تحلیل فیلوژنتیکی خانواده ژنی NAC در سورگوم دانه‌ای و بررسی الگوی بیانی اعضای دخیل در پاسخ به تنش خشکی

نوع مقاله: علمی پژوهشی

نویسندگان

1 دانشجوی دکتری بیوتکنولوژی گیاهی، گروه بیوتکنولوژی کشاورزی، دانشکده علوم کشاورزی دانشگاه گیلان، رشت، ایران

2 استادیار گروه بیوتکنولوژی کشاورزی، دانشکده علوم کشاورزی دانشگاه گیلان، رشت، ایران

3 استادیار گروه زیست‌شناسی سیستم‌ها، پژوهشگاه بیوتکنولوژی کشاورزی ایران، سازمان تحقیقات، آموزش و ترویج کشاورزی، کرج، ایران

4 استادیار گروه فیزیولوژی مولکولی، پژوهشکده بیوتکنولوژی کشاورزی ایران، سازمان تحقیقات، آموزش و ترویج کشاورزی، کرج، ایران

چکیده

سورگوم علی‌رغم تحمل قابل‌توجه به خشکی، در دوران قبل و بعد از گلدهی در صورت مواجهه با تنش خشکی، دچار کاهش عملکرد دانه‌ای می‌شود. عوامل رونویسیNAC ، نقش کلیدی در سازگاری سورگوم به خشکی ایفا می‌کنند. در این مطالعه، اطلاعات مربوط به خانواده پروتئینیNAC از پایگاه‌های اطلاعاتی جمع‌آوری شد. سپس، مدل مخفی مارکوف دمین NAC (PF02365) بر علیه پروتئین‌های سورگوم مورد جستجو قرار گرفت. در مجموع، 183 توالی پروتئینی کدشونده توسط 131 مکان ژنی شناسایی شدند. درخت فیلوژنی بر اساس دمینNAC خانواده ژنیNAC سورگوم، به‌همراه 11 توالی پروتئینی شناخته شده در سایر گیاهان، با روش نزدیک‌ترین همسایه‌ها ترسیم شد که این خانواده را به 15 زیرخانواده طبقه‌بندی نمود. 13 عضو از خانواده پروتئینی NAC سورگوم به زیرخانوادهSNAC های سایر گیاهان پیوستند که احتمالا در تحمل به تنش‌های غیرزیستی دخیل باشند. 14 نوع عنصر تنظیمی پاسخ‌دهنده به تنش‌ها و هورمون‌ها در راه‌انداز ژن‌های زیر‌گروه SNAC پیش‌بینی شد. به‌منظور بررسی الگوی بیانی نسبی ژن‌های SNAC، کشت مزرعه‌ای به‌صورت اسپلیت پلات در قالب طرح بلوک‌های کامل تصادفی اجرا شد. آبیاری در دو سطح شامل آبیاری معمولی و تنش خشکی (قطع آبیاری پس از گلدهی) و ارقام در دو سطح شامل کیمیا (متحمل) و سپیده (حساس) لحاظ گردید. با توجه به الگوی بیانی SbSNAC‌ها، انتظار می‌رود که برخی از اعضا به‌عنوان تنظیم‌کننده‌های رونویسی مثبت (سه عضو) و منفی (سه عضو) در پاسخ به تنش خشکی پس از گلدهی در سورگوم فعالیت کنند. همچنین، برخی در پیری برگ (دو عضو) و فرایند انتقال مجدد فلزات (دو عضو) نقش دارند.

کلیدواژه‌ها

موضوعات


عنوان مقاله [English]

Phylogenetic analysis of NAC gene family in grain Sorghum and expression pattern analysis of drought responsive members

نویسندگان [English]

  • Sepideh Sanjari 1
  • Reza Shirzadian-Khorramabad 2
  • Zahra-Sadat Shobbar 3
  • Maryam Shahbazi 4
1 Ph.D. Student, Department of Agricultural Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran.
2 Assistant Professor, Department of Agricultural Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran.
3 Assistant Professor, Department of Systems Biology, Agricultural Biotechnology Research Institute of Iran, Education and Extension Organization (AREEO), Karaj, Iran
4 Assistant Professor, Department of Molecular Physiology, Agricultural Biotechnology Research Institute of Iran, Education and Extension Organization (AREEO), Karaj, Iran
چکیده [English]

Sorghum, in spite of its great tolerance to drought stress, suffers from grain yield loss due to pre and post flowering -drought stress conditions. NAC TFs play key roles in Sorghum drought adaptation. In this study, NAC protein family data was collected from databases. Then, hidden Markov model profiles of NAM domain (PF02365) was obtained from Pfam database and used to find the putative NAC members against Sorghum proteins. Totally, 183 protein sequences encoded by 131 gene loci were identified. The unrooted phylogenetic tree was constructed based on NAC domains of Sorghum and 11 known NAC domains of other plants using the Neighbor-Joining method, which classified the family into 15 subfamilies. 13 members of the NAC protein family of Sorghum joined to the SNAC subfamily of other plants, which are expected to be involved in abiotic stress tolerance. 14 different stress and hormone responsive regulatory elements were predicted in promoters of SNAC subgroupgenes. To study the expression pattern of these genes, two extreme Sorghum cultivars including Kimia and Sepideh were planted based on Split-plot Randomized Complete Block Design with three replications in the field. Irrigation was performed in two levels including normal irrigation and drought stress (water holding from anthesis). Based on the SbSNAC expression pattern, we predict that some members are involved in response to drought stress at post-flowering stage as positive (3 members) and negative transcriptional regulators (3 members). As well, some of them play role in leaf senescence (2 members) and metal remobilization processes (2 members).

کلیدواژه‌ها [English]

  • NAC
  • Drought
  • Sorghum bicolor (L.) Moench
  • Phylogenetic tree
  • gene expression pattern
Casa AM, Mitchell S E, Hamblin MT, Sun H, Bowers J E, Paterson AH, Kresovich S (2005) Diversity and selection in sorghum: Simultaneous analyses using simple sequence repeats. Theoretical and Applied Genetics. 111(1): 23–30.

Christianson JA, Dennis ES, Llewellyn DJ,  Wilson IW (2010) ATAF NAC transcription factors: Regulators of plant stress signaling. Plant Signaling & Behavior. 5(4): 428–432.

Collinge M,  Boller T (2001) Differential induction of two potato genes, Stprx2 and StNAC, in response to infection by Phytophthora infestans and to wounding. Plant Molecular Biology. 46(5): 521–529.

Dalal M, Mayandi K,  Chinnusamy V (2012) Sorghum: Improvement of Abiotic Stress Tolerance. Improving Crop Resistance to Abiotic Stress 2: 923–950.

Dicko MH, Gruppen H, Traoré AS, Voragen  AGJ,  Van Berkel WJ H (2006) Sorghum grain as human food in Africa: relevance of content of starch and amylase activities. African Journal of Biotechnology. 5(5): 384–395.

Eppel A, Keren N, Salomon  E, Volis S,  Rachmilevitch S (2013) The response of Hordeum spontaneum desert ecotype to drought and excessive light intensity is characterized by induction of O 2 dependent photochemical activity and anthocyanin accumulation. Plant Science. 201: 74-80.

Fang Y, You J, Xie K, Xie W, Xiong L (2008) Systematic sequence analysis and identification of tissue-specific or stress-responsive genes of NAC transcription factor family in rice. Molecular Genetics and Genomics. 280(6): 547–563.

Finn RD, Coggill P, Eberhardt RY, Eddy SR, Mistry J, Mitchell AL, Bateman A (2016) The Pfam protein families database: Towards a more sustainable future. Nucleic Acids Research. 44(D1): 279–285.

Goodstein DM, Shu S, Howson R, Neupane R, Hayes RD, Fazo J, Rokhsar DS (2012) Phytozome: A comparative platform for green plant genomics. Nucleic Acids Research. 40(D1): 1178–1186.

 Harris K, Subudhi PK, Borrell A, Jordan D, Rosenow D, Nguyen H, Mullet J (2007) Sorghum stay-green QTL individually reduce post-flowering drought-induced leaf senescence. Journal of Experimental Botany. 58(2): 327–338.

Hu R, Qi G, Kong Y, Kong D, Gao Q,  Zhou G (2010) Comprehensive Analysis of NAC Domain Transcription Factor Gene Family in Populus trichocarpa. BMC Plant Biology. 10(1): 145-149.

Ibraheem O, Botha CEJ, Bradley G (2010) In silico analysis of cis-acting regulatory elements in 5′ regulatory regions of sucrose transporter gene families in rice (Oryza sativa Japonica) and Arabidopsis thaliana. Computational Biology and Chemistry. 34(5–6): 268–283.

Jin J, Tian, F, Yang DC, Meng YQ, Kong L, Luo J, Gao G (2017) PlantTFDB 4.0: Toward a central hub for transcription factors and regulatory interactions in plants. Nucleic Acids Research. 45(D1): 1040–1045.

Kapanigowda MH, Payne WA, Rooney LW, Mullet JE (2012) Transpiration Ratio in Sorghum [Sorghum bicolor (L.) Moench] for Increased Water-use Efficiency and Drought Tolerance. Journal of Arid Land Studies. 21(2):175–178.

Koyama T (2014) The roles of ethylene and transcription factors in the regulation of onset of leaf senescence. Frontiers in Plant Science. 5: 1–8.

Kumar S, Nei M, Dudley J, Tamura K (2006) MEGA: A biologist-centric software for evolutionary analysis of DNA and protein sequences. Brief Bioinformatics. 88(4): 559–566.

Larkin MA, Blackshields G, Brown NP, Chenna R, Mcgettigan PA, McWilliam H, Higgins DG (2007) Clustal W and Clustal X version 2.0. Bioinformatics. 23(21): 2947–2948.

Lata C, Muthamilarasan M, Prasad M (2015) Elucidation of Abiotic Stress Signaling in Plants. Springer-Verlag New York.

Letunic I, Doerks T, Bork P (2015) SMART: Recent updates, new developments and status in 2015. Nucleic Acids Research 43(D1): 257–260.

 Lu PL, Chen NZ, An R, Su Z, Qi BS, Ren F, Wang, X. C (2007) A novel drought-inducible gene, ATAF1, encodes a NAC family protein that negatively regulates the expression of stress-responsive genes in Arabidopsis. Plant Molecular Biology. 63 (2): 289–305.

Makita Y, Shimada S, Kawashima M, Kondou-Kuriyama T, Toyoda T, Matsui M (2015) MOROKOSHI: Transcriptome database in sorghum bicolor. Plant and Cell Physiology. 56 (1): e6.

Magali L, Patrice D, Gert T, Kathleen M, Yves M, Yves V, Pierre R, Stephane R (2002) PlantCARE, a database of plant cis-acting regulatory elements and a portal to tools for in silico analysis of promoter sequences. Nucleic Acids Research. 30 (1):325-327.

Nakashima, K, Takasaki H, Mizoi J, Shinozaki K, Yamaguchi-Shinozaki K (2012) NAC transcription factors in plant abiotic stress responses. Biochimica et Biophysica Acta - Gene Regulatory Mechanisms. 1819 (2): 97–103.

Pask, AJD, Pietragalla J, Mullan DM, Reynolds MP (2012) Physiological breeding II: a field guide to wheat phenotyping. CIMMYT.

Paterson AH, Bowers JE, Bruggmann R, Dubchak I, Grimwood J, Gundlach H, Rokhsar DS (2009) The Sorghum bicolor genome and the diversification of grasses. Nature, 457(7229): 551–556.

 Patil  JV, Rakshit S, Khot K B (2013) Genetics of post-flowering drought tolerance traits in post-rainy sorghum [Sorghum bicolor (L.) Moench]. Indian Journal of Genetics and Plant Breeding. 73 (1): 44–50.

Reddy TY, Reddy VR, Anbumozhi V (2003) Physiological responses of groundnut (Arachis hypogea L.) to drought stress and its amelioration: a critical review. Plant growth regulation. 41 (1): 75-88.

Ricachenevsky FK, Menguer PK,  Sperotto RA (2013) kNACking on heaven’s door: how important are NAC transcription factors for leaf senescence and Fe/Zn remobilization to seeds? Frontiers in Plant Science, 4: 1–7.

Riechmann JL, Heard J, Martin G, Reuber L ZC, Jiang L, Yu G (2000). Arabidopsis Transcription Factors: Genome-Wide Comparative Analysis Among Eukaryotes. Science. 290 (5499): 2105–2110.

Rosegrant MW (2003) Global Food Security: Challenges and Policies. Science. 302(5652): 1917–1919.

Sabadin PK, Malosetti M, Boer MP, Tardin FD, Santos FG, Guimarães CT, Magalhaes JV (2012) Studying the genetic basis of drought tolerance in sorghum by managed stress trials and adjustments for phenological and plant height differences. Theoretical and Applied Genetics. 124 (8): 1389–1402.

Sairam RK, Srivastava GC (2002) Changes in antioxidant activity in sub-cellular fractions of tolerant and susceptible wheat genotypes in response to long term salt stress. Plant Science. 162 (6): 897-904.

Shen H, Yin Y, Chen F, Xu Y, Dixon RA (2009) A bioinformatic analysis of NAC genes for plant cell wall development in relation to lignocellulosic bioenergy production. Bioenergy Research. 2(4): 217–232.

Singh A, Sharma V, Pal A (2013) Genome-wide organization and expression profiling of the NAC transcription factor family in potato (Solanum tuberosum L.). Dna (May): 403–423

Song SY, Chen Y, Chen J, Dai XY,  Zhang WH (2011) Physiological mechanisms underlying OsNAC5-dependent tolerance of rice plants to abiotic stress. Planta. 234 (2): 331–345.

Sperotto RA, Ricachenevsky FK, Duarte GL, Boff T, Lopes KL, Sperb ER, Fett JP (2009) Identification of up-regulated genes in flag leaves during rice grain filling and characterization of OsNAC5, a new ABA-dependent transcription factor. Planta. 230 (5): 985–1002.

Sudhakar Reddy P, Srinivas Reddy D, Sivasakthi K, Bhatnagar-Mathur P, Vadez V, Sharma KK (2016) Evaluation of Sorghum [Sorghum bicolor (L.)] Reference Genes in Various Tissues and under Abiotic Stress Conditions for Quantitative Real-Time PCR Data Normalization. Frontiers in Plant Science. 7: 1–14.

Sun L, Huang L, Hong Y, Zhang H, Song F, Li D (2015) Comprehensive analysis suggests overlapping expression of rice onac transcription factors in abiotic and biotic stress responses. International Journal of Molecular Sciences. 16(2): 4306–4326.

Thomas H,  Howarth C J (2000) Five ways to stay green. Journal of Experimental Botany. 51: 329–337.

Tran LSP, Nishiyama R, Yamaguchi-Shinozaki K,  Shinozaki K (2010) Potential utilization of NAC transcription factors to enhance abiotic stress tolerance in plants by biotechnological approach. GM Crops. 1(1): 32–39.

Tuteja N (2010) Cold, Salinity, and Drought Stress. Plant Stress Biology: From Genomics to Systems Biology. 444: 137–159.

Uauy C, Distelfeld A, Fahima T, Blechl A, Dubcovsky J (2006) A NAC Gene Regulating Senescence Improves Grain Protein, Zinc, and Iron Content in Wheat. Science. 314(5803): 1298–1301.

Wang N, Zheng Y, Xin H, Fang L, Li S (2013) Comprehensive analysis of NAC domain transcription factor gene family in Vitis vinifera. Plant Cell Reports. 32 (1): 61–75.

Wang YX, Liu ZW, Wu  Z J, Li H,  Zhuang J (2016) Transcriptome-wide identification and expression analysis of the NAC gene family in tea plant [camellia sinensis (L.) O. Kuntze]. PLoS ONE. 11(11): 1–26.

Wojciech R (2010) Primer analysis software OLIGO Version 7, 402, 209. Methods in Molecular Biology.  402: 35-59.

Wu XY, Hu WJ, Luo H, Xia Y, Zhao Y, Wang LD, Jing HC (2016) Transcriptome profiling of developmental leaf senescence in sorghum (Sorghum bicolor). Plant Molecular Biology. 92 (4–5): 555–580.

Yi-Hong W, Aniruddha A, Millie B, Robert RK, Patricia EK, Karl HH (2013) Mapping and candidate genes associated with saccharification yield in sorghum. Canadian Journal of Genetics and Cytology. 56 (11): 659-665.

Yilmaz A, Nishiyama MY, Fuentes BG, Souza GM, Janies D, Gray J,  Grotewold E (2009) GRASSIUS: a platform for comparative regulatory genomics across the grasses. Plant Physiology. 149 (1): 171–80.