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Wang L, Gao J, Li G, Cheng J, Yuan G, Zhang T, Zeng W, Lu H. Identification of Metabolites in Muscles of Lueyang Black-Bone Chickens: A Comparative Analysis of Caged and Cage-Free Rearing Modes Using Untargeted Metabolomic Techniques. Animals (Basel) 2024; 14:2041. [PMID: 39061503 PMCID: PMC11274139 DOI: 10.3390/ani14142041] [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: 06/17/2024] [Revised: 07/07/2024] [Accepted: 07/10/2024] [Indexed: 07/28/2024] Open
Abstract
The Lueyang black-bone chicken is a specific native chicken strain in China. This study aimed to investigate the effects of different rearing systems on the meat quality of Lueyang black-bone chickens. Six hundred Lueyang black-bone hens were randomly divided into two groups at 7 weeks of age and raised in cage and cage-free systems for 20 weeks. The carcass yield, meat quality, and total metabolites were measured in both the leg and breast muscles. By comparison, the carcass yield of hens in the cage-free (CF) group (1.26 ± 0.09 kg) was significantly lower than that in the caged rearing (CR) group (1.52 ± 0.15 kg). However, the shear force of leg muscles in the CF group (27.98 ± 2.43 N) was significantly greater than that in the CR group (24.15 ± 1.93 N). In addition, six samples from each group were randomly selected and their metabolites were detected by the non-targeted metabolomics technique. Among these metabolites, 408 and 354 significantly differentially abundant metabolites were identified in breast and leg muscles, which were mainly involved in glycerophospholipid metabolism, unsaturated fatty acid biosynthesis, arginine and proline metabolism, and nucleotide metabolism. We found that the levels of 19 phospholipids, mainly phosphatidylcholines and lysophosphatidylcholines, were significantly greater in the CF group than in the CR group. Additionally, the contents of eight unsaturated fatty acids, linoleic acid, and linolenic acid were dramatically greater in the CF group than in the caged group. The accumulation of 4-hydroxy-proline, glutamate, and adenosine 3'-monophosphate (AMP) was enhanced in the CF group. Moreover, many more volatile organic compounds were identified in the muscles of the cage-free group, enhancing the flavor of the chicken meat. In conclusion, the cage-free rearing mode facilitates the accumulation of nutrients and flavor substances in the chicken meat and is a better rearing system for Lueyang black-bone chickens.
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Affiliation(s)
- Ling Wang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, China
- Shaanxi University Engineering Research Center of Quality Improvement and Safety Control of Qinba Special Meat Products, Hanzhong 723001, China
- Qinba Mountain Area Collaborative Innovation Center of Bioresources Comprehensive Development, Shaanxi University of Technology, Hanzhong 723001, China
| | - Jie Gao
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, China
| | - Guojin Li
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, China
| | - Jia Cheng
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, China
- Shaanxi University Engineering Research Center of Quality Improvement and Safety Control of Qinba Special Meat Products, Hanzhong 723001, China
- Qinba State Key Laboratory of Biological Resources and Ecological Environment, Shaanxi University of Technology, Hanzhong 723001, China
| | - Guoqiang Yuan
- Shaanxi Baiweiyuan Network Technology Company, Hanzhong 724300, China
| | - Tao Zhang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, China
- Shaanxi University Engineering Research Center of Quality Improvement and Safety Control of Qinba Special Meat Products, Hanzhong 723001, China
- Qinba Mountain Area Collaborative Innovation Center of Bioresources Comprehensive Development, Shaanxi University of Technology, Hanzhong 723001, China
- Qinba State Key Laboratory of Biological Resources and Ecological Environment, Shaanxi University of Technology, Hanzhong 723001, China
| | - Wenxian Zeng
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, China
- Shaanxi University Engineering Research Center of Quality Improvement and Safety Control of Qinba Special Meat Products, Hanzhong 723001, China
- Qinba Mountain Area Collaborative Innovation Center of Bioresources Comprehensive Development, Shaanxi University of Technology, Hanzhong 723001, China
- Qinba State Key Laboratory of Biological Resources and Ecological Environment, Shaanxi University of Technology, Hanzhong 723001, China
| | - Hongzhao Lu
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, China
- Shaanxi University Engineering Research Center of Quality Improvement and Safety Control of Qinba Special Meat Products, Hanzhong 723001, China
- Qinba Mountain Area Collaborative Innovation Center of Bioresources Comprehensive Development, Shaanxi University of Technology, Hanzhong 723001, China
- Qinba State Key Laboratory of Biological Resources and Ecological Environment, Shaanxi University of Technology, Hanzhong 723001, China
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He L, Yang H, Lan F, Chen R, Jiang P, Jin W. Use of GC-IMS and Stoichiometry to Characterize Flavor Volatiles in Different Parts of Lueyang Black Chicken during Slaughtering and Cutting. Foods 2024; 13:1885. [PMID: 38928826 PMCID: PMC11202429 DOI: 10.3390/foods13121885] [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: 05/16/2024] [Revised: 06/07/2024] [Accepted: 06/12/2024] [Indexed: 06/28/2024] Open
Abstract
Chilled and cut chicken is preferred by consumers for its safeness and readiness to cook. To evaluate the quality characteristics of various chilled chicken products, differences in volatile organic components (VOCs) of six different cut parts (breast, back, leg, heart, liver, and gizzard) of Lueyang black chicken were characterized through gas chromatography-ion mobility spectroscopy (GC-IMS) combined with stoichiometry. A total of 54 peaks in the signal of VOCs were detected by GC-IMS, and 43 VOCs were identified by qualitative analysis. There were 22 aldehydes (20.66-54.07%), 8 ketones (25.74-62.87%), 9 alcohols (4.17-14.69%), 1 ether (0.18-2.22%), 2 esters (0.43-1.54%), and 1 furan (0.13-0.52%), in which aldehydes, ketones, and alcohols were the main categories. Among the six cut parts, the relative content of aldehydes (54.07%) was the highest in the gizzard, and the relative content of ketones (62.87%) was the highest in the heart. Meanwhile, the relative content of alcohols (14.69%) was the highest in the liver. Based on a stable and reliable predictive model established by orthogonal partial least squares-discriminant analysis (OPLS-DA), 3-hydroxy-2-butanone (monomer and dimer), acetone, 2-butanone monomer, hexanal (monomer and dimer), isopentyl alcohol monomer, and n-hexanol monomer were picked out as characteristic VOCs based on variable importance in projection (VIP value > 1.0, p < 0.05). Principal component analysis (PCA) and the clustering heatmap indicated that the characteristic VOCs could effectively distinguish the six cut parts of Lueyang black chicken. The specific VOCs responsible for flavor differences among six different cut parts of Lueyang black chicken were hexanal (monomer and dimer) for the gizzard, 2-butanone monomer and hexanal dimer for the breast, hexanal monomer for the back, 3-hydroxy-2-butanone monomer for the leg, 3-hydroxy-2-butanone (monomer and dimer) for the heart, and acetone and isopentyl alcohol monomer for the liver. These findings could reveal references for quality assessment and development of chilled products related to different cut parts of Lueyang black chicken in the future.
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Affiliation(s)
- Linlin He
- College of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, China; (L.H.); (F.L.); (R.C.)
- Shaanxi Province Key Laboratory of Bio-Resources, Shaanxi University of Technology, Hanzhong 723001, China
- Qinba Mountain Area Collaborative Innovation Center of Bioresources Comprehensive Development, State Key Laboratory of Biological Resources and Ecological Environment (Incubation), Hanzhong 723001, China
| | - Hui Yang
- Shaanxi Baisheng Biological Engineering Co., Ltd., Hanzhong 723001, China
| | - Fei Lan
- College of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, China; (L.H.); (F.L.); (R.C.)
| | - Rui Chen
- College of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, China; (L.H.); (F.L.); (R.C.)
- Shaanxi Province Key Laboratory of Bio-Resources, Shaanxi University of Technology, Hanzhong 723001, China
| | - Pengfei Jiang
- College of Food Science and Technology, Dalian Polytechnic University, Dalian 116034, China;
| | - Wengang Jin
- College of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, China; (L.H.); (F.L.); (R.C.)
- Shaanxi Province Key Laboratory of Bio-Resources, Shaanxi University of Technology, Hanzhong 723001, China
- Qinba Mountain Area Collaborative Innovation Center of Bioresources Comprehensive Development, State Key Laboratory of Biological Resources and Ecological Environment (Incubation), Hanzhong 723001, China
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Xue Z, Wang L, Tian Y, Yang Y, Li P, Yang G, Lu H, Wang S, Zeng W, Zhang T. A genome-wide scan to identify signatures of selection in Lueyang black -bone chicken. Poult Sci 2023; 102:102721. [PMID: 37186968 DOI: 10.1016/j.psj.2023.102721] [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: 02/07/2023] [Revised: 04/05/2023] [Accepted: 04/10/2023] [Indexed: 05/17/2023] Open
Abstract
Lueyang black-bone chicken is a domestic breed in China. The genetic mechanism of the formation of important economic traits of this breed has not been studied systematically. Therefore, in this study, whole genome resequencing was used to systematically analyze and evaluate the genetic diversity of the black-feather and white-feather populations, and to screen and identify key genes related to phenotypes. The results of principal component analysis and population structure analysis showed that Lueyang black-feathered chickens and white-feathered chickens could be divided into 2 subgroups, and the genetic diversity of black-feathered chicken was richer than that of white-feathered chickens. Linkage disequilibrium analysis also showed that the selection intensity of black-feathered chickens was lower than for white-feathered chickens, which was mainly due to the small population size of white-feathered chickens and a certain degree of inbreeding. Fixation index (FST) analysis revealed that the candidate genes related to feather color traits were G-gamma, FA, FERM, Kelch, TGFb, Arf, FERM, and melanin synthesis-related gene tyrosinase (TYR). Based on Kyoto Encyclopedia of Genes and Genomes enrichment analysis, Jak-STAT, mTOR, and TGF-β signaling pathways were mainly related to melanogenesis and plume color. The findings of this study supported important information for the evaluation and protection of chicken genetic resources and help to analyze the unique genetic phenotypes such as melanin deposition and feather color of Lueyang black-bone chicken. Additionally, it could provide basic research data for the improvement and breeding of Lueyang black-bone chicken with characteristic traits.
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Affiliation(s)
- Zhen Xue
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, Shaanxi, China
| | - Ling Wang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, Shaanxi, China; Engineering Research Center of quality improvement and safety control of Qinba special meat products, Universities of Shaanxi Province, Hanzhong 723001, Shaanxi, China; QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C., Shaanxi University of Technology, Hanzhong 723001 Shaanxi, China; Shaanxi Union Research Center of University and Enterprise for Zhenba Bacon, Hanzhong 723001, Shaanxi, China
| | - Yingmin Tian
- School of Mathematics and Computer Science, Shaanxi University of Technology, Hanzhong 723001, Shaanxi, China
| | - Yufei Yang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, Shaanxi, China
| | - Pan Li
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, Shaanxi, China
| | - Ge Yang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, Shaanxi, China
| | - Hongzhao Lu
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, Shaanxi, China; Engineering Research Center of quality improvement and safety control of Qinba special meat products, Universities of Shaanxi Province, Hanzhong 723001, Shaanxi, China; Shaanxi Union Research Center of University and Enterprise for Zhenba Bacon, Hanzhong 723001, Shaanxi, China
| | - Shanshan Wang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, Shaanxi, China; Engineering Research Center of quality improvement and safety control of Qinba special meat products, Universities of Shaanxi Province, Hanzhong 723001, Shaanxi, China; QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C., Shaanxi University of Technology, Hanzhong 723001 Shaanxi, China; Shaanxi Union Research Center of University and Enterprise for Zhenba Bacon, Hanzhong 723001, Shaanxi, China
| | - Wenxian Zeng
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, Shaanxi, China; Engineering Research Center of quality improvement and safety control of Qinba special meat products, Universities of Shaanxi Province, Hanzhong 723001, Shaanxi, China; Qinba State Key Laboratory of Biological Resources and Ecological Environment, Hanzhong 723001, Shaanxi, China
| | - Tao Zhang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong 723001, Shaanxi, China; Engineering Research Center of quality improvement and safety control of Qinba special meat products, Universities of Shaanxi Province, Hanzhong 723001, Shaanxi, China; QinLing-Bashan Mountains Bioresources Comprehensive Development C. I. C., Shaanxi University of Technology, Hanzhong 723001 Shaanxi, China; Shaanxi Union Research Center of University and Enterprise for Zhenba Bacon, Hanzhong 723001, Shaanxi, China; Qinba State Key Laboratory of Biological Resources and Ecological Environment, Hanzhong 723001, Shaanxi, China.
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Jin S, Xia J, Jia F, Jiang L, Wang X, Liu X, Liu X, Geng Z. Complete Mitochondrial Genome, Genetic Diversity and Phylogenetic Analysis of Pingpu Yellow Chicken ( Gallus gallus). Animals (Basel) 2022; 12:3037. [PMID: 36359161 PMCID: PMC9654125 DOI: 10.3390/ani12213037] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2022] [Revised: 10/27/2022] [Accepted: 10/31/2022] [Indexed: 09/11/2023] Open
Abstract
In this study, the complete mitochondrial genome sequence of one female Pingpu Yellow chicken (PYC) and the D-loop sequences obtained from 60 chickens were analyzed to investigate their genetic diversity and phylogeny. The total length of the PYC mitogenome is 16,785 bp and that of the complete D-loop is 1231 to 1232 bp. The mitogenome comprises 22 transfer ribonucleic acids (tRNAs), 2 ribosomal ribonucleic acids (rRNAs), 13 protein-coding genes (PCGs), and 1 non-coding control region (D-loop). Additionally, the total length of the 13 PCGs is 11,394 bp, accounting for 67.88% of the complete mitogenome sequence, and the PCGs region has 3798 codons. A majority of the PCGs have ATG as the start codon. The haplotype and nucleotide diversity of PYC were 1.00000 ± 0.00029 and 0.32678 ± 0.29756, respectively. In the D-Loop data set, we found 25 polymorphic sites, which determined 18 haplotypes and 3 major haplogroups (A-C). Therefore, PYC has a classical vertebrate mitogenome, with comparatively high nucleotide diversity and potentially three maternal lineages. The neighbor-joining (NJ) tree analysis results showed PYC grouped with the Luhua (MT555049.1) and Nandan chickens (KP269069.1), which indicates that PYC is closely related to these two breeds.
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Affiliation(s)
- Sihua Jin
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Anhui Provincial Key Laboratory of Local Animal Genetic Resources Conservation and Bio-Breeding, Hefei 230036, China
| | - Jingjing Xia
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Anhui Provincial Key Laboratory of Local Animal Genetic Resources Conservation and Bio-Breeding, Hefei 230036, China
| | - Fumin Jia
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Anhui Provincial Key Laboratory of Local Animal Genetic Resources Conservation and Bio-Breeding, Hefei 230036, China
| | - Lijun Jiang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Anhui Provincial Key Laboratory of Local Animal Genetic Resources Conservation and Bio-Breeding, Hefei 230036, China
| | - Xin Wang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Anhui Provincial Key Laboratory of Local Animal Genetic Resources Conservation and Bio-Breeding, Hefei 230036, China
| | - Xuling Liu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Anhui Provincial Key Laboratory of Local Animal Genetic Resources Conservation and Bio-Breeding, Hefei 230036, China
| | - Xing Liu
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Anhui Provincial Key Laboratory of Local Animal Genetic Resources Conservation and Bio-Breeding, Hefei 230036, China
| | - Zhaoyu Geng
- College of Animal Science and Technology, Anhui Agricultural University, Hefei 230036, China
- Anhui Provincial Key Laboratory of Local Animal Genetic Resources Conservation and Bio-Breeding, Hefei 230036, China
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Zhang S, Zhang J, Cao C, Cai Y, Li Y, Song Y, Bao X, Zhang J. Effects of Different Rearing Systems on Lueyang Black-Bone Chickens: Meat Quality, Amino Acid Composition, and Breast Muscle Transcriptome. Genes (Basel) 2022; 13:genes13101898. [PMID: 36292783 PMCID: PMC9601429 DOI: 10.3390/genes13101898] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Revised: 10/07/2022] [Accepted: 10/17/2022] [Indexed: 11/16/2022] Open
Abstract
The quality of poultry products depends on genotype, rearing system, and environment. The aim of this study was to investigate the effects of different rearing systems on meat quality, amino acid composition, and breast muscle transcriptome from Lueyang black-bone chickens. Lueyang black-bone chickens (n = 900) were randomly divided into three groups (cage, flat-net, and free-range groups), with three replicates per group (100 chickens per replicate). At 16 weeks, a total of 36 healthy chickens (six males and six females per group) were collected, and their breast muscles were sampled to detect meat quality parameters, amino acid composition, and fatty acid contents. Furthermore, breast muscles from six random hens in each group were used for RNA-seq analysis. The results revealed that the values of pH, shear force, inosine monophosphate (IMP), palmitic acid, and linoleic acid in the free-range group were significantly higher than those in the caged group (p < 0.05). Fat content in the free-range group was significantly lower than in the caged and flat-net groups (p < 0.05). Glutamate (Glu) levels, the amino acid crucial for the umami taste, was significantly higher in the free-range group than in the caged group (p < 0.05). Meanwhile, there was no significant difference between the free-range and flat-net groups (p > 0.05). The breast muscle transcriptome results showed that there were 291, 131, and 387 differently expressed genes (DEGs) among the three comparison groups (caged vs. free-range, flat-net vs. caged, and flat-net vs. free-range, respectively) that were mainly related to muscle development and amino acid metabolism pathways. To validate the accuracy of the transcriptome data, eight genes (GOS2, ASNS, NMRK2, GADL1, SMTNL2, SLC7A5, AMPD1, and GLUL) which relate to fat deposition, skeletal muscle function, and flavor formation were selected for Real-time Quantitative PCR (RT-qPCR) verification. In conclusion, these results suggested that rearing systems significantly influenced the meat quality and gene expression of Lueyang black-bone chickens. All the data proved that free-range and flat-net systems may provide better flavor to consumers by affecting the deposition of flavor substances and the expression of related genes. These findings will provide a valuable theoretical basis for the rearing system selection in the poultry industry.
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Yang X, E GX, Yang BG, Liu CL, Guo Y, Gong Y, Chen BE, Zhang DP, Li MH. Genetic Diversity and Phylogeny Pattern across Chongqing (China) Chicken Populations Using mtDNA D-Loop Sequences. RUSS J GENET+ 2022. [DOI: 10.1134/s1022795422080117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Hata A, Nunome M, Suwanasopee T, Duengkae P, Chaiwatana S, Chamchumroon W, Suzuki T, Koonawootrittriron S, Matsuda Y, Srikulnath K. Origin and evolutionary history of domestic chickens inferred from a large population study of Thai red junglefowl and indigenous chickens. Sci Rep 2021; 11:2035. [PMID: 33479400 PMCID: PMC7820500 DOI: 10.1038/s41598-021-81589-7] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2020] [Accepted: 01/07/2021] [Indexed: 01/29/2023] Open
Abstract
In this study, we aimed to elucidate the origin of domestic chickens and their evolutionary history over the course of their domestication. We conducted a large-scale genetic study using mitochondrial DNA D-loop sequences and 28 microsatellite DNA markers to investigate the diversity of 298 wild progenitor red junglefowl (Gallus gallus) across two subspecies (G. g. gallus and G. g. spadiceus) from 12 populations and 138 chickens from 10 chicken breeds indigenous to Thailand. Twenty-nine D-loop sequence haplotypes were newly identified: 14 and 17 for Thai indigenous chickens and red junglefowl, respectively. Bayesian clustering analysis with microsatellite markers also revealed high genetic diversity in the red junglefowl populations. These results suggest that the ancestral populations of Thai indigenous chickens were large, and that a part of the red junglefowl population gene pool was not involved in the domestication process. In addition, some haplogroups that are distributed in other countries of Southeast Asia were not observed in either the red junglefowls or the indigenous chickens examined in the present study, suggesting that chicken domestication occurred independently across multiple regions in Southeast Asia.
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Affiliation(s)
- Ayano Hata
- Laboratory of Avian Bioscience, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
- Tropical Animal Genetic Unit (TAGU), Department of Animal Science, Faculty of Agriculture, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Mitsuo Nunome
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Thanathip Suwanasopee
- Tropical Animal Genetic Unit (TAGU), Department of Animal Science, Faculty of Agriculture, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Prateep Duengkae
- Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand
| | - Soontorn Chaiwatana
- Department of National Parks, Wildlife and Plant Conservation, Chatuchak, Bangkok, 10900, Thailand
| | - Wiyada Chamchumroon
- Department of National Parks, Wildlife and Plant Conservation, Chatuchak, Bangkok, 10900, Thailand
| | - Takayuki Suzuki
- Laboratory of Avian Bioscience, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan
| | - Skorn Koonawootrittriron
- Tropical Animal Genetic Unit (TAGU), Department of Animal Science, Faculty of Agriculture, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand.
| | - Yoichi Matsuda
- Laboratory of Avian Bioscience, Department of Animal Sciences, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan.
- Avian Bioscience Research Center, Graduate School of Bioagricultural Sciences, Nagoya University, Nagoya, Aichi, 464-8601, Japan.
| | - Kornsorn Srikulnath
- Laboratory of Animal Cytogenetics and Comparative Genomics (ACCG), Department of Genetics, Faculty of Science, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand.
- Special Research Unit for Wildlife Genomics, Department of Forest Biology, Faculty of Forestry, Kasetsart University, Chatuchak, Bangkok, 10900, Thailand.
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Zang H, Wang Y, Yang HH, He PL, Pan SQ, Geng ZY, Jin SH. Characterisation of the complete mitochondrial genome, genetic diversity and maternal origin of Huainan Partridge chicken. Br Poult Sci 2021; 62:320-327. [PMID: 33263413 DOI: 10.1080/00071668.2020.1855628] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
1. The objectives of the present study were to investigate the complete mitochondrial genome, genetic diversity and maternal origin of Huainan Partridge chicken (HPC).2. One complete mitochondrial genome and 37 complete D-loop regions of HPC were sequenced. Moreover, 400 mitochondrial genome D-loop sequences of Chinese native chicken were downloaded from the National Centre for Biotechnology Information database.3. The complete HPC genome was 16,785 bp in size, including 22 tRNA genes, two rRNA genes, 13 protein-coding genes and one non-coding control region. The haplotype diversity and nucleotide diversity of HPC were 0.964, and 0.00615, respectively. Twenty-three variable sites defining 22 haplotypes were identified, and the 22 haplotypes were distributed into three haplogroups (A, B, and C).4. In conclusion, HPC has a typical vertebrate mitochondrial genome, relatively high haplotype diversity, relatively low nucleotide diversity, and potentially three maternal lineages. HPC showed considerable genetic information exchange with Southwest Chinese chicken populations and had not admixed with European commercial breeds in the course of domestication.
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Affiliation(s)
- H Zang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China.,Department of Poultry Genetics and Breeding, Anhui Provincial Key Laboratory of Local Animal Genetic Resources Conservation and Bio-breeding, Hefei, China
| | - Y Wang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China.,Department of Poultry Genetics and Breeding, Anhui Provincial Key Laboratory of Local Animal Genetic Resources Conservation and Bio-breeding, Hefei, China
| | - H H Yang
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - P L He
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - S Q Pan
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China
| | - Z Y Geng
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China.,Department of Poultry Genetics and Breeding, Anhui Provincial Key Laboratory of Local Animal Genetic Resources Conservation and Bio-breeding, Hefei, China
| | - S H Jin
- College of Animal Science and Technology, Anhui Agricultural University, Hefei, China.,Department of Poultry Genetics and Breeding, Anhui Provincial Key Laboratory of Local Animal Genetic Resources Conservation and Bio-breeding, Hefei, China
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Pal A, Pal A, Mallick AI, Biswas P, Chatterjee PN. Molecular characterization of Bu-1 and TLR2 gene in Haringhata Black chicken. Genomics 2020; 112:472-483. [PMID: 30902756 DOI: 10.1016/j.ygeno.2019.03.010] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2018] [Revised: 02/17/2019] [Accepted: 03/18/2019] [Indexed: 11/21/2022]
Abstract
Haringhata Black is the only registered indigenous poultry genetic resource of West Bengal till date. Molecular characterization of HB revealed that Bu-1 to be highly glycoylated transmembrane protein unlike mammalian Bu-1, whereas TLR2 of HB chicken was observed to be rich in Leucine rich repeat. HB chicken was observed to be genetically close to chicken of Japan, while distant to chicken breed of UK and Chicago. Avian species wise evolution study indicates genetic closeness of HB chicken with turkey. Differential mRNA expression profile for the immune response genes (TLR2, TLR4 and Bu1 gene) were studied for HB chicken with respect to other chicken breed and poultry birds, which reveals that HB chicken were better in terms of B cell mediated immunity and hence better response to vaccination. Hence HB chicken is one of the best poultry genetic resources to be reared under backyard system where biosecurity measures are almost lacking.
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Affiliation(s)
- Aruna Pal
- West Bengal University of Animal and Fishery Sciences, 37, K.B. Sarani, Kolkata 37, India.
| | - Abantika Pal
- Indian Institute of technology, Kharagpur, West Bengal, India
| | | | - P Biswas
- West Bengal University of Animal and Fishery Sciences, 37, K.B. Sarani, Kolkata 37, India
| | - P N Chatterjee
- West Bengal University of Animal and Fishery Sciences, 37, K.B. Sarani, Kolkata 37, India
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Yang G, Lu H, Wang L, Zhao J, Zeng W, Zhang T. Genome-Wide Identification and Transcriptional Expression of the METTL21C Gene Family in Chicken. Genes (Basel) 2019; 10:genes10080628. [PMID: 31434291 PMCID: PMC6723737 DOI: 10.3390/genes10080628] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 08/06/2019] [Accepted: 08/15/2019] [Indexed: 12/31/2022] Open
Abstract
The chicken is a common type of poultry that is economically important both for its medicinal and nutritional values. Previous studies have found that free-range chickens have more skeletal muscle mass. The methyltransferase-like 21C gene (METTL21C) plays an important role in muscle development; however, there have been few reports on the role of METTL21C in chickens. In this study, we performed a genome-wide identification of chicken METTL21C genes and analyzed their phylogeny, transcriptional expression profile, and real-time quantitative polymerase chain reaction (qPCR). We identified 10 GgMETTL21C genes from chickens, 11 from mice, and 32 from humans, and these genes were divided into six groups, which showed a large amount of variation among these three species. A total of 15 motifs were detected in METTL21C genes, and the intron phase of the gene structure showed that the METTL21C gene family was conservative in evolution. Further, both the transcript data and qPCR showed that a single gene’s (GgMETTL21C3) expression level increased with the muscle development of chickens, indicating that the METTL21C genes are involved in the development of chicken muscles. Our results provide some reference value for the subsequent study of the function of METTL21C.
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Affiliation(s)
- Ge Yang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi 723001, China
| | - Hongzhao Lu
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi 723001, China
| | - Ling Wang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi 723001, China
| | - Jiarong Zhao
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi 723001, China
| | - Wenxian Zeng
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi 723001, China
| | - Tao Zhang
- School of Biological Science and Engineering, Shaanxi University of Technology, Hanzhong, Shaanxi 723001, China.
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