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Yang X, Ma B, Zhao Q, Jia Y, Meng Q, Qin Y, Tang C, Zhang J. High temporal-resolution transcriptome landscape reveals the biological process and regulatory genes of melanin deposition in breast muscle of Silkie chickens during embryonic development. BMC Genomics 2025; 26:476. [PMID: 40360976 PMCID: PMC12070674 DOI: 10.1186/s12864-025-11654-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 04/29/2025] [Indexed: 05/15/2025] Open
Abstract
BACKGROUND Abnormal deposition of melanin in skeletal muscle is an interesting phenomenon and the Silkie is the most typical example. Melanin deposition involves multiple steps such as neural crest cell migration, melanocyte differentiation, melanosome assembly and melanin biosynthesis, which have already occurred during the embryonic stage of Silkies. However, there is no comprehensive understanding of the dynamic changes in the biological processes and regulatory mechanism underlying melanin deposition in skeletal muscle during chicken embryonic development. RESULTS In this study, high-performance liquid chromatography (HPLC) was used to accurately measure the melanin content in breast muscle across 13 embryonic time points. There was no melanin in breast muscle on embryonic day 8 (E08) to E10, a trace amount of melanin on E11 to E16 and a large amount of melanin on E17 to E21. According to melanin content and deposition pattern, the melanin deposition process in breast muscle was further divided into five stages, including E08 to E10, E11 to E14, E15 to E16, E17 to E18, and E19 to E21. High temporal-resolution transcriptome analysis was performed in the breast muscle of Silkies across 13 embryonic time points. The protein-coding genes (PCGs) and transcriptional factors (TFs) significantly specifically expressed at these five stages were identified. Among these stage-specific genes, stage-specific DEGs between Silkies and Wenchang chickens without melanosis were further screened at each stage. During E08 to E10, three stage-specific DEGs and one stage-specific TF act on neural crest cell migration and melanocyte stem cell differentiation. During E17 to E21, nine stage-specific DEGs and one stage-specific TF act on melanosome assembly and melanin biosynthesis. During E19 to E21, one stage-specific DEG enhances melanin biosynthesis. These stage-specific DEGs and TFs all affect the final melanin content of breast muscle. CONCLUSIONS This study reveals the critical stage of melanin deposition in breast muscle during the embryonic development, and identified the biological processes and functional genes at each stage. This study provides novel insights into the biological process and regulatory mechanism of melanin deposition in skeletal muscle and provides a reference for breeding Silkies with high muscle melanin content.
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Affiliation(s)
- Xinting Yang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Bowen Ma
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Qingyu Zhao
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yaxiong Jia
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Qingshi Meng
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Yuchang Qin
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China
| | - Chaohua Tang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
| | - Junmin Zhang
- State Key Laboratory of Animal Nutrition and Feeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193, China.
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Gao L, Liu C, Wu J, Cui Y, Zhang M, Bi C, Shan A, Dou X. EGCG improve meat quality, restore lipid metabolism disorder and regulate intestinal flora in high-fat fed broilers. Poult Sci 2025; 104:104875. [PMID: 39919564 PMCID: PMC11848460 DOI: 10.1016/j.psj.2025.104875] [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: 11/11/2024] [Revised: 01/22/2025] [Accepted: 02/01/2025] [Indexed: 02/09/2025] Open
Abstract
Excessive oil addition can easily result in decreased disease resistance in broilers, a drop in meat quality, and disorders of glucose and lipid metabolism. Epigallocatechin gallate (EGCG) is an important bioactive component of tea and has been shown to have promising effects on the metabolism of nutrients. This study was aimed at investigating the impact of EGCG supplementation through a high-fat diet (HFD) on production performance, meat quality, lipid metabolism and the influence of intestinal flora in broiler chickens. During the experimental phase, the broilers were segregated into three groups and provided with distinct diets: a basal diet, a high-fat diet, and a high-fat diet supplemented with EGCG, respectively. The results showed that EGCG increased lightness (L*) 24 h (P < 0.05), and decreased drip loss (P < 0.05) of chicken meat; Enhanced the presence of non-essential and flavor amino acids in muscle tissue and greatly enhanced the antioxidant capacity of broilers, leading to a noteworthy upregulation of antioxidant genes at the genetic level (P < 0.05); Reduced in blood lipids, blood glucose, liver and abdominal fat accumulation in high-fat diet-induced obese chickens (P < 0.05), markedly improved serum and liver biochemical parameters, and histological analysis results also demonstrated that EGCG markedly decreased hepatic lipid accumulation caused by HFD feeding. Compared to high-fat diet-induced obese chickens, supplementation of EGCG significantly lowered hepatic fatty acid synthase (FAS) expression and lipid synthesis metabolites, while fatty acid decomposition enzymes showed no significant changes. Furthermore, EGCG significantly decreased inflammation levels and oxidative damage in high-fat diet-induced obese chickens (P < 0.05). 16S rRNA gene sequencing revealed that dietary supplementation of EGCG reduced the abundance of Bacteroidota and Dielma, while increasing the abundance of Firmicutes, Turiciactor, Romboutsia, and Parasutterella, thereby modulating the microbial composition. Dietary EGCG may have induced some of the alterations due to increased activity of the enzymes catalase (CAT) and superoxide dismutase (SOD), as well as decreased oxidation of proteins and lipids. Collectively, EGCG shows potential as an effective dietary additive for improving the high fat feeding of broiler health, feed nutrient utilization, and meat quality and nutritional value. This experiment provides a powerful new idea for the efficient utilization of oil feed and has important theoretical significance.
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Affiliation(s)
- Lujia Gao
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China
| | - Chen Liu
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China
| | - Jiaqi Wu
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China
| | - Ying Cui
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China
| | - Man Zhang
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China
| | - Chongpeng Bi
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China
| | - Anshan Shan
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China
| | - Xiujing Dou
- Institute of Animal Nutrition, Northeast Agricultural University, Harbin 150030, China.
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Zhang H, Dai Y, Gu J, Li H, Wu R, Jia J, Shen J, Li W, Han R, Sun G, Li W, Liu X, Zhao Y, Li G. Multi-Omics Profiling of Lipid Variation and Regulatory Mechanisms in Poultry Breast Muscles. Animals (Basel) 2025; 15:694. [PMID: 40075981 PMCID: PMC11898432 DOI: 10.3390/ani15050694] [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: 02/10/2025] [Revised: 02/24/2025] [Accepted: 02/25/2025] [Indexed: 03/14/2025] Open
Abstract
This study aimed to elucidate the genetic basis of lipid composition in the breast muscles of poultry, including AA broilers, dwarf guinea fowl, quails, and pigeons, and the impact of artificial selection on lipid traits. By employing lipidomics and transcriptomic sequencing, the research analyzed the chest muscle tissues of these four poultry. A total of 1542 lipid molecules were identified, with 711 showing significant differences among species. These lipids primarily belonged to subclasses such as TG, PC, Phosphatidylethanolamine (PE), Ceramides (Cer), and Diglyceride (DG), with each species demonstrating distinct profiles in these subclasses. Additionally, 5790 orthologous genes were identified, with 763, 767, 24, and 8 genes in AA broilers, dwarf guinea fowl, quails, and pigeons, respectively, exhibiting positive selection (Ka/Ks > 1). Notably, 114 genes related to lipid metabolism displayed significant differential expression, particularly between AA broilers and dwarf guinea fowl. The findings revealed that the metabolic pathways of PC and LPC lipid molecules in the glycerophospholipid pathway, as well as TG lipid molecules in the glycerolipid pathway, exhibited marked interspecies differences, potentially contributing to variations in breast muscle lipid composition. These results provide a solid foundation for understanding the lipid composition and molecular regulatory mechanisms in diverse poultry, offering valuable insights for further research in poultry lipid metabolism and artificial breeding programs.
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Affiliation(s)
- Hongyuan Zhang
- The Shennong Laboratory, Henan Agricultural University, Zhengzhou 450046, China; (H.Z.); (Y.D.); (J.G.); (H.L.); (R.W.); (J.J.); (J.S.); (R.H.); (G.S.); (W.L.); (X.L.)
| | - Yaqi Dai
- The Shennong Laboratory, Henan Agricultural University, Zhengzhou 450046, China; (H.Z.); (Y.D.); (J.G.); (H.L.); (R.W.); (J.J.); (J.S.); (R.H.); (G.S.); (W.L.); (X.L.)
| | - Jinxing Gu
- The Shennong Laboratory, Henan Agricultural University, Zhengzhou 450046, China; (H.Z.); (Y.D.); (J.G.); (H.L.); (R.W.); (J.J.); (J.S.); (R.H.); (G.S.); (W.L.); (X.L.)
| | - Hongtai Li
- The Shennong Laboratory, Henan Agricultural University, Zhengzhou 450046, China; (H.Z.); (Y.D.); (J.G.); (H.L.); (R.W.); (J.J.); (J.S.); (R.H.); (G.S.); (W.L.); (X.L.)
| | - Ran Wu
- The Shennong Laboratory, Henan Agricultural University, Zhengzhou 450046, China; (H.Z.); (Y.D.); (J.G.); (H.L.); (R.W.); (J.J.); (J.S.); (R.H.); (G.S.); (W.L.); (X.L.)
| | - Jiyu Jia
- The Shennong Laboratory, Henan Agricultural University, Zhengzhou 450046, China; (H.Z.); (Y.D.); (J.G.); (H.L.); (R.W.); (J.J.); (J.S.); (R.H.); (G.S.); (W.L.); (X.L.)
| | - Jingqi Shen
- The Shennong Laboratory, Henan Agricultural University, Zhengzhou 450046, China; (H.Z.); (Y.D.); (J.G.); (H.L.); (R.W.); (J.J.); (J.S.); (R.H.); (G.S.); (W.L.); (X.L.)
| | - Wanli Li
- Institute of Animal Science, Henan Academy of Agricultural Sciences, Zhengzhou 450002, China;
| | - Ruili Han
- The Shennong Laboratory, Henan Agricultural University, Zhengzhou 450046, China; (H.Z.); (Y.D.); (J.G.); (H.L.); (R.W.); (J.J.); (J.S.); (R.H.); (G.S.); (W.L.); (X.L.)
| | - Guirong Sun
- The Shennong Laboratory, Henan Agricultural University, Zhengzhou 450046, China; (H.Z.); (Y.D.); (J.G.); (H.L.); (R.W.); (J.J.); (J.S.); (R.H.); (G.S.); (W.L.); (X.L.)
| | - Wenting Li
- The Shennong Laboratory, Henan Agricultural University, Zhengzhou 450046, China; (H.Z.); (Y.D.); (J.G.); (H.L.); (R.W.); (J.J.); (J.S.); (R.H.); (G.S.); (W.L.); (X.L.)
| | - Xiaojun Liu
- The Shennong Laboratory, Henan Agricultural University, Zhengzhou 450046, China; (H.Z.); (Y.D.); (J.G.); (H.L.); (R.W.); (J.J.); (J.S.); (R.H.); (G.S.); (W.L.); (X.L.)
| | - Yinli Zhao
- College of Biological Engineering, Henan University of Technology, Zhengzhou 450001, China
| | - Guoxi Li
- The Shennong Laboratory, Henan Agricultural University, Zhengzhou 450046, China; (H.Z.); (Y.D.); (J.G.); (H.L.); (R.W.); (J.J.); (J.S.); (R.H.); (G.S.); (W.L.); (X.L.)
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Cui Z, Amevor FK, Lan X, Tang B, Qin S, Fu P, Liu A, Liu L. Integrative metabolomics and transcriptomics analysis revealed specific genes and metabolites affecting meat quality of chickens under different rearing systems. Poult Sci 2024; 103:103994. [PMID: 38991385 PMCID: PMC11296026 DOI: 10.1016/j.psj.2024.103994] [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: 05/18/2024] [Revised: 06/07/2024] [Accepted: 06/19/2024] [Indexed: 07/13/2024] Open
Abstract
Different rearing systems have varying effect on animal welfare and meat quality of poultry. Currently, there are no established standards for the rearing systems of Chinese indigenous chickens. Our study aimed to investigate the effects of different rearing systems on the meat quality, gene profiles, and metabolites of Chinese indigenous chickens (Nanchuan chicken). 10-wk-old Nanchuan chickens (n=360) were randomly divided into 3 groups (cage, net, and free-range groups), with 6 replicates per group (20 chickens per replicate). The experiment lasted for 12 wk. At 154-days-old, 36 healthy chickens (6 males and 6 females per group) were randomly selected, euthanized, and their breast muscles were collected to assess the meat quality parameters and histomorphological characteristics. Additionally, breast muscles from 18 random hens (3 males and 3 females per group) were used for metabolomics and RNA-seq analysis. The results showed that rearing systems significantly affected the meat quality and myofiber characteristics. The meat quality of breast muscles from free-range chickens was superior to that of caged chickens, characterized by more tender meat and smaller myofiber cross-sectional areas. Integrative metabolomics and transcriptomics analysis revealed that the differentially expressed genes of chicken breast muscles were primarily involved in the myofiber differentiation. Mechanically, the improved meat quality of breast muscle in free-range chickens were mainly associated with enhanced skeletal muscle differentiation facilitated by fibromodulin, increased levels of up-regulated Acetyl-L-carnitine and Propionylcarnitine level, and decreased levels of Nonanoic acid and Elaidic acid abundance (Graphical abstract). This provides a comprehensive understanding of the most effective and sustainable breeding, production, and rearing systems for Chinese indigenous chickens. It also contributes to the current knowledge of the molecular mechanisms underlying the effects of rearing systems on growth performance and meat quality of chickens.
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Affiliation(s)
- Zhifu Cui
- College of Animal Science and Technology, Southwest University, Beibei, 400715 Chongqing, P. R. China
| | - Felix Kwame Amevor
- State Key Laboratory of Swine and Poultry Industry, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan Province, P. R. China
| | - Xi Lan
- College of Animal Science and Technology, Southwest University, Beibei, 400715 Chongqing, P. R. China
| | - Bincheng Tang
- College of Animal Science and Technology, Southwest University, Beibei, 400715 Chongqing, P. R. China
| | - Simeng Qin
- College of Animal Science and Technology, Southwest University, Beibei, 400715 Chongqing, P. R. China
| | - Penghui Fu
- College of Animal Science and Technology, Southwest University, Beibei, 400715 Chongqing, P. R. China
| | - Anfang Liu
- College of Animal Science and Technology, Southwest University, Beibei, 400715 Chongqing, P. R. China
| | - Lingbin Liu
- College of Animal Science and Technology, Southwest University, Beibei, 400715 Chongqing, P. R. China.
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Horecka B, Wojciechowski W, Drabik K, Wengerska K, Batkowska J. Characterization of the Coding Sequence of the MC1R (Melanocortin 1 Receptor) Gene of Ayam Cemani Black Chickens. Animals (Basel) 2024; 14:2507. [PMID: 39272291 PMCID: PMC11394068 DOI: 10.3390/ani14172507] [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: 08/02/2024] [Revised: 08/21/2024] [Accepted: 08/27/2024] [Indexed: 09/15/2024] Open
Abstract
Plumage color is one of the most important traits characterizing chicken breeds. Black-boned chickens constitute a specific group of breeds with a unique phenotype. One of the representatives is the Indonesian Ayam Cemani. The extraordinary black phenotype results from a specific chromosomal rearrangement. We used complete CDS of crucial color-related gene MC1R, which plays a key role in melanin distribution but has not been previously studied in Ayam Cemani. It turned out that Ayam Cemani individuals possess a newly found non-synonymous mutation G355A resulting in amino acid substitution D119N. Together with the presence of G274A (E92K), the new missense variant enabled us to distinguish a new extended black allele at the E locus. All of the investigated birds were heterozygous in terms of the new mutation. Previous studies and our own results indicate a high level of genetic variation within the MC1R gene within and between chicken breeds. Besides the key mutations that make it possible to distinguish particular major alleles, there are also numerous substitutions that give haplotypes more characteristics for individual breeds.
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Affiliation(s)
- Beata Horecka
- Institute of Biological Basis of Animal Production, University of Life Sciences in Lublin, 20-950 Lublin, Poland
| | - Witold Wojciechowski
- Institute of Biological Basis of Animal Production, University of Life Sciences in Lublin, 20-950 Lublin, Poland
| | - Kamil Drabik
- Institute of Biological Basis of Animal Production, University of Life Sciences in Lublin, 20-950 Lublin, Poland
| | - Karolina Wengerska
- Institute of Biological Basis of Animal Production, University of Life Sciences in Lublin, 20-950 Lublin, Poland
| | - Justyna Batkowska
- Institute of Biological Basis of Animal Production, University of Life Sciences in Lublin, 20-950 Lublin, Poland
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Zhao J, Ge X, Li T, Yang M, Zhao R, Yan S, Wu H, Liu Y, Wang K, Xu Z, Jia J, Liu L, Dou T. Integrating metabolomics and transcriptomics to analyze the differences of breast muscle quality and flavor formation between Daweishan mini chicken and broiler. Poult Sci 2024; 103:103920. [PMID: 38909504 PMCID: PMC11253666 DOI: 10.1016/j.psj.2024.103920] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2024] [Revised: 05/23/2024] [Accepted: 05/28/2024] [Indexed: 06/25/2024] Open
Abstract
The quality and flavor of chicken are affected by muscle metabolites and related regulatory genes, and the molecular regulation mechanism of meat quality is different among different breeds of chicken. In this study, 40 one-day-old Daweishan mini chicken (DM) and Cobb broiler (CB) were selected from each group, with 4 replicates and 10 chickens in each replicate. The chickens were reared until 90 d of age under the same management conditions. Then, metabolomics and transcriptomics data of 90-day-old DM (n = 4) and CB (n = 4) were integrated to analyze metabolites affecting breast muscle quality and flavor, and to explore the important genes regulating meat quality and flavor related metabolites. The results showed that a total of 38 significantly different metabolites (SDMs) and 420 differentially expressed genes (DEGs) were detected in the breast muscle of the 2 breeds. Amino acid and lipid metabolism may be the cause of meat quality and flavor difference between DM and CB chickens, involving metabolites such as L-methionine, betaine, N6, N6, N6-Trimethyl-L-lysine, L-anserine, glutathione, glutathione disulfide, L-threonine, N-Acetyl-L-aspartic acid, succinate, choline, DOPC, SOPC, alpha-linolenic acid, L-palmitoylcarnitine, etc. Important regulatory genes with high correlation with flavor amino acids (GATM, GSTO1) and lipids (PPARG, LPL, PLIN1, SCD, ANGPTL4, FABP7, GK, B4GALT6, UGT8, PLPP4) were identified by correlation analysis, and the gene-metabolite interaction network of breast muscle mass and flavor formation in DM chicken was constructed. This study showed that there were significant differences in breast metabolites between DM and CB chickens, mainly in amino acid and lipid metabolites. These 2 kinds of substances may be the main reasons for the difference in breast muscle quality and flavor between the 2 breeds. In general, this study could provide a theoretical basis for further research on the molecular regulatory mechanism of the formation of breast muscle quality and flavor differences between DM and CB chickens, and provide a reference for the development, utilization and genetic breeding of high-quality meat chicken breeds.
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Affiliation(s)
- Jingying Zhao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Xuehai Ge
- College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Tao Li
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Min Yang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Ruohan Zhao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Shixiong Yan
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Hao Wu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Yong Liu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; Yunnan Rural Revitalization Education Institute, Yunnan Open University, Kunming 650101, China
| | - Kun Wang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Zhiqiang Xu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; College of Food Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Junjing Jia
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Lixian Liu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; Institute of Science and Technology, Chuxiong Normal University, Chuxiong 675099, China
| | - Tengfei Dou
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, 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: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [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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Che S, Pham PH, Barbut S, Bienzle D, Susta L. Transcriptomic Profiles of Pectoralis major Muscles Affected by Spaghetti Meat and Woody Breast in Broiler Chickens. Animals (Basel) 2024; 14:176. [PMID: 38254345 PMCID: PMC10812457 DOI: 10.3390/ani14020176] [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: 12/11/2023] [Revised: 01/03/2024] [Accepted: 01/04/2024] [Indexed: 01/24/2024] Open
Abstract
Spaghetti meat (SM) and woody breast (WB) are breast muscle myopathies of broiler chickens, characterized by separation of myofibers and by fibrosis, respectively. This study sought to investigate the transcriptomic profiles of breast muscles affected by SM and WB. Targeted sampling was conducted on a flock to obtain 10 WB, 10 SM, and 10 Normal Pectoralis major muscle samples from 37-day-old male chickens. Total RNA was extracted, cDNA was used for pair-end sequencing, and differentially expressed genes (DEGs) were determined by a false discovery rate of <0.1 and a >1.5-fold change. Principal component and heatmap cluster analyses showed that the SM and WB samples clustered together. No DEGs were observed between SM and WB fillets, while a total of 4018 and 2323 DEGs were found when comparing SM and WB, respectively, against Normal samples. In both the SM and WB samples, Gene Ontology terms associated with extracellular environment and immune response were enriched. The KEGG analysis showed enrichment of cytokine-cytokine receptor interaction and extracellular matrix-receptor interaction pathways in both myopathies. Although SM and WB are macroscopically different, the similar transcriptomic profiles suggest that these conditions may share a common pathogenesis. This is the first study to compare the transcriptomes of SM and WB, and it showed that, while both myopathies had profiles different from the normal breast muscle, SM and WB were similar, with comparable enriched metabolic pathways and processes despite presenting markedly different macroscopic features.
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Affiliation(s)
- Sunoh Che
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON N1G2W1, Canada; (S.C.); (P.H.P.)
| | - Phuc H. Pham
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON N1G2W1, Canada; (S.C.); (P.H.P.)
| | - Shai Barbut
- Department of Food Science, Ontario Agricultural College, University of Guelph, Guelph, ON N1G2W1, Canada;
| | - Dorothee Bienzle
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON N1G2W1, Canada; (S.C.); (P.H.P.)
| | - Leonardo Susta
- Department of Pathobiology, Ontario Veterinary College, University of Guelph, Guelph, ON N1G2W1, Canada; (S.C.); (P.H.P.)
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9
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Li X, Wang X, Yu X, Yang C, Lin L, Huang Y. The draft genome of the Temminck's tragopan (Tragopan temminckii) with evolutionary implications. BMC Genomics 2023; 24:751. [PMID: 38062370 PMCID: PMC10702090 DOI: 10.1186/s12864-023-09857-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2023] [Accepted: 11/29/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND High-quality genome data of birds play a significant role in the systematic study of their origin and adaptive evolution. The Temminck's tragopan (Tragopan temminckii) (Galliformes, Phasianidae), a larger pheasant, is one of the most abundant and widely distributed species of the genus Tragopan, and was defined as class II of the list of national key protected wild animals in China. The absence of a sequenced genome has restricted previous evolutionary trait studies of this taxa. RESULTS The whole genome of the Temminck's tragopan was sequenced using Illumina and PacBio platform, and then de novo assembled and annotated. The genome size was 1.06 Gb, with a contig N50 of 4.17 Mb. A total of 117.22 Mb (11.00%) repeat sequences were identified. 16,414 genes were predicted using three methods, with 16,099 (98.08%) annotated as functional genes based on five databases. In addition, comparative genome analyses were conducted across 12 Galliformes species. The results indicated that T. temminckii was the first species to branch off from the clade containing Lophura nycthemera, Phasianus colchicus, Chrysolophus pictus, Syrmaticus mikado, Perdix hodgsoniae, and Meleagris gallopavo, with a corresponding divergence time of 31.43 million years ago (MYA). Expanded gene families associated with immune response and energy metabolism were identified. Genes and pathways associated with plumage color and feather development, immune response, and energy metabolism were found in the list of positively selected genes (PSGs). CONCLUSIONS A genome draft of the Temminck's tragopan was reported, genome feature and comparative genome analysis were described, and genes and pathways related to plumage color and feather development, immune response, and energy metabolism were identified. The genomic data of the Temminck's tragopan considerably contribute to the genome evolution and phylogeny of the genus Tragopan and the whole Galliformes species underlying ecological adaptation strategies.
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Affiliation(s)
- Xuejuan Li
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Xiaoyang Wang
- School of Biological and Environmental Engineering, Xi'an University, Xi'an, China
| | - Xiaoping Yu
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Chao Yang
- Shaanxi Institute of Zoology, Xi'an, China
| | - Liliang Lin
- College of Life Sciences, Shaanxi Normal University, Xi'an, China
| | - Yuan Huang
- College of Life Sciences, Shaanxi Normal University, Xi'an, China.
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10
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Zhao J, Duan X, Yan S, Liu Y, Wang K, Hu M, Chai Q, Liu L, Ge C, Jia J, Dou T. Transcriptomics reveals the molecular regulation of Chinese medicine formula on improving bone quality in broiler. Poult Sci 2023; 102:103044. [PMID: 37717480 PMCID: PMC10507442 DOI: 10.1016/j.psj.2023.103044] [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: 05/19/2023] [Revised: 08/12/2023] [Accepted: 08/15/2023] [Indexed: 09/19/2023] Open
Abstract
Skeletal disorder is of concern to the poultry industry as it affects animal welfare and production performance. Traditional Chinese medicine could improve bone quality and reduce the incidence of bone disease, but the molecular regulation of Chinese medicine formula (CMF) on improving bone quality in broilers is still unclear. This study was performed to research the effects of CMF on skeletal performance of Cobb broilers and reveal the molecular regulation. A total of 120 one-day-old Cobb broilers were randomly allocated into 4 equal groups of 30 chickens, with 5 replicates and 6 chickens in each replicate. The control (CON) group was fed a diet without CMF, while the CMF1, CMF2, and CMF3 groups were supplemented with different CMF at 6,000 mg/kg diet, respectively. The broilers were raised to 60 d of age, then bone tissues were collected for biomechanical properties, micro-CT detection and transcriptomic sequencing analysis. The results showed that CMF3 improved the biomechanical properties of broiler tibia, via increasing the elastic modulus (P < 0.05), yield strength (P > 0.05), maximum stress (P < 0.05) and fracture stress (P < 0.05) of the tibia. Micro-CT analysis indicated that CMF3 increased the bone mineral density (BMD), bone volume/total volume (BV/TV), bone surface density (BS/TV), trabecular number (Tb.N), trabecular thickness (Tb.Th), and decreased the trabecular separation (Tb.Sp) of femur cancellous bone (P < 0.05). RNA-seq analysis revealed 2,177 differentially expressed genes (DEGs) (|log2FoldChange| ≥ 1, FDR < 0.05) between the CMF3 group and CON group. Kyoto Encyclopedia of Genes and Genomes pathway (KEGG) analysis showed 13 pathways mostly associated with bone growth and development and bone metabolism, and we identified 39 bone-related DEGs. This study suggests that CMF3 could improve bone strength and bone microstructure of broilers, and showed a positive effect on bone performance. Our research could provide a theoretical reference for the development of pollution-free feed additives to improve the skeletal performance of broilers, which could help promote healthy farming of chickens.
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Affiliation(s)
- Jingying Zhao
- Faculty of Animal Science and Technology, Yunnan Agricultural University, 650201 Kunming, China
| | - Xiaohua Duan
- Faculty of Animal Science and Technology, Yunnan Agricultural University, 650201 Kunming, China; Yunnan University of Chinese Medicine, 650500 Kunming, China
| | - Shixiong Yan
- Faculty of Animal Science and Technology, Yunnan Agricultural University, 650201 Kunming, China
| | - Yong Liu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, 650201 Kunming, China
| | - Kun Wang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, 650201 Kunming, China
| | - Mei Hu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, 650201 Kunming, China
| | - Qian Chai
- Faculty of Animal Science and Technology, Yunnan Agricultural University, 650201 Kunming, China
| | - Lixian Liu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, 650201 Kunming, China; Yunnan Vocational and Technical College of Agriculture, 650031 Kunming, China
| | - Changrong Ge
- Faculty of Animal Science and Technology, Yunnan Agricultural University, 650201 Kunming, China
| | - Junjing Jia
- Faculty of Animal Science and Technology, Yunnan Agricultural University, 650201 Kunming, China
| | - Tengfei Dou
- Faculty of Animal Science and Technology, Yunnan Agricultural University, 650201 Kunming, China.
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11
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Song HY, Deng ML, Yang JF, Ma J, Shu FF, Cheng WJ, Zhu XQ, Zou FC, He JJ. Transcriptomic, 16S ribosomal ribonucleic acid and network pharmacology analyses shed light on the anticoccidial mechanism of green tea polyphenols against Eimeria tenella infection in Wuliangshan black-boned chickens. Parasit Vectors 2023; 16:330. [PMID: 37726789 PMCID: PMC10510215 DOI: 10.1186/s13071-023-05922-x] [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: 06/03/2023] [Accepted: 08/09/2023] [Indexed: 09/21/2023] Open
Abstract
BACKGROUND Eimeria tenella is an obligate intracellular parasitic protozoan that invades the chicken cecum and causes coccidiosis, which induces acute lesions and weight loss. Elucidating the anticoccidial mechanism of action of green tea polyphenols could aid the development of anticoccidial drugs and resolve the problem of drug resistance in E. tenella. METHODS We constructed a model of E. tenella infection in Wuliangshan black-boned chickens, an indigenous breed of Yunnan Province, China, to study the efficacy of green tea polyphenols against the infection. Alterations in gene expression and in the microbial flora in the cecum were analyzed by ribonucleic acid (RNA) sequencing and 16S ribosomal RNA (rRNA) sequencing. Quantitative real-time polymerase chain reaction was used to verify the host gene expression data obtained by RNA sequencing. Network pharmacology and molecular docking were used to clarify the interactions between the component green tea polyphenols and the targeted proteins; potential anticoccidial herbs were also analyzed. RESULTS Treatment with the green tea polyphenols led to a reduction in the lesion score and weight loss of the chickens induced by E. tenella infection. The expression of matrix metalloproteinase 7 (MMP7), MMP1, nitric oxide synthase 2 and ephrin type-A receptor 2 was significantly altered in the E. tenella infection plus green tea polyphenol-treated group and in the E. tenella infection group compared with the control group; these genes were also predicted targets of tea polyphenols. Furthermore, the tea polyphenol (-)-epigallocatechin gallate acted on most of the targets, and the molecular docking analysis showed that it has good affinity with interferon induced with helicase C domain 1 protein. 16S ribosomal RNA sequencing showed that the green tea polyphenols had a regulatory effect on changes in the fecal microbiota induced by E. tenella infection. In total, 171 herbs were predicted to act on two or three targets in MMP7, MMP1, nitric oxide synthase 2 and ephrin type-A receptor 2. CONCLUSIONS Green tea polyphenols can directly or indirectly regulate host gene expression and alter the growth of microbiota. The results presented here shed light on the mechanism of action of green tea polyphenols against E. tenella infection in chickens, and have implications for the development of novel anticoccidial products.
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Affiliation(s)
- Hai-Yang Song
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China
- Key Laboratory of Veterinary Public Health of Yunnan Province, College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China
| | - Meng-Ling Deng
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China
- Key Laboratory of Veterinary Public Health of Yunnan Province, College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China
| | - Jian-Fa Yang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China
- Key Laboratory of Veterinary Public Health of Yunnan Province, College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China
| | - Jun Ma
- Key Laboratory of Veterinary Public Health of Yunnan Province, College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China
| | - Fan-Fan Shu
- Key Laboratory of Veterinary Public Health of Yunnan Province, College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China
| | - Wen-Jie Cheng
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China
| | - Xing-Quan Zhu
- Key Laboratory of Veterinary Public Health of Yunnan Province, College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China
- Laboratory of Parasitic Diseases, College of Veterinary Medicine, Shanxi Agricultural University, Taigu, 030801, Shanxi, People's Republic of China
| | - Feng-Cai Zou
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China.
- Key Laboratory of Veterinary Public Health of Yunnan Province, College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China.
| | - Jun-Jun He
- Key Laboratory of Veterinary Public Health of Yunnan Province, College of Veterinary Medicine, Yunnan Agricultural University, Kunming, 650201, Yunnan, People's Republic of China.
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12
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Shinde SS, Sharma A, Vijay N. Decoding the fibromelanosis locus complex chromosomal rearrangement of black-bone chicken: genetic differentiation, selective sweeps and protein-coding changes in Kadaknath chicken. Front Genet 2023; 14:1180658. [PMID: 37424723 PMCID: PMC10325862 DOI: 10.3389/fgene.2023.1180658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 06/05/2023] [Indexed: 07/11/2023] Open
Abstract
Black-bone chicken (BBC) meat is popular for its distinctive taste and texture. A complex chromosomal rearrangement at the fibromelanosis (Fm) locus on the 20th chromosome results in increased endothelin-3 (EDN3) gene expression and is responsible for melanin hyperpigmentation in BBC. We use public long-read sequencing data of the Silkie breed to resolve high-confidence haplotypes at the Fm locus spanning both Dup1 and Dup2 regions and establish that the Fm_2 scenario is correct of the three possible scenarios of the complex chromosomal rearrangement. The relationship between Chinese and Korean BBC breeds with Kadaknath native to India is underexplored. Our data from whole-genome re-sequencing establish that all BBC breeds, including Kadaknath, share the complex chromosomal rearrangement junctions at the fibromelanosis (Fm) locus. We also identify two Fm locus proximal regions (∼70 Kb and ∼300 Kb) with signatures of selection unique to Kadaknath. These regions harbor several genes with protein-coding changes, with the bactericidal/permeability-increasing-protein-like gene having two Kadaknath-specific changes within protein domains. Our results indicate that protein-coding changes in the bactericidal/permeability-increasing-protein-like gene hitchhiked with the Fm locus in Kadaknath due to close physical linkage. Identifying this Fm locus proximal selective sweep sheds light on the genetic distinctiveness of Kadaknath compared to other BBC.
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Affiliation(s)
| | | | - Nagarjun Vijay
- Computational Evolutionary Genomics Lab, Department of Biological Sciences, IISER Bhopal, Bhauri, Madhya Pradesh, India
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13
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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: 5] [Impact Index Per Article: 2.5] [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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14
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Yu H, Raza SHA, Pan Y, Cheng G, Mei C, Zan L. Integrative Analysis of Blood Transcriptomics and Metabolomics Reveals Molecular Regulation of Backfat Thickness in Qinchuan Cattle. Animals (Basel) 2023; 13:ani13061060. [PMID: 36978600 PMCID: PMC10044415 DOI: 10.3390/ani13061060] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/27/2023] [Revised: 03/11/2023] [Accepted: 03/14/2023] [Indexed: 03/17/2023] Open
Abstract
A crucial goal of reducing backfat thickness (BFT) is to indirectly improve feed conversion efficiency. This phenotype has been reported in certain papers; however, the molecular mechanism has yet to be fully revealed. Two extreme BFT groups, consisting of four Qinchuan cattle, were chosen for this study. We performed metabolite and transcriptome analyses of blood from cattle with a high BFT (H-BFT with average = 1.19) and from those with a low BFT (L-BFT with average = 0.39). In total, 1106 differentially expressed genes (DEGs) and 86 differentially expressed metabolites (DEMs) were identified in the extreme trait. In addition, serum ceramide was strongly correlated with BFT and could be used as a potential biomarker. Moreover, the most notable finding was that the functional genes (SMPD3 and CERS1) and metabolite (sphingosine 1-phosphate (S1P)) were filtered out and significantly enriched in the processes related to the sphingolipid metabolism. This investigation contributed to a better understanding of the subcutaneous fat depots in cattle. In general, our results indicated that the sphingolipid metabolism, involving major metabolites (serum ceramide and S1P) and key genes (SMPD3 and CERS1), could regulate BFT through blood circulation.
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Affiliation(s)
- Hengwei Yu
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (H.Y.); (S.H.A.R.)
| | - Sayed Haidar Abbas Raza
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (H.Y.); (S.H.A.R.)
- Guangdong Provincial Key Laboratory of Food Quality and Safety/Nation-Local Joint Engineering Research Center for Machining and Safety of Livestock and Poultry Products, South China Agricultural University, Guangzhou 510642, China
| | - Yueting Pan
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (H.Y.); (S.H.A.R.)
| | - Gong Cheng
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (H.Y.); (S.H.A.R.)
| | - Chugang Mei
- College of Grassland Agriculture, Northwest A&F University, Xianyang 712100, China
- National Beef Cattle Improvement Center, Xianyang 712100, China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China; (H.Y.); (S.H.A.R.)
- National Beef Cattle Improvement Center, Xianyang 712100, China
- Correspondence:
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15
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Alsoufi MA, Liu Y, Cao C, Zhao J, Kang J, Li M, Wang K, He Y, Ge C. Integrated Transcriptomics Profiling in Chahua and Digao Chickens' Breast for Assessment Molecular Mechanism of Meat Quality Traits. Genes (Basel) 2022; 14:95. [PMID: 36672833 PMCID: PMC9859260 DOI: 10.3390/genes14010095] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2022] [Revised: 11/27/2022] [Accepted: 12/02/2022] [Indexed: 12/31/2022] Open
Abstract
Meat quality traits are an important economic trait and remain a major argument, from the producer to the consumer. However, there are a few candidate genes and pathways of chicken meat quality traits that were reported for chicken molecular breeding. The purpose of the present study is to identify the candidate genes and pathways associated with meat quality underlying variations in meat quality. Hence, transcriptome profiles of breast tissue in commercial Digao (DG, 5 male) and Chahua (CH, 5 male) native chicken breeds were analyzed at the age of 100 days. The results found 3525 differentially expressed genes (DEGs) in CH compared to DG with adjusted p-values of ≤0.05 and log2FC ≥ 0.1 FDR ≤ 0.05. Functional analysis of GO showed that the DEGs are mainly involved in the two types of processes of meat quality, such as positive regulation of the metabolic process, extracellular structure organization, collagen trimer, cellular amino acid metabolic process, cellular amino acid catabolic process, and heme binding. Functional analysis of KEGG showed that the DEGs are mainly involved in the two types of processes of meat quality, such as oxidative phosphorylation, carbon metabolism, valine, leucine, and isoleucine degradation, and fatty acid degradation. Many of the DEGs are well known to be related to meat quality, such as COL28A1, COL1A2, MB, HBAD, HBA1, ACACA, ACADL, ACSL1, ATP8A1, CAV1, FADS2, FASN, DCN, CHCHD10, AGXT2, ALDH3A2, and MORN4. Therefore, the current study detected multiple pathways and genes that could be involved in the control of the meat quality traits of chickens. These findings should be used as an essential resource to improve the accuracy of selection for meat traits in chickens using marker-assisted selection based on differentially expressed genes.
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Affiliation(s)
- Mohammed Abdulwahid Alsoufi
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
- Department of Animal Production, Faculty of Agriculture, Sana’a University, Alwehdah Street, Sana’a P.O. Box 19509, Yemen
| | - Yong Liu
- College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Changwei Cao
- Department of Food Science and Engineering, College of Biological Sciences, Southwest Forestry University, Kunming 650224, China
| | - Jinbo Zhao
- 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
| | - Mengyuan Li
- 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
| | - Yang He
- 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
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16
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Wang Y, Zhou H, Zhou K, Han Q, Wang Z, Xu B. Study on the roles of microorganisms and endogenous enzymes in the evolution of metabolic characteristics of lean portion during traditional Chinese bacon processing. Food Res Int 2022; 162:112087. [DOI: 10.1016/j.foodres.2022.112087] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Revised: 09/11/2022] [Accepted: 10/24/2022] [Indexed: 11/25/2022]
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17
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Zhou H, Yang Y, Wang L, Ye S, Liu J, Gong P, Qian Y, Zeng H, Chen X. Integrated multi-omic data reveal the potential molecular mechanisms of the nutrition and flavor in Liancheng white duck meat. Front Genet 2022; 13:939585. [PMID: 36046229 PMCID: PMC9421069 DOI: 10.3389/fgene.2022.939585] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2022] [Accepted: 07/14/2022] [Indexed: 12/01/2022] Open
Abstract
The Liancheng white (LW) duck is one of the most valued Chinese indigenous poultry breeds. Its meat is rich in nutrients and has distinct flavors, but the molecular mechanisms behind them are unknown. To address this issue, we measured and compared multi-omic data (genome, transcriptome, and metabolome) of breast meat from LW ducks and the Mianyang Shelduck (MS) ducks. We found that the LW duck has distinct breed-specific genetic features, including numerous mutant genes with differential expressions associated with amino acid metabolism and transport activities. The metabolome driven by genetic materials was also seen to differ between the two breeds. For example, several amino acids that are beneficial for human health, such as L-Arginine, L-Ornithine, and L-lysine, were found in considerably higher concentrations in LW muscle than in MS duck muscle (p < 0.05). SLC7A6, a mutant gene, was substantially upregulated in the LW group (p < 0.05), which may lead to excessive L-arginine and L-ornithine accumulation in LW duck meat through transport regulation. Further, guanosine monophosphate (GMP), an umami-tasting molecule, was considerably higher in LW muscle (p < 0.05), while L-Aspartic acid was significantly abundant in MS duck meat (p < 0.05), showing that the LW duck has a different umami formation. Overall, this study contributed to our understanding of the molecular mechanisms driving the enriched nutrients and distinct umami of LW duck meat, which will provide a useful reference for duck breeding.
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Affiliation(s)
- Hao Zhou
- Insitute of Animal Husbandry and Veterinary, Wuhan Academy of Agricultural Science, Wuhan, China
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Yu Yang
- Insitute of Animal Husbandry and Veterinary, Wuhan Academy of Agricultural Science, Wuhan, China
| | - Lixia Wang
- Insitute of Animal Husbandry and Veterinary, Wuhan Academy of Agricultural Science, Wuhan, China
| | - Shengqiang Ye
- Insitute of Animal Husbandry and Veterinary, Wuhan Academy of Agricultural Science, Wuhan, China
| | - Jiajia Liu
- Department of Animal Science, School of Agriculture and Biology, Shanghai Jiao Tong University, Shanghai, China
| | - Ping Gong
- Insitute of Animal Husbandry and Veterinary, Wuhan Academy of Agricultural Science, Wuhan, China
| | - Yunguo Qian
- Insitute of Animal Husbandry and Veterinary, Wuhan Academy of Agricultural Science, Wuhan, China
| | - Huijun Zeng
- Wuhan Institute for Food and Cosmetic Control, Wuhan, China
- Key Laboratory of Edible Oil Quality and Safety for State Market Regulation, Wuhan, China
- *Correspondence: Huijun Zeng, ; Xing Chen,
| | - Xing Chen
- Insitute of Animal Husbandry and Veterinary, Wuhan Academy of Agricultural Science, Wuhan, China
- *Correspondence: Huijun Zeng, ; Xing Chen,
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Transcriptomics and Metabolomics Analysis of the Ovaries of High and Low Egg Production Chickens. Animals (Basel) 2022; 12:ani12162010. [PMID: 36009602 PMCID: PMC9404446 DOI: 10.3390/ani12162010] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2022] [Revised: 08/04/2022] [Accepted: 08/05/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary The ovarian tissues of different breeds of hens during egg production were investigated through transcriptomics and metabolomics to provide a more comprehensive understanding of the molecular mechanisms of the ovary during egg production. Four genes involved in egg production were predicted by the transcriptome, including P2RX1, INHBB, VIPR2, and FABP3, and several close metabolites associated with reproduction were identified in the metabolome, including 17α-hydroxyprogesterone, iloprost, spermidine and adenosine. Correlation analysis of specific differential genes and differential metabolites identified important gene-metabolite pairs VIPR2–Spermidine and P2RX1–Spermidine in the reproductive process. Abstract Egg production is a pivotal indicator for evaluating the fertility of poultry, and the ovary is an essential organ for egg production and plays an indispensable role in poultry production and reproduction. In order to investigate different aspects of egg production mechanisms in different poultry, in this study we performed a metabolomic analysis of the transcriptomic combination of the ovaries of two chicken breeds, the high-production Ninghai indigenous chickens and the low-production Wuliangshan black-boned chickens, to analyze the biosynthesis and potential key genes and metabolic pathways in the ovaries during egg production. We predicted four genes in the transcriptomic that are associated with egg production, namely P2RX1, INHBB, VIPR2, and FABP3, and identified three important pathways during egg production, “Calcium signaling pathway”, “Neuroactive ligand–receptor interaction” and “Cytokine–cytokine receptor interaction”, respectively. In the metabolomic 149 significantly differential metabolites were identified, 99 in the negative model and 50 in the positive model, of which 17α-hydroxyprogesterone, iloprost, spermidine, and adenosine are important metabolites involved in reproduction. By integrating transcriptomics and metabolomics, the correlation between specific differential genes and differential metabolites identified important gene-metabolite pairs “VIPR2-Spermidine” and “P2RX1-Spermidine” in egg production. In conclusion, these data provide a better understanding of the molecular differences between the ovaries of low- and high-production hens and provide a theoretical basis for further studies on the mechanics of poultry egg production.
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