. We compared global gene expression in chicken breast muscles with differing carnosine contents and meat toughness produced through dietary supplementation with β-alanine or L-histidine. We identified differentially expressed genes involved in regulating myosin, collagen, intramuscular fat, and calpain—factors that may affect meat tenderness. Pathway enrichment analysis indicated that the insulin-related and adipocytokine signaling pathways were altered by dietary supplementation with β-alanine or L-histidine. These data will be useful for future studies on carnosine content and meat toughness in slow-growing chickens. Abstract Korat chicken (KRC) is a slow-growing chicken bred in Thailand, whose meat exhibits a unique toughness. A previous study produced KRC breast meat containing high carnosine content through dietary supplementation with β-alanine or L-histidine; however, the KRC that were fed an L-histidine-supplemented diet produced meat that was significantly more tender. Herein, we performed RNA-Seq to identify candidate genes involved in the regulation of carnosine content and meat toughness. Total RNA was isolated from five female KRC breast muscles in each treatment group that KRC fed diets without supplementation, supplemented with β-alanine or L-histidine. Compared to the non-supplemented group, we identified 118 and 198 differentially expressed genes (DEGs) in the β-alanine or L-histidine supplementation groups, respectively. Genes potentially related to meat tenderness—i.e., those regulating myosin, collagen, intramuscular fat, and calpain—were upregulated (LOC107051274, ACSBG1, and CAPNS2) and downregulated (MYO7B, MYBPH, SERPINH1, and PGAM1). However, carnosine synthase gene was not identified. Functional enrichment analysis identified pathways affected by dietary supplementation, including the insulin signaling pathway (β-alanine supplementation) and the insulin resistance and adipocytokine signaling pathways (L-histidine supplementation). The FoxO signaling pathway was identified as a regulatory network for both supplementation groups. The identified genes can be used as molecular markers of meat tenderness in slow-growing chickens.
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15
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Huang X, Weng Z, He Y, Miao Y, Luo W, Zhang X, Zhong F, Du B. Mitochondrial DNA diversity and demographic history of Black-boned chickens in China. Mitochondrial DNA B Resour 2021; 6:1462-1467. [PMID: 33969196 PMCID: PMC8079009 DOI: 10.1080/23802359.2021.1912668] [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: 02/21/2020] [Accepted: 03/29/2021] [Indexed: 11/30/2022] Open
Abstract
Black-boned chickens (Gallus domesticus, herein abbreviated BBCs) are well known for their unique appearance and medicinal properties and have a long breeding history in China. However, the genetic diversity and demographic history of BBCs remain unclear. In this study, we analyzed 844 mitochondrial DNA D-loop sequences, including 346 de novo sequences and 498 previously published sequences from 20 BBC breeds. We detected a generally high level of genetic diversity among the BBCs, with average haplotype and nucleotide diversities of 0.917 ± 0.0049 and 0.01422, respectively. Nucleotide diversity was highest in populations from Southwest China (0.01549 ± 0.00026), particularly in Yunnan Province (0.01624 ± 0.00025). Significant genetic divergence was detected between most breeds, particularly between Yunnan chickens and those from all other provinces. Haplogroups F and G had the highest levels of genetic diversity and were restricted to Southwest China, particularly Yunnan Province. Based on neutrality tests and mismatch distribution analyses, we did not obtain evidence for rapid population expansions and observed similar demographic histories in BBCs and local non-BBCs. Our results suggest that Chinese BBCs have complex breeding histories and may be selected in situ from local domestic chickens. These results improve our understanding of the genetic heritage and breeding histories of these desirable chickens.
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Affiliation(s)
- Xunhe Huang
- Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas, Guangdong Innovation Centre for Science and Technology of Wuhua Yellow Chicken, School of Life Science, JiaYing University, Meizhou, China
| | - Zhuoxian Weng
- Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas, Guangdong Innovation Centre for Science and Technology of Wuhua Yellow Chicken, School of Life Science, JiaYing University, Meizhou, China
- College of Animal Science and Technology, Hunan Agricultural University,Changsha, China
| | - Yujing He
- Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas, Guangdong Innovation Centre for Science and Technology of Wuhua Yellow Chicken, School of Life Science, JiaYing University, Meizhou, China
| | - Yongwang Miao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, China
| | - Wei Luo
- College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Xiquan Zhang
- College of Animal Science, South China Agricultural University, Guangzhou, China
| | - Fusheng Zhong
- Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas, Guangdong Innovation Centre for Science and Technology of Wuhua Yellow Chicken, School of Life Science, JiaYing University, Meizhou, China
- College of Animal Science and Technology, Hunan Agricultural University,Changsha, China
| | - Bingwang Du
- Guangdong Provincial Key Laboratory of Conservation and Precision Utilization of Characteristic Agricultural Resources in Mountainous Areas, Guangdong Innovation Centre for Science and Technology of Wuhua Yellow Chicken, School of Life Science, JiaYing University, Meizhou, China
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Analysis of MC1R, MITF, TYR, TYRP1, and MLPH Genes Polymorphism in Four Rabbit Breeds with Different Coat Colors. Animals (Basel) 2021; 11:ani11010081. [PMID: 33466315 PMCID: PMC7824738 DOI: 10.3390/ani11010081] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2020] [Revised: 12/31/2020] [Accepted: 12/31/2020] [Indexed: 12/28/2022] Open
Abstract
Simple Summary Coat color is an important breed characteristic and economic trait for rabbits, and it is regulated by a few genes. In this study, the gene frequencies of some pigmentation genes were investigated in four Chinese native rabbit breeds with different coat colors. A total of 14 genetic variants were detected in the gene fragments of MC1R, MITF, TYR, TYRP1, and MLPH genes, and there was low-to-moderate polymorphism in the populations. The gene frequency showed significant differences among the four rabbit populations. The above results suggest that these genetic variations play an important role in regulating the coat color of rabbits. This study will provide potential molecular markers for the breeding of coat color traits in rabbits. Abstract Pigmentation genes such as MC1R, MITF, TYR, TYRP1, and MLPH play a major role in rabbit coat color. To understand the genotypic profile underlying coat color in indigenous Chinese rabbit breeds, portions of the above-mentioned genes were amplified and variations in them were analyzed by DNA sequencing. Based on the analysis of 24 Tianfu black rabbits, 24 Sichuan white rabbits, 24 Sichuan gray rabbits, and 24 Fujian yellow rabbits, two indels in MC1R, three SNPs in MITF, five SNPs (single nucleotide polymorphisms) in TYR, one SNP in TYRP1, and three SNPs in MLPH were discovered. These variations have low-to-moderate polymorphism, and there are significant differences in their distribution among the different breeds (p < 0.05). These results provide more information regarding the genetic background of these native rabbit breeds and reveal their high-quality genetic resources.
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Khwatenge CN, Kimathi BM, Nahashon SN. Transcriptome Analysis and Expression of Selected Cationic Amino Acid Transporters in the Liver of Broiler Chicken Fed Diets with Varying Concentrations of Lysine. Int J Mol Sci 2020; 21:E5594. [PMID: 32764289 PMCID: PMC7460557 DOI: 10.3390/ijms21165594] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2020] [Revised: 07/24/2020] [Accepted: 08/03/2020] [Indexed: 11/28/2022] Open
Abstract
Amino acids are known to play a key role in gene expression regulation. Amino acid signaling is mediated via two pathways: the mammalian target of rapamycin complex 1 (mTORC1) and the amino acid responsive (AAR) pathways. Cationic amino acid transporters (CATs) are crucial in these pathways due to their sensing, signaling and transport functions. The availability of certain amino acids plays a key role in the intake of other amino acids, hence affecting growth in young birds. However, the specific mechanism for regulating lysine transport for growth is not clear. In this study, we analyze the transcriptome profiles and mRNA expression of selected cationic amino acid transporters in the livers of broilers fed low and high lysine diets. Birds consumed high-lysine (1.42% lysine) or low-lysine (0.85% lysine) diets while the control group consumed 1.14% lysine diet. These concentrations of lysine represent 125% (high lysine), 75% (low lysine) and 100% (control), respectively, of the National Research Council's (NRC) recommendation for broiler chickens. After comparing the two groups, 210 differentially expressed genes (DEGs) were identified (fold change >1 and false discovery rate (FDR) <0.05). When comparing the high lysine and the low lysine treatments, there were 67 upregulated genes and 143 downregulated genes among these DEGs. Analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG) and the Gene Ontology (GO) enrichment analysis show that cellular growth, lipid metabolism and lysine metabolism pathways were among the significantly enriched pathways. This study contributes to a better understanding of the potential molecular mechanisms underlying the correlation between lysine intake, body weight gain (BWG) and feed intake (FI) in broiler chickens. Moreover, the DEGs obtained in this study may be used as potential candidate genes for further investigation of broiler growth customized responses to individualized nutrients such as amino acids.
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Affiliation(s)
- Collins N. Khwatenge
- Department of Biological Sciences, Tennessee State University, Nashville, TN 37209, USA; (C.N.K.); (B.M.K.)
- Department of Agricultural and Environmental Sciences, Tennessee State University, Nashville, TN 37209, USA
| | - Boniface M. Kimathi
- Department of Biological Sciences, Tennessee State University, Nashville, TN 37209, USA; (C.N.K.); (B.M.K.)
- Department of Agricultural and Environmental Sciences, Tennessee State University, Nashville, TN 37209, USA
| | - Samuel N. Nahashon
- Department of Agricultural and Environmental Sciences, Tennessee State University, Nashville, TN 37209, USA
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SFRP5 inhibits melanin synthesis of melanocytes in vitiligo by suppressing the Wnt/β-catenin signaling. Genes Dis 2020; 8:677-688. [PMID: 34291139 PMCID: PMC8278527 DOI: 10.1016/j.gendis.2020.06.003] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2020] [Revised: 05/25/2020] [Accepted: 06/05/2020] [Indexed: 01/16/2023] Open
Abstract
Secreted frizzled-related protein 5 (SFRP5) plays a pivotal role in regulating the development of many tissues and organs, however, as an inhibitor of Wnt signaling, the role of SFRP5 in vitiligo remains unknown. Hence, we speculated that SFRP5 might be associated with melanogenesis in melanocytes by regulating Wnt signaling in vitiligo. In this study, we found that SFRP5 was overexpressed in the skin lesions of patients with vitiligo. Compared with that in normal epidermal melanocytes (PIG1), the expression of SFRP5 was increased in vitiligo melanocytes (PIG3V). To investigate the effect of SFRP5 on melanin synthesis, PIG1 cells were infected with recombinant SFRP5 adenovirus (AdSFRP5), and PIG3V cells were infected with recombinant siSFRP5 adenovirus (AdsiSFRP5). The results showed that SFRP5 overexpression inhibited melanin synthesis in PIG1 cells through downregulation of microphthalmia-associated transcription factor (MITF) and its target proteins via suppression of the Wnt/β-catenin signaling pathway. Accordingly, SFRP5 silencing increased melanin synthesis and activated the Wnt signaling pathway in PIG3V cells. Moreover, SFRP5 overexpression also downregulated the transcriptional activity of T cell factor/lymphoid enhancer factor (TCF/LEF) in PIG1 cells. Furthermore, this inhibitory effect of SFRP5 on melanin synthesis was reversed by treatment with the β-catenin agonist, SKL2001. The inhibitory action of SFRP5 in pigmentation was further confirmed in vivo using a nude mouse model. Hence, our results indicate that SFRP5 can inhibit melanogenesis in melanocytes. Additionally, our findings showed that SFRP5 plays a vital role in the development of vitiligo, and thus may serve as a potential therapeutic target for vitiligo.
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