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Fang W, Wang E, Liu P, Gao X, Hou X, Hu G, Li G, Cheng J, Jiang C, Yan L, Wu C, Xu Z, Liu P. The relativity analysis of hypoxia inducible factor-1α in pulmonary arterial hypertension (ascites syndrome) in broilers: a review. Avian Pathol 2024:1-10. [PMID: 38887084 DOI: 10.1080/03079457.2024.2358882] [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: 12/27/2023] [Accepted: 05/17/2024] [Indexed: 06/20/2024]
Abstract
Ascites syndrome (AS) in broiler chickens, also known as pulmonary arterial hypertension (PAH), is a significant disease in the poultry industry. It is a nutritional metabolic disease that is closely associated with hypoxia-inducible factors and rapid growth. The rise in pulmonary artery pressure is a crucial characteristic of AS and is instrumental in its development. Hypoxia-inducible factor 1α (HIF-1α) is an active subunit of a key transcription factor in the oxygen-sensing pathway. HIF-1α plays a vital role in oxygen homeostasis and the development of pulmonary hypertension. Studying the effects of HIF-1α on pulmonary hypertension in humans or mammals, as well as ascites in broilers, can help us understand the pathogenesis of AS. Therefore, this review aims to (1) summarize the mechanism of HIF-1α in the development of pulmonary hypertension, (2) provide theoretical significance in explaining the mechanism of HIF-1α in the development of pulmonary arterial hypertension (ascites syndrome) in broilers, and (3) establish the correlation between HIF-1α and pulmonary arterial hypertension (ascites syndrome) in broilers. HIGHLIGHTSExplains the hypoxic mechanism of HIF-1α.Linking HIF-1α to pulmonary hypertension in broilers.Explains the role of microRNAs in pulmonary arterial hypertension in broilers.
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Affiliation(s)
- Weile Fang
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, People's Republic of China
| | - Enqi Wang
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, People's Republic of China
| | - Pei Liu
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, People's Republic of China
| | - Xiaona Gao
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, People's Republic of China
| | - Xiaolu Hou
- Guangxi Vocational University of Agriculture, Nanning, People's Republic of China
| | - Guoliang Hu
- Guangxi Vocational University of Agriculture, Nanning, People's Republic of China
| | - Guyue Li
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, People's Republic of China
| | - Juan Cheng
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, People's Republic of China
| | - Chenxi Jiang
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, People's Republic of China
| | - Linjie Yan
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, People's Republic of China
| | - Cong Wu
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, People's Republic of China
| | - Zheng Xu
- Department of Mathematics and Statistics, Wright State University, Dayton, OH, USA
| | - Ping Liu
- Jiangxi Provincial Key Laboratory for Animal Health, Institute of Animal Population Health, College of Animal Science and Technology, Jiangxi Agricultural University, Nanchang, People's Republic of China
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Li H, Chen Y. Whole-genome resequencing to explore genome‑wide single nucleotide polymorphisms and genes associated with avian leukosis virus subgroup J infection in chicken. 3 Biotech 2023; 13:417. [PMID: 38031589 PMCID: PMC10682322 DOI: 10.1007/s13205-023-03834-2] [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: 02/21/2023] [Accepted: 10/24/2023] [Indexed: 12/01/2023] Open
Abstract
Avian leukosis virus subgroup J (ALV-J) is an oncogenic virus that causes serious economic loss in the poultry industry. Currently, no effective vaccine or drug is available against this virus. Therefore, it is imperative to explore and understand the molecular regulatory mechanisms underlying ALV-J infection. In this study, blood samples from 21 ALV-J-infected and 22 ALV-J-uninfected (DZ) chickens (JZ) were analyzed by whole-genome resequencing (WGR). By combining the fixation index (FST) with the nucleotide diversity (π) ratio based on WGR data, 425 candidate genes were identified. Kyoto Encyclopedia of Genes and Genomes pathway enrichment analysis revealed the top 20 enriched pathways, among which 9 pathways were significantly associated with diseases, including endometrial cancer, Chagas disease, PD-L1 expression and PD-1 checkpoint pathway in cancer, colorectal cancer, endocrine resistance, fluid shear stress, atherosclerosis, basal cell carcinoma, non-small cell lung cancer, and melanoma. Fourteen single nucleotide polymorphisms related to twelve genes showed a notable difference between DZ and JZ group chickens. The genes included COMMD3, PPP1CB, VEGFA, GTF2H1, NOTCH2, ITPR1, FGFR4, GNAS, NECTIN1, WNT2B, PPP1CC, and MRC2. These findings may provide a valuable foundation for further exploration of the pathogenesis of ALV-J in chickens.
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Affiliation(s)
- Hongwei Li
- School of Life Science, Huizhou University, No. 46 Yanda Road, Huizhou, 516007 China
| | - Yuan Chen
- School of Life Science, Huizhou University, No. 46 Yanda Road, Huizhou, 516007 China
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Xiong X, Liu J, Rao Y. Whole Genome Resequencing Helps Study Important Traits in Chickens. Genes (Basel) 2023; 14:1198. [PMID: 37372379 DOI: 10.3390/genes14061198] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2023] [Revised: 05/23/2023] [Accepted: 05/25/2023] [Indexed: 06/29/2023] Open
Abstract
The emergence of high-throughput sequencing technology promotes life science development, provides technical support to analyze many life mechanisms, and presents new solutions to previously unsolved problems in genomic research. Resequencing technology has been widely used for genome selection and research on chicken population structure, genetic diversity, evolutionary mechanisms, and important economic traits caused by genome sequence differences since the release of chicken genome sequence information. This article elaborates on the factors influencing whole genome resequencing and the differences between these factors and whole genome sequencing. It reviews the important research progress in chicken qualitative traits (e.g., frizzle feather and comb), quantitative traits (e.g., meat quality and growth traits), adaptability, and disease resistance, and provides a theoretical basis to study whole genome resequencing in chickens.
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Affiliation(s)
- Xinwei Xiong
- Key Laboratory for Genetic Improvement of Indigenous Chicken Breeds of Jiangxi Province, Nanchang Normal University, Nanchang 330032, China
| | - Jianxiang Liu
- Key Laboratory for Genetic Improvement of Indigenous Chicken Breeds of Jiangxi Province, Nanchang Normal University, Nanchang 330032, China
| | - Yousheng Rao
- Key Laboratory for Genetic Improvement of Indigenous Chicken Breeds of Jiangxi Province, Nanchang Normal University, Nanchang 330032, China
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Qin Y, Yang J, Liang C, Liu J, Deng Z, Yan B, Fu Y, Luo Y, Li X, Wei X, Li W. Pan-cancer analysis identifies migrasome-related genes as a potential immunotherapeutic target: A bulk omics research and single cell sequencing validation. Front Immunol 2022; 13:994828. [PMID: 36405728 PMCID: PMC9669594 DOI: 10.3389/fimmu.2022.994828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022] Open
Abstract
Introduction The migrasome is a newly discovered organelle that resembles extracellular vesicles in structure. However, the function of the migrasome in tumors, particularly in relation to tumor immunity and tumor microenvironment, is unclear. Methods Gene expression data, copy number variation raw data, and methylation data of 33 cancer types were downloaded from The Cancer Genome Atlas database. Immunohistochemistry (IHC) based on 114 case of colorectal cancer was used to validate the expression of the migrasome hub-gene. We analyzed the expression, prognosis, genetic variation, and drug sensitivity profiles of migrasome-related genes (MRGs) in pan-cancer datasets. A migrasome score was constructed based on gene set enrichment analysis, and the correlation of migrasomes with the tumor microenvironment was assessed. The CancerSEA was used to perform a single-cell level functional analysis of the migrasome. Additionally, we also analyzed the correlation between migrasomes and tumor mutational burden (TMB), microsatellite instability (MSI), and tumor immune dysfunction and exclusion scores. Single-cell transcriptome sequencing (scRNA-seq) data was used to assess the activation state of migrasomes in the tumor microenvironment. Results PIGK expression was significantly up-regulated in 22 of 33 tumors, and high expression of migrasome was estimated to have contributed to poor prognosis. Missense mutations are the most common type of mutation in MRGs. We identified piperlongumine as a potential drug targeting migrasomes. The migrasome score was significantly and positively correlated with the tumor immunity score and the stroma score. In most tumors, the abundance of macrophages in the tumor microenvironment was significantly and positively correlated with the migrasome score. Additionally, the migrasome scores were significantly correlated with the immune checkpoint genes in pan-cancer as well as immune checkpoint therapy-related markers including TMB and MSI. According to scRNA-seq analysis, migrasome differed significantly among cells of the tumor microenvironment. IHC confirmed low expression of ITGA5 and PIGK in colorectal cancer. Discussion We performed the first pan-cancer analysis of migrasomes and discovered that they play an important role in tumor development and immune escape. Our study provides new insights into the role of migrasomes in tumor prognosis and immunotherapy.
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Affiliation(s)
- Yan Qin
- Department of Health Management, The People’s Hospital of Guangxi Zhuang Autonomous Region and Research center of Health Management, Guangxi Academy of Medical Sciences, Nanning, Guangxi, China
| | - Jie Yang
- Department of Health Management, The People’s Hospital of Guangxi Zhuang Autonomous Region and Research center of Health Management, Guangxi Academy of Medical Sciences, Nanning, Guangxi, China
| | - Cao Liang
- Department of Surgical Oncology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
| | - Jun Liu
- Department of Surgical Oncology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
| | - Zhixing Deng
- Department of Surgical Oncology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
| | - Binli Yan
- Department of Surgical Oncology, Guangxi Medical University Cancer Hospital, Nanning, Guangxi, China
| | - Ying Fu
- Department of Health Management, The People’s Hospital of Guangxi Zhuang Autonomous Region and Research center of Health Management, Guangxi Academy of Medical Sciences, Nanning, Guangxi, China
| | - Yinghua Luo
- Department of Health Management, The People’s Hospital of Guangxi Zhuang Autonomous Region and Research center of Health Management, Guangxi Academy of Medical Sciences, Nanning, Guangxi, China
| | - Xiaozhen Li
- Department of Health Management, The People’s Hospital of Guangxi Zhuang Autonomous Region and Research center of Health Management, Guangxi Academy of Medical Sciences, Nanning, Guangxi, China
- *Correspondence: Wei Li, ; Xiaoying Wei, ; Xiaozhen Li,
| | - Xiaoying Wei
- Department of Health Management, The People’s Hospital of Guangxi Zhuang Autonomous Region and Research center of Health Management, Guangxi Academy of Medical Sciences, Nanning, Guangxi, China
- *Correspondence: Wei Li, ; Xiaoying Wei, ; Xiaozhen Li,
| | - Wei Li
- Department of Health Management, The People’s Hospital of Guangxi Zhuang Autonomous Region and Research center of Health Management, Guangxi Academy of Medical Sciences, Nanning, Guangxi, China
- *Correspondence: Wei Li, ; Xiaoying Wei, ; Xiaozhen Li,
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Hossain ME, Akter N. Further insights into the prevention of pulmonary hypertension syndrome (ascites) in broiler: a 65-year review. WORLD POULTRY SCI J 2022. [DOI: 10.1080/00439339.2022.2090305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/17/2022]
Affiliation(s)
- Md. Emran Hossain
- Department of Animal Science and Nutrition, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Zakir Hossain Road, Khulshi, Bangladesh
| | - Nasima Akter
- Department of Dairy and Poultry Science, Faculty of Veterinary Medicine, Chattogram Veterinary and Animal Sciences University, Zakir Hossain Road, Khulshi, Bangladesh
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Lee KP, Anthony NB, Orlowski SK, Rhoads DD. SNP-based breeding for broiler resistance to ascites and evaluation of correlated production traits. Hereditas 2022; 159:9. [PMID: 35090566 PMCID: PMC8796538 DOI: 10.1186/s41065-022-00228-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/13/2022] [Indexed: 01/12/2023] Open
Abstract
Abstract
Background
The goal of this study was to evaluate marker-assisted selection (MAS) in broiler chickens using previously mapped gene regions associated with ascites syndrome incidence. The second-generation MAS products were assessed for impact on ascites phenotype and whether there were associated changes in important production traits. Previously, we used whole genome resequencing (WGR) to fine-map 28 chromosomal regions as associated with ascites phenotype in our experimental ascites broiler line (Relaxed, REL) based on a hypobaric chamber challenge. Genotypes for single nucleotide polymorphisms (SNPs) in mapped regions on chromosomes 2 and 22, were used for MAS in our REL line. After two generations, birds homozygous for the genotypes associated with resistance for both chromosomal regions were established. The MAS F2 generation was then compared to the REL line for ascites susceptibility and 25 production traits.
Results
Selection based on SNPs in the carboxypeptidase Q (CPQ, Gga2) and leucine rich repeat transmembrane neuronal 4 (LRRTM4, Gga22) gene regions resulted in a sex- and simulated altitude- dependent reduction of ascites incidence in two F2 cohorts of the MAS line. Comparisons of the F2 MAS and REL lines for production traits when reared at ambient pressure found no significant negative impacts for feed intake (FI), feed conversion ratio (FCR), or deboned part yields for either sex for two F2 cohorts. There were, however, improvements in the MAS for full-trial body weight gain (BWG), FCR, absolute and relative tender weights, and relative drumstick weight.
Conclusions
These results validate the mapping of the 28 chromosomal regions and demonstrate that fine mapping by WGR is an effective strategy for addressing a complex trait; it also stands as the first successful SNP-based selection program against a complex disease trait, such as ascites. The MAS line is comparable and, in some instances, superior, in growth performance to the REL control while being more resistant to ascites. This study indicates that MAS based on WGR can provide significant breeding potential in agricultural systems.
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Preparation of ribosomal protein S14 polyclonal antibody in broiler pulmonary artery: Its application in broiler ascites syndrome. Int J Biol Macromol 2021; 193:328-336. [PMID: 34699893 DOI: 10.1016/j.ijbiomac.2021.10.130] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2021] [Revised: 10/18/2021] [Accepted: 10/18/2021] [Indexed: 01/13/2023]
Abstract
RPS14 (ribosomal protein S14) gene maintains the normal physiological activities of the body by regulating the biosynthesis of ribosomes and the translation of important proteins. This study aims to explore the potential role of RPS14 in broiler ascites syndrome (BAS). We successfully prepared polyclonal antibody against RPS14 and studied the localization and expression of RPS14 protein in a variety of animal key tissues. In this experiment, the recombinant expression plasmid PET28a-RPS14 was constructed using the prokaryotic expression technology of foreign genes. Under the conditions of IPTG induction, a His-RPS14 protein with a molecular weight of about 22 kDa was expressed, and the purified recombinant protein was used as an antigen to prepare rabbit anti-chicken serum. Western blot results showed that the serum could specifically identify RPS14 protein in important tissues of broilers. Immunofluorescence combined with homology analysis showed that the antiserum had significant species specificity. Compared with other species, the expression of this protein in key tissues of broilers and ducks was more significant. More importantly, western blotting and immunofluorescence showed that BAS significantly reduced the expression level of RPS14. This further indicated that RPS14 protein can be used as one of the important entry points for BAS research.
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Zhang D, Zhang X, Li F, Liu T, Hu Z, Gao N, Yuan L, Li X, Zhao Y, Zhao L, Zhang Y, Xu D, Song Q, Cheng J, Wang W. Whole-genome resequencing identified candidate genes associated with the number of ribs in Hu sheep. Genomics 2021; 113:2077-2084. [PMID: 33965549 DOI: 10.1016/j.ygeno.2021.05.004] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 04/12/2021] [Accepted: 05/04/2021] [Indexed: 10/21/2022]
Abstract
The number of ribs is an important economic trait in the sheep industry when the sheep are raised for mutton. However, in sheep, the genetic mechanisms regulating rib number are poorly understood. In the present study, we aimed to identify important candidate genes that affect the increase in rib number in sheep. Whole-genome resequencing of 36 Hu sheep with an increased number of ribs (R14) and 36 sheep with normal (R13) rib numbers was carried out. Analysis using three methods (fixation index (FST), Fisher's exact test, and Chi-squared test) showed that 219 single nucleotide polymorphism sites overlapped among the results of the three methods, which represented 206 genes. Gene ontology and Kyoto Encyclopedia of Genes and Genomes analyses indicated that the genes were mainly associated with regulation of developmental process, inorganic anion transport, cellular biosynthetic process, tight junction, the oxytocin signaling pathway, and arrhythmogenic right ventricular cardiomyopathy. Four mutations were selected according to the significantly selected genomic regions and important pathways for genotyping and association analysis. The result demonstrated that three synonymous mutations correlated significantly with the rib number. Importantly, we revealed that the CPOX (encoding coproporphyrinogen oxidase), KCNH1 (encoding potassium voltage-gated channel subfamily H member 1), and CPQ (encoding carboxypeptidase Q) genes have a combined effect on rib number in Hu sheep. Our results identified candidate molecular markers for rib number in sheep breeding.
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Affiliation(s)
- Deyin Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Xiaoxue Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Fadi Li
- Engineering Laboratory of Sheep Breeding and Reproduction Biotechnology in Gansu Province, Minqin 733300, China; The State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Teng Liu
- Suzhou Zelgen Biopharmaceuticals Co., Ltd., Kunshan, Jiangsu 215300, China
| | - Zhihong Hu
- Changxing Yongsheng Animal Husbandry Co. Ltd., Huzhou, Zhejiang 313100, China
| | - Ning Gao
- Changxing Yongsheng Animal Husbandry Co. Ltd., Huzhou, Zhejiang 313100, China
| | - Lvfeng Yuan
- Engineering Laboratory of Sheep Breeding and Reproduction Biotechnology in Gansu Province, Minqin 733300, China
| | - Xiaolong Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Yuan Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Liming Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Yukun Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Dan Xu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Qizhi Song
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Jiangbo Cheng
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Weimin Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China.
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Abolfathi ME, Tabeidian SA, Foroozandeh Shahraki AD, Tabatabaei SN, Habibian M. Ethanol extract of elecampane (Inula helenium L.) rhizome attenuates experimental cold-induced ascites (pulmonary hypertension syndrome) in broiler chickens. Anim Feed Sci Technol 2021. [DOI: 10.1016/j.anifeedsci.2020.114755] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
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Varmaghany S, Jafari H, Javad. Evaluation of cardiac status, ascites related factors and growth performance of five commercial strains of broiler chickens. ACTA SCIENTIARUM: ANIMAL SCIENCES 2020. [DOI: 10.4025/actascianimsci.v43i1.50295] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The aim of the current study was to evaluate cardiac status, ascites susceptibility, thyroid hormones, some hematological parameters and performance of five commercial broiler strains. Chicks were selected from strains of Cobb, Hubbard, Ross 308, Arbor Acres, and Arian (Iranian commercial broiler strain). Management and nutritional conditions were the same for all strains. Ascites related factors, and growth performance were measured. The highest and lowest, RV weight/live weight at 21 day of age were related to Arian and Ross 308 strains, respectively (p < 0.05). The TV weight, TV weight/live weight and the RV weight/live weight were significantly different between various strains at 49 and 54 days of age (p < 0.05). Strain had no effect on RV/TV. Performance, T3 and T4 hormones, hematological parameters, and mortalities were not significantly different among the strains (p > 0.05). Ascites mortalities in the Ross 308 was zero; however, it had no significant difference with other strains (p > 0.05). It was concluded that, based on performance and physiological status, even though considered broiler strains did not differ significantly because of the same genetic programs probably, but according to the prices and market conditions each can be selected for breeding.
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Parveen A, Jackson CD, Dey S, Tarrant K, Anthony N, Rhoads DD. Identification and validation of quantitative trait loci for ascites syndrome in broiler chickens using whole genome resequencing. BMC Genet 2020; 21:54. [PMID: 32434464 PMCID: PMC7240924 DOI: 10.1186/s12863-020-00859-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 05/13/2020] [Indexed: 12/17/2022] Open
Abstract
BACKGROUND Ascites syndrome is a hypertensive, multifactorial, multigene trait affecting meat-type chickens imposing significant economic losses on the broiler industry. A region containing the CPQ gene has been previously identified as significantly affecting ascites phenotype. The region was discovered through whole genome resequencing focused on chicken chromosome 2. The association was confirmed through further genotyping in multiple broiler populations. RESULTS The whole genome resequencing analyses have now been extended to the current chicken genome assembly. DNA samples were pooled according to gender and phenotype and the pools subjected to next generation sequencing. Loci were identified as clusters of single nucleotide polymorphisms where frequencies of the polymorphisms differed between resistant and susceptible chickens. The chickens are an unselected line descended from a commercial elite broiler line. Regions identified were specific to one or both genders. The data identify a total of 28 regions as potential quantitative trait loci for ascites. The genes from these regions have been associated with hypertensive-related traits in human association studies. One region on chicken chromosome 28 contains the LRRTM4 gene. Additional genotyping for the LRRTM4 region demonstrates an epistatic interaction with the CPQ region for ascites phenotype. CONCLUSIONS The 28 regions identified were not previously identified in a multi-generational genome wide association study using 60k Single Nucleotide Polymorphism panels. This work demonstrates the utility of whole genome resequencing as a cost effective, direct, and efficient method for identifying specific gene regions affecting complex traits. The approach is applicable to any organism with a genome assembly and requires no a priori assumptions.
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Affiliation(s)
- Alia Parveen
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR, 72701, USA
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Christa D Jackson
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR, 72701, USA
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Shatovisha Dey
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR, 72701, USA
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Katy Tarrant
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR, 72701, USA
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Nicholas Anthony
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR, 72701, USA
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Douglas D Rhoads
- Program in Cell and Molecular Biology, University of Arkansas, Fayetteville, AR, 72701, USA.
- Department of Biological Sciences, University of Arkansas, Fayetteville, AR, 72701, USA.
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Franco-Martínez L, Martínez-Subiela S, Cerón JJ, Tecles F, Eckersall PD, Oravcova K, Tvarijonaviciute A. Biomarkers of health and welfare: A One Health perspective from the laboratory side. Res Vet Sci 2019; 128:299-307. [PMID: 31869596 DOI: 10.1016/j.rvsc.2019.12.012] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2019] [Revised: 11/22/2019] [Accepted: 12/10/2019] [Indexed: 10/25/2022]
Abstract
A biomarker is any measurement reflecting an interaction between a biological system and a potential hazard, which may be chemical, physical, or biological. The One World, One Health concept established that human and animal health and the environmental state are highly interconnected, sharing common aspects that can be applied globally in these three components. In this paper, we review how the concept of One Health can be applied to biomarkers of health and welfare, with a special focus on five points that can be applied to any biomarker when it is expected to be used to evaluate the human, animal or environmental health. Three of these points are: (1) the different biomarkers that can be used, (2) the different sample types where the biomarkers can be analysed, and (3) the main methods that can be used for their measurement. In addition, we will evaluate two key points needed for adequate use of a biomarker in any situation: (4) a proper analytical validation in the sample that it is going to be used, and (5) a correct selection of the biomarker. It is expected that this knowledge will help to have a broader idea about the use of biomarkers of health and welfare and also will contribute to a better and more accurate use of these biomarkers having in mind their One Health perspective.
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Affiliation(s)
- Lorena Franco-Martínez
- Interdisciplinary Laboratory of Clinical Analysis (Interlab-UMU), Veterinary School, Campus of Excellence Mare Nostrum, University of Murcia, Espinardo, 30100 Murcia, Spain.
| | - Silvia Martínez-Subiela
- Interdisciplinary Laboratory of Clinical Analysis (Interlab-UMU), Veterinary School, Campus of Excellence Mare Nostrum, University of Murcia, Espinardo, 30100 Murcia, Spain.
| | - José Joaquín Cerón
- Interdisciplinary Laboratory of Clinical Analysis (Interlab-UMU), Veterinary School, Campus of Excellence Mare Nostrum, University of Murcia, Espinardo, 30100 Murcia, Spain.
| | - Fernando Tecles
- Interdisciplinary Laboratory of Clinical Analysis (Interlab-UMU), Veterinary School, Campus of Excellence Mare Nostrum, University of Murcia, Espinardo, 30100 Murcia, Spain.
| | - Peter David Eckersall
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Bearsden Rd, Glasgow G61 1QH, UK.
| | - Katarina Oravcova
- Institute of Biodiversity, Animal Health and Comparative Medicine, University of Glasgow, Bearsden Rd, Glasgow G61 1QH, UK.
| | - Asta Tvarijonaviciute
- Interdisciplinary Laboratory of Clinical Analysis (Interlab-UMU), Veterinary School, Campus of Excellence Mare Nostrum, University of Murcia, Espinardo, 30100 Murcia, Spain.
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Fu CZ, Guang XM, Wan QH, Fang SG. Genome Resequencing Reveals Congenital Causes of Embryo and Nestling Death in Crested Ibis (Nipponia nippon). Genome Biol Evol 2019; 11:2125-2135. [PMID: 31298688 PMCID: PMC6685491 DOI: 10.1093/gbe/evz149] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/14/2019] [Indexed: 12/18/2022] Open
Abstract
The crested ibis (Nipponia nippon) is endangered worldwide. Although a series of conservation measures have markedly increased the population size and distribution area of these birds, the high mortality of embryos and nestlings considerably decreases the survival potential of this bird species. High-throughput sequencing technology was utilized to compare whole genomes between ten samples from dead crested ibises (including six dead embryos and four dead nestlings aged 0-45 days) and 32 samples from living birds. The results indicated that the dead samples all shared the genetic background of a specific ancestral subpopulation. Furthermore, the dead individuals were less genetically diverse and suffered higher degrees of inbreeding compared with these measures in live birds. Several candidate genes (KLHL3, SETDB2, TNNT2, PKP1, AK1, and EXOSC3) associated with detrimental diseases were identified in the genomic regions that differed between the alive and dead samples, which are likely responsible for the death of embryos and nestlings. In addition, in these regions, we also found several genes involved in the protein catabolic process (UBE4A and LONP1), lipid metabolism (ACOT1), glycan biosynthesis and metabolism (HYAL1 and HYAL4), and the immune system (JAM2) that are likely to promote the normal development of embryos and nestlings. The aberrant conditions of these genes and biological processes may contribute to the death of embryos and nestlings. Our data identify congenital factors underlying the death of embryos and nestlings at the whole genome level, which may be useful toward informing more effective conservation efforts for this bird species.
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Affiliation(s)
- Chun-Zheng Fu
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, P.R. China
| | - Xuan-Min Guang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, P.R. China
| | - Qiu-Hong Wan
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, P.R. China
| | - Sheng-Guo Fang
- MOE Key Laboratory of Biosystems Homeostasis & Protection, State Conservation Centre for Gene Resources of Endangered Wildlife, College of Life Sciences, Zhejiang University, Hangzhou, P.R. China
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