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Study on the muscle transcriptome of two diverse Indian backyard poultry breeds acclimatized to different agro-ecological conditions. Mol Biol Rep 2023; 50:2453-2461. [PMID: 36598628 DOI: 10.1007/s11033-022-08223-1] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Accepted: 12/19/2022] [Indexed: 01/05/2023]
Abstract
OBJECTIVE Free-range (FR) poultry production systems are associated with quality products and improved welfare. All the 19 diverse chicken breeds of India have evolved under the FR system and are adapted to different agro-climatic conditions. It is vital to explore indigenous germplasm with modern genomic tools to have insights into genomic characteristics of production traits and adaptation. METHODS In this study, breast tissue transcriptome profiles were generated and analyzed from four biological replicates of two indigenous backyard poultry breeds of India-Ankaleshwar, a breed of the mainland, and Nicobari, a breed adapted to islands. The read quality of sequences was checked by FASTQC and processed reads were aligned to the reference genome (bGalGal1). RESULTS More than 94% mapping to the reference genome was observed for all samples. A total of 12,790 transcripts were common across both groups, while 657 were expressed only in Ankaleshwar and 169 in Nicobari. The highest expressed genes across both groups were associated mainly with muscle structure, contraction, and energy metabolism. The highly expressed genes identified in Ankaleshwar were involved in fatty acid catabolism and oxidative stress mitigation. Functional terms, pathways, and hub genes in Nicobari participated in muscle fiber growth, adipogenesis, and fatty acid anabolism. A key hub gene (RAC1) in Nicobari is a potential candidate affecting the laying rate in chickens. The qRT-PCR results also substantiate the RNA-seq results. CONCLUSION The findings provide a precious molecular resource to advance understanding of the genetic basis of adaptation, meat quality, and egg production in backyard chickens.
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Removal of roosters alters the domestic phenotype and microbial and genetic profile of hens. SCIENCE CHINA-LIFE SCIENCES 2021; 64:1964-1976. [PMID: 33587265 DOI: 10.1007/s11427-020-1770-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/01/2020] [Accepted: 07/14/2020] [Indexed: 12/15/2022]
Abstract
Hens are raised apart from roosters in modern poultry production, a substantial change from their natural social structure. We compared productivity, injuries, behavior, physiology, microbiome and transcriptome of hens housed with (R+) or without (R-) roosters to quantify the effects of this change in social structure. Hens were raised free-range from 70 to 280 days when 30 birds per treatment were assigned to battery cages until Day 315 (R+C vs. R-C), while 30 birds per treatment remained in free-range pens (R+F vs. R-F). Response to a novel environment and object, behavioral time budgets, cecum microbiome, blood composition and transcriptomic sequencing of thigh muscle and spleen were analyzed. Hens housed without roosters showed better survival, consumed less food, produced more eggs and had better feed conversion. R+F hens clustered around the rooster and were less mobile in the novel environment and object tests. R+F hens displayed the richest microbiome, and the presence of roosters resulted in differentially expressed genes related to muscle development, cellular processes, environmental information processing and immune function. Removing roosters from housed hens intensified desirable characteristics favored by domestication probably operating by deprivation of mating behavior and reduced fear, along with altered microbial and genetic function.
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Hu S, Cheng L, Wang J, Li L, He H, Hu B, Ren X, Hu J. Genome-wide transcriptome profiling reveals the mechanisms underlying muscle group-specific phenotypic changes under different raising systems in ducks. Poult Sci 2020; 99:6723-6736. [PMID: 33248588 PMCID: PMC7704955 DOI: 10.1016/j.psj.2020.09.027] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2020] [Revised: 08/23/2020] [Accepted: 09/03/2020] [Indexed: 11/26/2022] Open
Abstract
Although a number of nongenetic factors have been reported to be able to modulate skeletal muscle phenotypes in meat-type birds, neither the underlying mechanisms nor the muscle group–specific phenotypic and molecular responses have been fully understood. In the present study, a total of 240 broiler ducks were used to compare the effects of floor raising system (FRS) and net raising system (NRS) on the physicochemical properties and global gene expression profiles of both breast and thigh muscles at the posthatching week 4 (W4), W8, and W13. Our results showed that compared with FRS, NRS generally induced higher pH, lower lightness (L∗) and yellowness (b∗), lower drip loss and cooking loss, and lower shear force in either breast or thigh muscles during early posthatching stages but subsequently showed less pronounced or even reverse effects. Meanwhile, it was observed that the raising system differently changed the myofiber characteristics depending on the muscle group and the developmental stage. Genome-wide transcriptome analysis showed that compared with FRS, NRS induced the most extensive gene expression changes in breast muscle (BM) at W4 but in thigh muscle (TM) at W13, suggesting the asynchronous molecular responses of BM and TM to the raising system and period. Most of differentially expressed genes in either BM or TM between NRS and FRS were enriched in the Gene Ontology and Kyoto Encyclopedia of Genes and Genomes terms associated with regulation of muscle cellular functions, metabolic and contractile activities, and tissue remodeling, indicating similar molecular mechanisms principally responsible for the raising system-caused phenotypic changes in both muscle groups. Nevertheless, several crucial pathways (e.g., adipocytokine signaling, AGE-RAGE signaling, and apoptosis) and genes (e.g., ANO6, ACER2, UCP3, DTL, and TMEM120A) were tightly related to the muscle group–specific adaptive remodeling on different raising systems. These data could not only contribute to a better understanding of the molecular mechanisms behind meat quality but also provide novel insights into the molecular causes of the muscle group–specific adaptive remodeling in response to environmental stimuli.
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Affiliation(s)
- Shenqiang Hu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Chengdu Campus, Sichuan Agricultural University 611130, Chengdu, China
| | - Lumin Cheng
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Chengdu Campus, Sichuan Agricultural University 611130, Chengdu, China
| | - Jiwen Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Chengdu Campus, Sichuan Agricultural University 611130, Chengdu, China.
| | - Liang Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Chengdu Campus, Sichuan Agricultural University 611130, Chengdu, China
| | - Hua He
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Chengdu Campus, Sichuan Agricultural University 611130, Chengdu, China
| | - Bo Hu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Chengdu Campus, Sichuan Agricultural University 611130, Chengdu, China
| | - Xufang Ren
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Chengdu Campus, Sichuan Agricultural University 611130, Chengdu, China
| | - Jiwei Hu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Chengdu Campus, Sichuan Agricultural University 611130, Chengdu, China
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Chen S, Yan C, Xiang H, Xiao J, Liu J, Zhang H, Wang J, Liu H, Zhang X, Ou M, Chen Z, Li W, Turner SP, Zhao X. Transcriptome changes underlie alterations in behavioral traits in different types of chicken. J Anim Sci 2020; 98:5841043. [PMID: 32432320 DOI: 10.1093/jas/skaa167] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2019] [Accepted: 05/14/2020] [Indexed: 12/16/2022] Open
Abstract
In recent decades, artificial selection has contributed greatly to meeting the demands for animal meat, eggs, and milk. However, it has also resulted in changes in behavior, metabolic and digestive function, and alterations in tissue development, including the brain and skeleton. Our study aimed to profile the behavioral traits and transcriptome pattern of chickens (broilers, layers, and dual-purpose breeds) in response to artificial selection. Broilers spent less time gathered as a group in a novel arena (P < 0.01), suggesting reduced fearfulness in these birds. Broilers also showed a greater willingness to approach a model predator during a vigilance test but had a greater behavioral response when first exposed to the vocalization of the predator. Genes found to be upregulated and downregulated in previous work on chickens divergently selected for fear responses also showed consistent differences in expression between breeds in our study and indicated a reduction in fearfulness in broilers. Gene ACTB_G1 (actin) was differentially expressed between breeds and is a candidate gene involved with skeletal muscle growth and disease susceptibility in broilers. Furthermore, breed-specific alterations in the chicken domestic phenotype leading to differences in growth and egg production were associated with behavioral changes, which are probably underpinned by alterations in gene expression, gene ontology terms, and Kyoto Encyclopedia of Genes and Genomes pathways. The results highlight the change in behavior and gene expression of the broiler strain relative to the layer and a dual-purpose native breed.
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Affiliation(s)
- Siyu Chen
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, China.,College of Animal Science and Technology, China Agricultural University, Beijing, China.,Guizhou Nayong Professor Workstation of China Agricultural University, Bijie, China
| | - Chao Yan
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,Guizhou Nayong Professor Workstation of China Agricultural University, Bijie, China
| | - Hai Xiang
- College of Animal Science and Technology, China Agricultural University, Beijing, China.,Guizhou Nayong Professor Workstation of China Agricultural University, Bijie, China
| | - Jinlong Xiao
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jian Liu
- Guizhou Nayong Professor Workstation of China Agricultural University, Bijie, China
| | - Hui Zhang
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jikun Wang
- Key Laboratory of Qinghai-Tibetan Plateau Animal Genetic Resource Reservation and Utilization, Ministry of Education; Institute of Qinghai-Tibetan Plateau, Southwest University for Nationalities, Chengdu, China
| | - Hao Liu
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xiben Zhang
- Guizhou Nayong Professor Workstation of China Agricultural University, Bijie, China
| | - Maojun Ou
- Guizhou Nayong Professor Workstation of China Agricultural University, Bijie, China
| | - Zelin Chen
- Guizhou Nayong Professor Workstation of China Agricultural University, Bijie, China
| | - Weibo Li
- Guizhou Nayong Professor Workstation of China Agricultural University, Bijie, China
| | - Simon P Turner
- Animal and Veterinary Sciences Department, Scotland's Rural College, Edinburgh, UK
| | - Xingbo Zhao
- Guangdong Provincial Key Laboratory of Animal Molecular Design and Precise Breeding, School of Life Science and Engineering, Foshan University, Foshan, China.,College of Animal Science and Technology, China Agricultural University, Beijing, China.,Guizhou Nayong Professor Workstation of China Agricultural University, Bijie, China
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Cheng Y, Sihua Z, Lu Q, Zhang W, Wen G, Luo Q, Shao H, Zhang T. Evaluation of young chickens challenged with aerosolized Salmonella Pullorum. Avian Pathol 2020; 49:507-514. [PMID: 32543216 DOI: 10.1080/03079457.2020.1783433] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
Abstract
Salmonella enterica serovar Pullorum (S. Pullorum) is an important pathogen specific to avian species, which poses a serious threat to the poultry industry. The transmission of S. Pullorum occurs both horizontally and vertically but the airborne transmission of S. Pullorum has been neglected historically. In this study, the effects of aerosolized S. Pullorum on young chickens were investigated. The results showed that the colonization and morbidity induced by bioaerosol infection are dose dependent. The bacteria colonized in chicken lung for more than 14 days following the exposure to ≥ 1.25 × 106 CFU/m3 of aerosolized S. Pullorum. Tachypnoea and depression were present in all the chickens between 5 and 7 days after infection, and some died, following the exposure to ≥1.25 × 108 CFU/m3 of aerosolized S. Pullorum. RT-PCR results showed that significant expressions of inflammatory cytokines, including tumour necrosis factor α, interleukin 1β (IL-1β), IL-6, and IL-8 were noted in the lung and spleen. Histopathological examination showed lung swelling, with obvious lesions, including inflammatory cell infiltration, tissue injury, and acute haemorrhage. These results suggest that uncontrolled and detrimental inflammation is caused by a high dose of aerosolized S. Pullorum. These results further extend our understanding of the pathogenicity of air-transmitted S. Pullorum on chickens. RESEARCH HIGHLIGHTS Aerosolized S. Pullorum caused tachypnoea, depression, and lung swelling in chickens. The colonization and morbidity caused by aerosolized S. Pullorum are dose dependent. Detrimental inflammation is caused by high doses of aerosolized S. Pullorum in lung.
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Affiliation(s)
- Yiluo Cheng
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, People's Republic of China
| | - Zhang Sihua
- Wuhan Animal Disease Prevention and Control Center, Wuhan, People's Republic of China
| | - Qin Lu
- Hubei Provincial Key Laboratory of Animal Pathogenic Microbiology, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, People's Republic of China
| | - Wenting Zhang
- Hubei Provincial Key Laboratory of Animal Pathogenic Microbiology, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, People's Republic of China
| | - Guoyuan Wen
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, People's Republic of China
| | - Qingping Luo
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, People's Republic of China
| | - Huabin Shao
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, People's Republic of China.,Hubei Provincial Key Laboratory of Animal Pathogenic Microbiology, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, People's Republic of China
| | - Tengfei Zhang
- Key Laboratory of Prevention and Control Agents for Animal Bacteriosis, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, People's Republic of China.,Hubei Provincial Key Laboratory of Animal Pathogenic Microbiology, Institute of Animal Husbandry and Veterinary, Hubei Academy of Agricultural Sciences, Wuhan, People's Republic of China
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Qiaoxian Y, Hui C, Yingjue X, Chenxuan H, Jianzhong X, Rongyan Z, Lijun X, Han W, Ye C. Effect of housing system and age on products and bone properties of Taihang chickens. Poult Sci 2020; 99:1341-1348. [PMID: 32111310 PMCID: PMC7587717 DOI: 10.1016/j.psj.2019.10.052] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2019] [Revised: 10/15/2019] [Accepted: 10/18/2019] [Indexed: 11/24/2022] Open
Abstract
The aim of this study was to compare egg quality, carcass, meat characteristics, and bone properties of Taihang chickens in 2 different housing systems at various ages. A total of 168 birds were selected and randomly allocated to 2 groups at 23 wks and raised in conventional cage (CC) or flattening on floor (FF) housing system, respectively. FF hens' egg weight, albumen height, and Haugh unit were higher (P < 0.05), and yolk weight was lower (P < 0.001) than those of the CC hens. Egg quantity of FF hens was higher than that of the CC hens (P < 0.01). The FF hens' weight (P < 0.05) and breast meat percent (P < 0.01) were higher than those of the CC hens. The highest live body and carcass weight were observed at 57 wk (both P < 0.01), whereas the highest semieviscerated percentage (P < 0.01) and meat weight of breast and thigh (P < 0.05) were shown at 49 wk. The highest eviscerated percentage and thigh meat were displayed at 41 and 32 wk, respectively (P < 0.01). For meat color, the lightness of both breast and thigh meat in the FF group was significantly reduced compared with those of the CC group (P < 0.01 and P < 0.05). FF hens' humerus weight and breaking strength (both P < 0.01) and tibia breaking strength (P < 0.05) were significantly higher than those of the CC hens. Femur breaking strength was significantly affected by hens' age (P < 0.01). Egg weight, albumen height, Haugh unit, yolk color (all P < 0.01), pH of thigh meat, semieviscerated, and eviscerated weight (all P < 0.05) were influenced by the interaction of housing system and age, whereas no change in moisture loss rate, meat color, shearing force, and bone quality was found (P > 0.05). In summary, in the 2 housing systems, hens' age and their interaction could affect slaughter performance, quality of egg, meat, and bone of Taihang chickens. In addition, the results of the present study support a theoretical basis for the development and utilization of Taihang chickens in accordance with the FF system.
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Affiliation(s)
- Yue Qiaoxian
- College of Animal Science and Technology,Hebei Agricultural University, Baoding 071000, China
| | - Chen Hui
- College of Animal Science and Technology,Hebei Agricultural University, Baoding 071000, China
| | - Xu Yingjue
- College of Animal Science and Technology,Hebei Agricultural University, Baoding 071000, China
| | - Huang Chenxuan
- College of Animal Science and Technology,Hebei Agricultural University, Baoding 071000, China
| | - Xi Jianzhong
- College of Animal Science and Technology,Hebei Agricultural University, Baoding 071000, China
| | - Zhou Rongyan
- College of Animal Science and Technology,Hebei Agricultural University, Baoding 071000, China.
| | - Xu Lijun
- Baoding Municipal Bureau of Agriculture, Baoding 071000, China
| | - Wang Han
- College of Animal Science and Technology,Hebei Agricultural University, Baoding 071000, China
| | - Chen Ye
- College of Animal Science and Technology,Hebei Agricultural University, Baoding 071000, China
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7
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Chen S, Xiang H, Zhang H, Zhu X, Wang D, Wang J, Yin T, Liu L, Kong M, Li H, Zhao X. Rearing system causes changes of behavior, microbiome, and gene expression of chickens. Poult Sci 2019; 98:3365-3376. [PMID: 30916350 DOI: 10.3382/ps/pez140] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/09/2018] [Accepted: 03/11/2019] [Indexed: 12/26/2022] Open
Abstract
It has been long demonstrated that cage rearing (CR) deprives the animal of the possibility to express natural behaviors and results in stress. However, the effect of the rearing system on gene expression and the molecular levels of the gut microbiome are unknown. 10-wk-old Beijing You chickens were studied in parallel CR and free-range (FR) systems for 30 wk, to investigate the effect of rearing systems on behavior, microbiota composition, and gene expression. From week 40, a match-mismatch design was conducted for 5 wk. The results indicated that CR deprives the animals of natural behaviors, evidenced by sham dust-bathing behavior. A decreased alpha diversity of gut microbiome composition of CR chickens was seen in FR compared to CR-FR chickens (P < 0.001), and the alpha diversity of gut microbiome composition of FR-CR was decreased as compared to FR chickens (P = 0.045). The heat map and beta-diversity analysis showed that the cluster of gut microbial compositions were similar between the mismatch groups (FR-CR and CR-FR), while those of CR showed the lowest diversity from the 4 groups. The relative abundance of gut microbes at genera and species levels was different between comparisons (P < 0.05). Moreover, the CR (both CR and FR-CR) triggered the downregulation of most Kyoto encyclopedia of genes and genomes pathways, while it was upregulated in 2 genetic information processing pathways, compared to FR hens regardless of long or short term. In conclusion, CR deprived chickens of their normal behavior and resulted in changes in the microbiome diversity and pathways and gene expression of chickens.
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Affiliation(s)
- Siyu Chen
- School of Life Science and Engineering, Foshan University, Foshan 528225, China.,College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Hai Xiang
- School of Life Science and Engineering, Foshan University, Foshan 528225, China.,College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Hui Zhang
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Xu Zhu
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Dan Wang
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Jikun Wang
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Tao Yin
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Langqing Liu
- College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Minghua Kong
- School of Life Science and Engineering, Foshan University, Foshan 528225, China.,College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Hua Li
- School of Life Science and Engineering, Foshan University, Foshan 528225, China
| | - Xingbo Zhao
- School of Life Science and Engineering, Foshan University, Foshan 528225, China.,College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
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