مطالعه شبکه ژنی آنژیوژنز در جوجه‌های مرغ آرین حساس به آسیت با استفاده از داده‌های RNA-Seq

پژوهشهای علوم دامی ایران

مقاله 6، دوره 10، شماره 2، آبان 1397، صفحه 249-262   

نوع مقاله: علمی پژوهشی- ژنتیک و اصلاح دام و طیور

شناسه دیجیتال (DOI): 10.22067/ijasr.v10i2.65215

نویسندگان

وحید تقی زاده^{* 1}؛ محمدرضا نصیری²؛ مجتبی طهمورث پور²؛ محمدرضا بختیاری زاده³؛ علی جوادمنش²

¹پردیس واحد بین‌الملل دانشگاه فردوسی مشهد

²گروه علوم دامی، دانشکده کشاورزی، دانشگاه فردوسی مشهد، مشهد، ایران.

³گروه علوم دام و طیور، پردیس ابوریحان، دانشگاه تهران، تهران، ایران

چکیده

سندروم آسیت یک عارضه متابولیکی است که در سنین بالا در پرندگان گوشتی بروز می‌کند و به سویه تجاری آرین که تنها لاین اصلاح شده مرغ گوشتی ایران می باشد آسیب جدی وارد کرده است. مطالعات گذشته نقش عوامل ژنتیکی در بروز این سندروم را اثبات کرده است. از آنجا که ارگان‌های متعددی در بروز آسیت دخالت دارند و نقش قلب در آنها از همه بارزتر است، از مطالعات ژنومی استفاده شد تا ژن‌های مرتبط با مسیر آنژیوژنز در هایپرتروفی بطن راست قلب شناسایی شوند. در این تحقیق تعداد 464 پرنده از خط پدری B لاین آرین تحت تنش سرمایی پرورش داده شد و در بررسی آنالیز داده هایRNA-seq بین دو گروه سالم و مبتلا به آسیت، پروفایل بیان ژن‌ها در بطن راست قلب مرغان حساس و مقاوم به آسیت با استفاده از تکنولوژی توالی‌یابی نسل آینده مورد مقایسه قرار گرفت. نتایج بررسی ترنسکریپتومی ژنهای مسیر آنژیوژنز نشان داد که تعداد 59 ژن بین دو تیمار سالم و آسیتی تفاوت بیان معنی‌دار داشتند )05/0P

کلیدواژه‌ها

آسیت؛ آنالیز مسیر؛ آنژیوژنز؛ شبکه ژنی؛ هستی شناسی ژن؛ RNA-seq

مراجع

1- Alinaghizadeh, H., M. R. Mohammad Abadi, and S. Zakizadeh. 2010 Exon 2 of BMP15 gene polymorphismin Jabal Barez Red Goat. Journal of Agricultural Biotechnology 2 (1): 69-80. (In Persian).

2- Azizian, M., S. Rahimi, M. A. Kamali, Karimi M. A. Torshizi, and M. R. Zobdeh 2013. Comparison of the susceptibility of six male broiler hybrids to ascites by using hematological and pathological parameters. Journal of Agricultural Science and Technology, 15: 517-525.

3- Bakar, S. 1996. How to control Ascites in Broilers. Misset-World Poultry. 12:55-57

4- Balog, J. M., B. D. Kidd, G. R. Huff, W. E. Huff, N. C. Rath, and N. B. Anthony. 2003. Effect of cold stress on broilers selected for resistance or susceptibility to ascites syndrome. Poultry Science, 82: 1383-1387.

5- Bellon G, T. Caulet, Y. Cam, M. Pluot, G. Poulin, M. Pytlinska, and M. H. Bernard. 1985. Immunohisto chemical localisation of macromolecules of the basement membrane and extracellular matrix of human gliomas and meningiomas. Acta Neuropathol, 66(3):245-252. [PubMed: 3893018]

6- Bolger, A. M., M. Lohse, and B. Usadel. 2014. Trimmomatic: A flexible trimmer for Illumina sequence data. Bioinformatics, doi: 10.1093/bioinformatics/btu170.

7- Bozorgmehri M., B. Shoja doost, A. Akbari, G. Koleidari, and N. Sheikhi. 1996. Guides for poultry disease, Department of education and research of Kowsar economic organization. (In Persian).

8- Closter, A. M. 2014. Quantitative genetic analysis of ascites in broilers. PhD thesis. Wageningen University.

9- Coble D. J., D. Fleming, M. E. Persia, C. M. Ashwell, M. F. Rothschild, C. J. Schmidt, and S. J. Lamont. 2014. RNA Seq analysis of broiler liver transcriptome reveals novel responses to high ambient temperature. BMC Genomics, 15: 1084.

10- Decuypere, E., J. Buyse, and N. Buys. 2000. Ascites in broiler chickens: exogenous and endogenous structural and functional causal factors. World's Poultry Science Journal, 56:367-377.

11- Diril, M. K., C. K. Ratnacaram, V. C. Padmakumar, T. Du, M. Wasser, and V. Coppola. 2012. Cyclin-dependent kinase 1 (Cdk1) is essential for cell division and suppression of DNA re-replication but not for liver regeneration. roceedings of the National Academy of Sciences of the United States of America, 109 (10):3826-31.

12- Dominguez-Avila, N., G. Ruiz-Castañeda, J. Gonzalez-Ramirez, N. Fernandez-Jaramillo, J. Escoto, F. Sanchez-Muñoz, R. Marquez-Velasco, R. Bojalil, R. Espinosa-Cervantes, and F. Sanchez. 2013. Over and under expression of endothelia 1 and TGF-beta family ligands and receptors in lung tissue of broilers with pulmonary hypertension. BioMed Research International, 1-7.

13- Druyan, S. 2012. Ascites syndrome in broiler chickens-A physiological sydrome affected by red blood cells. In: Blood cell-an overview of studies in hematology. (Edited by Terry E. Moschandreou). INTECH. CC BY 3.0 license. Chapter, 13pp:243-270.

14- Ford H. L. and A. B. Pardee. 1999. Cancer and the cell cycle. Journal of Cellular Biochemistry, 75(S32):166-72.

15- Hamal, K. R., F. Robert Wideman, B. Nicholas Anthony, and F. E. Gisela. 2010. Differential gene expression of proinflammatory chemokines and cytokines in lungs of ascites-resistant and -susceptible broiler chickens following intravenous cellulose microparticle injection. Veterinary Immunology and Immunopathology, 133: 250-255.

16- Hartgring, S. A., J. A. van Roon, M. Wenting-van Wijk, K. M. Jacobs, Z. N. Jahangier, and C. R. Willis. 2009. Elevated expression of interleukin-7 receptor in inflamed joints mediates interleukin-7-induced immune activation in rheumatoid arthritis. Arthritis & Rheumatology, 60(9):2595-605. [PubMed:19714586]

17- Hasanpoor K., M. R. Nassiri, G. A. Hoseini Salkandeh, R. Vaez torshizi, A. Pakdel, and H. Kermanshahi. 2016. Transcriptom analysis and gene expression profile of chicken susceptible to ascites. Thesis for PhD degree, Department of animal science, Ferdowsi University of Mashhad, Iran. (In Persian)

18- Javanmard, A., M. R. Mohammadabadi, G. E. Zarrigabayi, A. A. Gharahedaghi, M. R. Nassiry, A. Javadmansh, and N. Asadzadeh. 2008. Polymorphism within the intron region of the bovine leptin gene in Iranian Sarabi cattle (Iranian Bos taurus). Russian Journal of Genetics, 44 (4): 495-497.

19- Julian, R. J. 1987. The Effect of Increased Sodium in the Drinking Water on Right Ventricular Hypertrophy, Right Ventricular Failure and Ascites in Broiler Chickens. Avian Pathology, 16:61-71

20- Julian, R. J., G. W. Friars, H. French, and M. Quinton .1987. The Relationship of Right Ventricular Hypertrophy, Right Ventricular Failure and Ascites to Weight Gain Broiler and Roster Chickens. Avian Diseases, 31:130-135

21- Julian, J. R. 1989. Lung volume of meat-type chickens. Avian Disease, 33: 174-176.

22- Kalluri, R. 2003. Basement membranes: structure, assembly and role in tumour angiogenesis. Nature Reviews Cancer, 3(6):422-433. [PubMed: 12778132]

23- Krishnamoorthy, S., C. D. Smith, A. A. Al-Rubaye, G. F. Erf, R. F. Wideman, N. B. Anthony, and D. D. Rhoads. 2014. A quantitative trait locus for ascites on chromosome 9 in broiler chicken lines. Poultry Science, 93: 307-317.

24- Luger, D., D. Shinder, D. Wolfenson, and S. Yahav. 2003. Erythropoiesis regulation during the development of ascites syndrome in broiler chickens: a possible role of corticosterone on egg production. Journal of Animal Science, 81:784-790.

25- Maxwell, M. H., and G. W. Robeson. l997. World Broiler Ascites Survey l996. Poultry Int. April. l 6-30

26- Moazeni, S., M. R. Mohammadabadi, M. Sadeghi, H. Shahrbabak, A. Koshkoieh, and F. Bordbar, 2016a. Association between UCP Gene Polymorphisms and Growth, Breeding Value of Growth and Reproductive Traits in Mazandaran Indigenous Chicken. Open Journal of Animal Sciences, 6 (1): 1-8.

27- Moazeni, S. M., M. R. Mohammadabadi, M. Sadeghi, H. Moradi Shahrbabak, and A. K. Esmailizadeh. 2016b. Association of the melanocortin-3(MC3R) receptor gene with growth and reproductive traits in Mazandaran indigenous chicken. Journal of Livestock Science and Technologies, 4 (2): 51-56.

28- Mohammadabadi, M. R., M. Nikbakhti, H. R. Mirzaee, A. Shandi, D. A. Saghi, M. N. Romanov, and I. G. Moiseyeva. 2010. Genetic variability in three native Iranian chicken populations of the Khorasan province based on microsatellite markers. Russian Journal of Genetics, 46 (4): 505-509.

29- Mohammadi, A., M. R. Nassiry, J. Mosafer, M. R. Mohammadabadi, and G. E. Sulimova. 2009. Distribution of BoLA-DRB3 allelic frequencies and identification of a new allele in the Iranian cattle breed Sistani (Bos indicus). Russian Journal of Genetics, 45(2): 198-202.

30- Mohammadifar, A., and M. R. Mohammadabadi. 2011. Application of microsatellite markers for a study of Kermani sheep genome. Iranian Journal of Animal Science, 42(4): 337-344.

31- Mousavizadeh, A., M. R. Mohammad Abadi, A. Torabi, M. R. Nassiry, H. Ghiasi, and A. K. Esmailizadeh. 2009. Genetic polymorphism at the growth hormone locus in Iranian Talli goats by polymerase chain reaction-single strand conformation polymorphism (PCR-SSCP). Iranian Journal of Biotechnology, 7 (1): 51-53.

32- Nigg, E. A. 1995. Cyclin-dependent protein kinases: key regulators of the eukaryotic cell cycle. BioEssays News Rev Mol Cell Dev Biol. 17(6):471-80.

33- Odom, T. W. 1993. Ascites Syndrome: Overview and Up-To-Date. Poultry Digest, 52:14-22.

34- Olkowski, A. A., C. Wajnarowicz, B. M. Rathgeber, J. A. Abbott, and H. L. Classen. 2003. Lesions of pericardium and their significance in the aetiology of heart failure in broiler chick-ens. Research in Veterinary Science, 74:203-211.

35- Pakdel, A., J. A. Van Arendonk, A. L. Vereijken, and H. Bovenhuis. 2002. Direct and maternal genetic effects for ascites-related traits in broilers. Poultry Science, 81(9):1273-9.

36- Pavlidis, H. O., J. M. Balog, L. K. Stamps, J. D. Hughes, W. E. Huff, and N. B. Anthony. 2007. Divergent selection for ascites incidence in chickens. Poultry Science, 86:2517-2529.

37- Pickens, S. R., N. D. Chamberlain, M. V. Volin, R. M. Pope, N. E. Talarico, A. M. Mandelin II, and S. Shahrara. 2011. Characterization of IL-7 and IL-7R in the pathogenesis of Rheumatoid Arthritis Arthritis Rheum. 2011 October; 63(10): 2884-2893. doi:10.1002/art.30493.

38- Rabie, T., R. P. M. A. Crooijmans, H. Bovenhuis, A. L. J. Vereijken, T. Veenendaal, J. J. van der Poel, J. A. M. Van Arendonk, A. Pakdel, and M. A. M. Groenen. 2005. Genetic mapping of quantitative trait loci affecting susceptibility in chicken to develop pulmonary hypertension syndrome. International Society for Animal Genetics, Animal Genetics, 36: 468-476.

39- Rabie, T., R. P. M. A. Crooijmans, H. Bovenhuis, A. L. J. Vereijken, T. Veenendaal, J. J. van der Poel, J. A. M. van Arendonk, A. Pakdel, and M. A. M. Groenen. 2005. Genetic mapping of quantitative trait loci affecting susceptibility in chicken to develop pulmonary hypertension syndrome. Animal Genetics, 36: 468-476.

40- Rabie, T., R. Crooijmans, H. Bovenhuis, A. L. J. Vereijken, A. Veenendaal, J. J. Van der Poel, J. A. M. Van Arendonk, and M. A. M. Groenen. 2007. Pulmonary hypertension syndrome (PHS) in broilers: validation and fine-scale mapping of quantitative trait loci affecting PHS using advanced intercross line. In utilisation of diversity in land use systems: Sustainable and organic approaches to meet human needs. Tropentag, October 9-11, 2007, Witzenhausen.

41- Rowland, K., A. Alban, N. B. Anthony, and B. W. Kong. 2013. Whole-genome sequencing of ascites resistant and susceptible lines of broilers. Poultry Science, 92(E-Suppl. 1): P. 53.

42- Schmidt, C. J., M. E. Persia, E. Feierstein, B. Kingham, and W.W. Saylor. 2009. Comparison of a modern broiler line and a heritage line unselected since the 1950s. Poultry Science, 88: 2610-2619.

43- Shahdadnejad, N., M. R. Mohammadabadi, and M. Shamsadini, 2016. Typing of Clostridium Perfringens Isolated from Broiler Chickens Using Multiplex PCR. Genetics in the 3rd millennium, 14 (4).

44- Shi, S., Y. Shen, Z. Zhao, Z. Hou, Y. Yang, and H. Zhou .2014. Integrative analysis of transcriptomic and metabolomic profiling of ascites syndrome in broiler chickens induced by low temperature. Molecular BioSystems, 10: 2984-2993. DOI: 10.1039/c4mb00360h PMID: 25178933.

45- Shi S., Y. Shen, S. Zhang, Z. Zhao, Z. Hou, H. Zhou, J. Zou, and Y. Guo. 2017. Combinatory Evaluation of Transcriptome and Metabolome Profiles of Low Temperatureinduced Resistant Ascites Syndrome in Broiler Chickens. Scientific Reports, 7: 2389. DOI: 10.1038/s41598-017-02492-8.

46- Shojaei, M., M. R. Mohammad Abadi, M. Asadi Fozi, O. Dayani, A. Khezri, and M. Akhondi. 2010. Association of growth trait and Leptin gene polymorphism in Kermani sheep. Journal of Cell and Molecular Research, 2: 67-73

47- Szklarczyk, D., A. Franceschini, S. Wyder, K. Forslund, D. Heller, J. Huerta-Cepas, and C. von Mering. 2015. STRING v10: protein–protein interaction networks, integrated over the tree of life. Nucleic Acids Research, 43(Database issue), D447–D452. http://doi.org/10.1093/nar/gku1003.

48- Tekeli, A. 2014. Effects of ascites on blood gas, blood oximetry parameters and heart sections of broilers growth at high altitude. Journal of Animal and Plant Sciences, 24:998-1002.

49- Trapnell, C., L. Pachter, and S. Salzberg. 2009. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics, 25: 1105-1111.

50- Trapnell, C., B. A. Williams, G. Pertea, A. Mortazavi, G. Kwan, M. J. van Baren, S. L. Salzberg, B. J. Wold, and L. Pachter. 2010. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nature Biotechnology, 28: 511-515.

51- Trapnell, C., D. G. Hendrickson, M. Sauvageau, L. Goff, J. L. Rinn, and L. Pachter. 2013. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nature Biotechnolgy, 31: 46-53.

52- Wang, D., J. C. Anderson, C. L. Gladson. 2005. The role of the extracellular matrix in angiogenesis in malignant glioma tumors. Brain Pathol, 15(4):318-326. [PubMed: 16389944]

53- Wideman, R. F. 1998. Causes and control of ascites in broilers. In: National Mtg. Poultry Health and Processing. Delmarva Poultry Industry Inc. Georgetown, DE. 33:56-85.

54- Yang, F., H. Cao, Q. Xiao, X. Guo, Y. Zhuang, and C. Zhang. 2016. Transcriptome Analysis and Gene Identification in the Pulmonary Artery of Broilers with Ascites Syndrome. PLoS ONE 11(6): e0156045. https://doi.org/10.1371/journal.pone.0156045

55- Zamani, P., M. Akhondi, M. R. Mohammadabadi, A. A. Saki, A. Ershadi, M. H. Banabazi, and A. R. Abdolmohammadi. 2013. Genetic variation of Mehraban sheep using two intersimple sequence repeat (ISSR) markers. African Journal of Biotechnology, 10: 1812-1817.

56- Zandi, E., M. R. Mohammadabadi, M. Ezzatkhah, and A. K. Esmailizadeh. 2014. Typing of Toxigenic Isolates of Clostridium Perfringens by Multiplex PCR in Ostrich. Iranian Journal of Applied Animal Science, 4: 509-514.

57- Zhao, Y., X. M. Meng, Y. J. Wei, X. W. Zhao, D. Q. Liu, H. Q. Cao, C. C. Liew, and J. F. Ding. 2003. Cloning and characterization of a novel cardiac-specific kinase that interacts specifically with cardiac troponin I. Journal of Molecular Medicine, 81: 297-304.

58- Zhou, H. J., Y. Wang, S. J. Lamont, and P. Ross. 2012. Re-annotation of chicken genome using RNA-seq data. Poultry Science, 92(E-Suppl. 1).