مطالعه جامع ژن‌های غیرکدکننده بلند مرتبط با سندرم آسیت طیور

نوع مقاله : مقاله پژوهشی

نویسندگان

1 گروه علوم دامی دانشکده کشاورزی دانشگاه تبریز

2 گروه علوم دامی دانشگاه تبریز

چکیده

اهداف: سندرم آسیت ، عارضه‌ای است که معمولا، در جوجه‌های گوشتی در حال رشد در تمام نقاط دنیا رخ می-دهد واین بیماری یکی از علل مهم تلفات در بسیاری از گله‌ها می‌باشد. درسبب‌شناسی این عارضه درپرندگان حساس نسبت به پرندگان مقاوم، علاوه بر فاکتور‌های محیطی، پروفایل بیان متفاوت ژن‌ها احتمالا، در حین یا قبل از بروز بیماری دخیل می‌باشد. همچنین، عامل این تفاوت بیان ژن، ممکن است تحت تاثیر RNAهای غیرکدکننده طویل باشد. لذا هدف از تحقیق حاضر، شناسایی و کشف ژن‌های غیرکدکننده بلند طولانی موثر برسندرم آسیت در جوجه‌های گوشتی بود.
مواد و روش‌ها: بدین منظور، از شش مجموعه داده متعلق به چهاربافت (کبد، کلیه، قلب و سرخرگ ششی) استفاده شد. جهت شناسایی ژن‌های غیرکدکننده بلند طولانی از انواع نرم‌افزارها (CPC2, CNIT PLEK, FEELNC, PLIT) و انواع بلاستها بر علیه پایگاه داده های مختلف NR و Refseq و همچنین، سایر ابزارهای شناسایی رونوشت‌ها استفاده شد. برای انجام متاآنالیز ازنرم‌افزار meta-RNAseq و روش فیشر استفاده شد.
یافته‌ها: بررسی نتایج این تحقیق نشان داد که 188 رونوشت lncRNA به عنوان RNA غیرکدکننده بلند طولانی جدید در بافت‌های مورد بررسی کشف و شناسایی شدند. از این تعداد، 166 lncRNA در فاصله 50±هزار بازنوکلئوتیدی با 689 تعداد ژن همجوار بودند. آنالیز همبیانی نشان داد که بین 13عدد lncRNA وتعداد 17 ژن همجوار همبستگی بالای 90/0 وجود داشت. از این 17تعداد ژن همجوار،6 تعداد ژن کدکننده شناخته شده بودند. بررسی سطح معنی‌داری بین گروه پرندگان سالم و آسیتی نشان داد که در بافت سرخرگ ششی بیان 4 ژن به صورت معنی داری متفاوت بود که این 4 ژن همجوار کدکننده با3 تا lncRNA ارتباط بیانی داشتند. بعبارت دیگر، یک lncRNA دو ژن همجوار را کنترل می‌کرد. درمتاآنالیز نیز تعداد 9 ژن lncRNA بین پرندگان سالم و آسیتی بطور معنی داری دارای بیان افتراقی بود که بررسی های بیشتر آنها نشان دهنده ارتباطات آنها با سندروم آسیت بود.
نتیجه گیری: نتایج این تحقیق به روشنی نشان داد که lncRNA ها نقش مهمی در بروز بیماری آسیت ایفا می-کنند و با مدیریت ژنتیکی گله‌های مرغان تجاری می‌توان بروز این عارضه در مرغداری‌ها را کم و ضررهای اقتصادی را کنترل کرد.
واژه‌های کلیدی: آسیت، متاآنالیز، RNAهای غیرکدکننده بلند طولانی، فیشر

کلیدواژه‌ها

موضوعات

عنوان مقاله [English]

A comprehensive study of long noncoding genes associated with ascites syndrome in poultry

نویسندگان [English]

  • Mina aghazadeh 1
  • abbas rafat 2
  • arash javanmard 2
  • karim hassanpour 1
1 Department of Animal Science, Faculty of Agriculture, University of Tabriz
2 Tabriz
چکیده [English]

Objectives Objectives: Ascites syndrome occurs in growing broilers in all parts of the world and is a major cause of losses in many flocks. In addition to genetic and non-genetic factors, differential expression of genes in susceptible chickens compared to resistant chickens during or before onset of the disease is likely involved. This difference in gene expression can be influenced by long non-coding RNAs. Therefore, the aim of this research was to identify and discover long non-coding genes effective in ascites syndrome in four tissues of broilers.Ascites.
Materials and methods: Six data sets in four tissues (liver, kidney, heart and pulmonary artery) were used for this research. Hisat2 software was used to align the reads with chicken reference genome and Sting Tie software package was used to assemble the transcripts. To identify long non-coding genes, we used various software (CPC2, CNIT PLEK, FEELNC, PLIT) and BLAST methods. meta-RNAseq software and Fisher's method were used to perform meta-analysis.
Results: Examination of the results of this research revealed that 188 lncRNAs were detected in the examined tissues and identified as new long non-coding RNAs. Of these, 160 lncRNAs were located within 50,000 contiguous 689 genes. Coexpression analysis showed that there was a correlation of 0.9 between 13 lncRNAs and 17 neighboring genes. Of these 17 neighboring genes, 6 coding genes were known. Examination of the level of significance between the healthy group and the ascites group in the examined tissues showed that in the pulmonary artery tissue the expression of 4 genes was significantly different and these 4 adjacent coding genes with 3 lncRNAs, i.e. H. an lncRNA that controls two adjacent genes. In the meta-analysis, 9 lncRNA genes were differentially expressed between healthy chickens and ascites chickens.
Conclusion: The results of this research showed that lncRNAs play an important role in the
occurrence of ascites disease and that genetic management can reduce the occurrence of this
complication in poultry farms and control economic losses.
Key words: Ascites, Fisher, Long non-coding RNAs, Meta-analysis

Objectives Objectives: Ascites syndrome occurs in growing broilers in all parts of the world and is a major cause of losses in many flocks. In addition to genetic and non-genetic factors, differential expression of genes in susceptible chickens compared to resistant chickens during or before onset of the disease is likely involved. This difference in gene expression can be influenced by long non-coding RNAs. Therefore, the aim of this research was to identify and discover long non-coding genes effective in ascites syndrome in four tissues of broilers.Ascites.
Materials and methods: Six data sets in four tissues (liver, kidney, heart and pulmonary artery) were used for this research. Hisat2 software was used to align the reads with chicken reference genome and Sting Tie software package was used to assemble the transcripts. To identify long non-coding genes, we used various software (CPC2, CNIT PLEK, FEELNC, PLIT) and BLAST methods. meta-RNAseq software and Fisher's method were used to perform meta-analysis.
Results: Examination of the results of this research revealed that 188 lncRNAs were detected in the examined tissues and identified as new long non-coding RNAs. Of these, 160 lncRNAs were located within 50,000 contiguous 689 genes. Coexpression analysis showed that there was a correlation of 0.9 between 13 lncRNAs and 17 neighboring genes. Of these 17 neighboring genes, 6 coding genes were known. Examination of the level of significance between the healthy group and the ascites group in the examined tissues showed that in the pulmonary artery tissue the expression of 4 genes was significantly different and these 4 adjacent coding genes with 3 lncRNAs, i.e. H. an lncRNA that controls two adjacent genes. In the meta-analysis, 9 lncRNA genes were differentially expressed between healthy chickens and ascites chickens.
Conclusion: The results of this research showed that lncRNAs play an important role in the
occurrence of ascites disease and that genetic management can reduce the occurrence of this
complication in poultry farms and control economic losses.
Key words: Ascites, Fisher, Long non-coding RNAs, Meta-analysis

Objectives Objectives: Ascites syndrome occurs in growing broilers in all parts of the world and is a major cause of losses in many flocks. In addition to genetic and non-genetic factors, differential expression of genes in susceptible chickens compared to resistant chickens during or before onset of the disease is likely involved. This difference in gene expression can be influenced by long non-coding RNAs. Therefore, the aim of this research was to identify and discover long non-coding genes effective in ascites syndrome in four tissues of broilers.Ascites.
Materials and methods: Six data sets in four tissues (liver, kidney, heart and pulmonary artery) were used for this research. Hisat2 software was used to align the reads with chicken reference genome and Sting Tie software package was used to assemble the transcripts. To identify long non-coding genes, we used various software (CPC2, CNIT PLEK, FEELNC, PLIT) and BLAST methods. meta-RNAseq software and Fisher's method were used to perform meta-analysis.
Results: Examination of the results of this research revealed that 188 lncRNAs were detected in the examined tissues and identified as new long non-coding RNAs. Of these, 160 lncRNAs were located within 50,000 contiguous 689 genes. Coexpression analysis showed that there was a correlation of 0.9 between 13 lncRNAs and 17 neighboring genes. Of these 17 neighboring genes, 6 coding genes were known. Examination of the level of significance between the healthy group and the ascites group in the examined tissues showed that in the pulmonary artery tissue the expression of 4 genes was significantly different and these 4 adjacent coding genes with 3 lncRNAs, i.e. H. an lncRNA that controls two adjacent genes. In the meta-analysis, 9 lncRNA genes were differentially expressed between healthy chickens and ascites chickens.
Conclusion: The results of this research showed that lncRNAs play an important role in the
occurrence of ascites disease and that genetic management can reduce the occurrence of this
complication in poultry farms and control economic losses.
Key words: Ascites, Fisher, Long non-coding RNAs, Meta-analysis

کلیدواژه‌ها [English]

  • Ascites
  • Fisher
  • Long non-coding RNAs
  • Meta-analysis

مراجع

آلبوشکه. سیدنادر، بختیارزاده محمدرضا. 1398. شناسایی lncRNAهای مرتبط با رشد عضله سینه مرغ به وسیله روش RNA-seq. 2:165-180.
حسن­پور کریم. 1394. بررسی ترنسکریپتوم و پروفایل بیان ژن مرغان حساس به آسیت. رساله دکتری دانشکده کشاورزی، دانشگاه فردوسی مشهد.
حسن زاده، محمد. 1387. بیماریهای متابولیکی طیور، چاپ اول، انتشارات دانشگاه تهران. صفحات 89-86.
جباری رقیه. 1398. آنالیز پروفایل ترنسکریپتومی و فاکتور­های متابولیکی سندرم آسیت القا شده در یک لاین مرغ گوشتی، رساله دکتری دانشکده کشاورزی، دانشگاه تبریز.
محمدی فر آمنه، فقیه ایمانی سید علی، محمدآبادی محمد رضا، سفلایی محمد. (1392). تأثیر ژن TGFb3 بر ارزش های فنوتیپی و ارثی صفات وزن بدن در مرغ بومی استان فارس. مجله بیوتکنولوژی کشاورزی 5(4)، 136-125.
Chen L, Zhang SH, Huang J, Zhang G, Xie K, Wang J, Wu H and Dai G, 2019. identification of Long Non-Coding RNA-Assocciated Competing Endogenous RNA Network in the Differentiation of chicken Preadipocytes Animal Genetics and Genomics. 10,795, doi.org/10.3390/10100795.
Gupta P, Peter S, Jung M, Lewin A, Hemmrich-Stainsak G, Franke A, Kleist M., Schutte C, Einspanier R., Shabati S and Brugge J, 2019. Analysis of long non-coding RNA and mRNA expression in bovine macrophages brings up novel aspects of Mycobacterium avium subspecies paratuberculosis infections. Scientific Reports, 9:1571. https://doi.org/10.1038/s41598-018-38141-x.
Khabiri A, Toroghi R, Mohammadabadi M, Tabatabaeizadeh S, 2023. Introduction of a Newcastle disease virus challenge strain (sub-genotype VII. 1.1) isolated in Iran. Vet Res Forum 14 (4): 221-228.
Liu J, Zhou Y, Hu X, Yang J, Lei Q, Liu W, Han H, Li F and Cao D, 2021. Transcriptome analysis reveals the profile of long non-coding RNAs during chicken muscle development. Sec. Developmental Physiology. Volume 12, https://, doi.org/10.3389/fphys.2021.660370.
Li D, Li F, Jiang K, Zhang M, Han R, Jiang R, 2019. Integrative analysis of long noncoding RNA and mRNA reveals candidate lncRNAs responsible for meat quality at different physiological stages in Gushi chicken. PLoS ONE14(4): e0215006. https://doi.org/10.1371/journal. pone.0215006.
Liu L, Ren L, Liu A,Wang J, Wang, J and Wang Q, 2022. Genome-wide identification and characterization of long non-coding RNAs in embryo muscle of chicken. Animals 12, 1274. https://doi.org/10.3390/ani12101274.
Marot A, Trepo E, Doerig C, Moreno C, Moradpour D and Deltenre P. 2015. Systematic review with meta-analysis: self-expanding metalstents in patients with cirrhosis and severe or refractoryoesophageal variceal bleeding. Journal Evidence based on Medicine. 42:1250–1260. doi:10.1111/apt.13424125.
Mohammadabadi MR, Nikbakhti M, Mirzaee HR, Shandi A, Saghi DA, Romanov DA, Moiseyeva IG. 2010. Genetic variability in three native Iranian chicken populations of the Khorasan province based on microsatellite markers. Russian Journal of Genetics. 46, 505-509.
Mohammadifar A, Faghih Imani SA, Mohammadabadi MR, Soflaei M, 2014. The effect of TGFb3 gene on phenotypic and breeding values of body weight traits in Fars native fowls. Agricultural Biotechnology Journal. 5, 125-136 (In Persian).
Mohammadifar A and Mohammadabadi MR, 2017. the effect of uncoupling protein polymorphisms on growth, breeding value of growth and reproductive traits in the fars indigenous chicken. Iranian Journal of Applied Animal Science. 7: 679-685.
Mohammadifar A and Mohammadabadi MR, 2018. Melanocortin-3 receptor (mc3r) gene association with growth and egg production traits in Fars indigenous chicken. Malays Appl Biol 47: 85–90.
Ramasamy A, Mondry A, Holmes A and Altman D, 2008. key issues in conducting a meta-analysis of gene expression microarray datasets. Plos Medicine, doi.org/10.137/journal.pmed.0050184.
Shahdadnejad N, Mohammadabadi MR and Shamsadini M, 2016. Typing of Clostridium perfringens isolated from broiler chickens using multiplex PCR. Genetics Third Millennium. 14 (4): 4368-4374.
Tingting L, Suya W, Rimao W, Xueya Z, Dahai Z and Yong Z, 2012, Identification of long non-protein coding RNAs in chicken skeletal muscle using next generation sequencing, Genomics 99(5): 292-298.
Wang Y, Guo Y, Ning D, Peng Y, Cai H, Tan J, Yang Y and Liu D, 2012. Changes of hepatic biochemical parameters and proteomics in broilers with cold-induced ascites. Journal of animal science and biotechnology, 3(1), 41-49.
Xu C, Yang M, Tian J, Wang X and Li Z, (2011) MALAT-1, a long non-coding RNA and its important 3'end functional motif in colorectal cancer metastasis. International Journal of Oncology 39(1): 169-75. doi: 10.3892/ijo.2011.1007.
Yang Y, Gao M, Wu Z and Guo Y. 2010. Genistein attenuates low temperature induced pulmonary hypertension in broiler chicks by modulating endothelial function. European Journal of Pharmacology 649: 242-248.
Zhai B, Zhao Y, Fan SH, Yuan P, Li H, Li SH, Li Y, Zhang Y, Huang H, Li H, Kangand H and Li G, 2021. Differentially expressed lncRNAs related to the development of abdominal fat in Gushi chickens and their interaction regulatory network. Livestock Genomics. 12: 1-12 https://doi.org/10.3389/fgene.2021.802857.
پژوهش های علوم دامی (دانش کشاورزی)
دوره 34، شماره 2
شهریور 1403
صفحه 31-44

فایل ها

سابقه مقاله

  • تاریخ دریافت: 05 تیر 1402
  • تاریخ بازنگری: 10 بهمن 1402
  • تاریخ پذیرش: 10 بهمن 1402

هم رسانی

ارجاع به این مقاله

آمار