آمار
| تعداد نشریات | 28 |
| تعداد شماره‌ها | 426 |
| تعداد مقالات | 4,164 |
| تعداد مشاهده مقاله | 6,739,264 |
| تعداد دریافت فایل اصل مقاله | 4,988,760 |
Evaluation of Drought Stress-responsive Genes Expression of Durum Wheat Using Comparative Genomics | ||
| Journal of Genetic Resources | ||
| دوره 8، شماره 2، آذر 2022، صفحه 147-157 اصل مقاله (352.12 K) | ||
| نوع مقاله: Research Article | ||
| شناسه دیجیتال (DOI): 10.22080/jgr.2022.22737.1290 | ||
| نویسندگان | ||
| Shadi Heidari1؛ Peivand Heidari1؛ Baharak Heidari* 2 | ||
| 1Department of Plant Breeding, Science and Research Branch, Islamic Azad University, Tehran, Iran. | ||
| 2Department of Computer Engineering, Kermanshah Branch, Islamic Azad University, Kermanshah, Iran. | ||
| تاریخ دریافت: 21 مرداد 1400، تاریخ بازنگری: 21 دی 1400، تاریخ پذیرش: 07 آذر 1400 | ||
| چکیده | ||
| As the water resources become more limited, the production levels of crops are declining, and following the rapid increase in population, the use of mankind from staple food products has increased. So, the development of drought-tolerant crops aimed at cultivation in the arid regions will be of great worth to provide the country's nutritional necessity. The following research aimed to elucidate the drought tolerance of durum wheat (Triticum turgidum ssp. durum) through comparative expressed sequence tags/EST analysis of unstressed library with 2534 EST and drought-stressed library with 4485 EST. Preliminary data were gathered from the Harvard university database. All unigenes were assembled using EGassembler software to detect similarities between the two libraries and were then analyzed through X-blast by CLCbio software against a non-redundant protein database. To identify statistically differentially expressed genes, the IDEG6 web tool was used. Over 150 differentially ESTs were detected by Audic-Claverie statistics of IDEG6 software, in which over 85% ESTs were upregulated in response to drought. The GoMapMan comparative classification tool was used to categorize gene functional annotations. All significant differential unigenes were divided into seven functional categories i.e., photosynthesis and energy (19%), regulatory pathways (25%), transport (5%), hormones, plant defense, response to drought stress (11%), cell metabolism (19%), cell organization and development (4%) and miscellaneous as well as unclassified processes (17%). Comparative analysis revealed that some of the promising traits in T. turgidum are specifically regulated in drought stress including genes related to response to stress and hormones pathways, development and growth (helicases and CPL phosphatase), maintenance of cell water content (transporters and osmolites), membrane stability (HSP) and preventing the accumulation of toxins. This study prominently demonstrates the helicase role under durum wheat’s drought tolerance as well as provides indices for assessing the drought tolerance of T. turgidum aims to the use of tolerant varieties in breeding programs in arid and semi-arid regions in Iran. | ||
| کلیدواژه‌ها | ||
| Comparative genomics؛ Drought-tolerant cultivar؛ Expressed sequence tags؛ Functional catalogs؛ Gene expression analysis؛ Physiological processes | ||
| مراجع | ||
|
Ali GM, Komatsu S. 2006. Proteomic analysis of rice leaf sheath during drought stress. J Proteome Res 5: 396-403.
Antonescu C, Antonescu V, Sultana R, Quackenbush J. 2010. Using the dfci gene index databases for biological discovery. Curr Protoc Bioinform 29(1): 1-6.
Bassel GW, Glaab E, Marquez J, Bacardit J. 2011. Functional network construction in Arabidopsis using rule-based machine learning on large-scale data sets. Plant Cell 23(9): 3101-3116.
Bell SP, Dutta A. 2002. DNA replication in eukaryot cells. Annu Rev Biochem 71(1): 333-374.
Bennetzen JL. 2002. Mechanism and rate of genome expansion and contraction in flower plant. Genetica 115(1): 29-36.
Berridge MJ. 2005. Unlocking the secrets of cell signaling. Annu Rev Physiol 67: 1-21.
Chen CW, Yang YW, Lur HS, Tsai YG, Chang MC. 2006. A novel function of abscisic acid in the regulation of rice (Oryza sativa L.) root growth and development. Plant Cell Physiol 47(1): 1-13.
Choi WG, Toyota M, Kim SH, Hilleary R, Gilroy S. 2014. Salt stress-induced Ca2+ waves are associated with rapid, long-distance root-to-shoot signaling in plants. Proc Natl Acad Sci 111(17): 6497-6502.
Dang HQ, Tran NQ, Gill SS, Tuteja R, Tuteja N. 2011. A single subunit MCM6 from pea promotes salinity stress tolerance without affecting yield. Plant Mol Biol 76(1): 19-34.
Dodd AN, Kudla J, Sanders D. 2010.The language of calcium signaling. Annu Rev Plant Biol 61: 593-620.
Farooq M, Wahid A, Kobayashi NSMA, Fujita DBSMA, Basra SMA. 2009. Plant drought stress: effects, mechanisms and management. J Sustain Agric 29: 185-212.
Guan Q, Yue X, Zeng H, Zhu J. 2014. The protein phosphatase RCF2 and its interacting partner NAC019 are critical for heat stress–responsive gene regulation and thermotolerance in Arabidopsis. Plant Cell 26(1): 438-453
Heidari P, Etminan A, Azizinezhad R, Khosroshahli M. 2018. In vitro-examination of genetic parameters and estimation of seedling physiological traits under drought and normal conditions in durum wheat. Indian J Genet Plant Breed 78(02): 217-227.
Heidari Sh, Azizinezhad R, Haghparast R, Heidari P. 2019. evaluation of the association among yield and contributing characters through path coefficient analysis in advanced lines of durum wheat under diverse conditions. J Anim Plant Sci 29: 1325-1335.
Heidari Sh, Heidari P, Azizinezhad R, Etminan A, Khosroshahli M. 2020. Assessment of genetic variability, heritability and genetic advance for agro-morphological and some in-vitro related-traits in durum wheat. Bulg J Agric Sci 26: 120-127.
Heidari P, Maleki Zanjani B, Heidary S. 2012. A study of gene expression and functional genomics of wheat, rice, cotton and festuca plants under drought stress by analyzing expressed sequence tags (EST). Mod Genet J 7: 129-140.
Henty-Ridilla JL, Shimono M, Li J, Chang JH, Day B, Staiger CJ. 2013. The plant actin cytoskeleton responds to signals from microbe-associated molecular patterns. PLoS Pathog 9(4): e1003290.
Higaki T, Sano T, Hasezawa S. 2007. Actin microfilament dynamics and actin side-binding proteins in plants. Curr Opin Plant Biol 10(4): 549-556.
Huang YC, Huang WL, Hong CY, Lur HS, Chang MC. 2012. Comprehensive analysis of differentially expressed rice actin depolymerizing factor gene family and heterologous overexpression of OsADF3 confers Arabidopsis thaliana drought tolerance. Rice 5(1): 1-14.
Jongeneel CV. 2000. Searching the expressed sequence tag databases panning for genes. Brief Bioinform 1(1): 76-92.
Kapilan R, Vaziri M, Zwiazek JJ. 2018. Regulation of aquaporin plant under stress. Biol Res 51(1): 1-11.
Kappachery S, Baniekal-Hiremath G, Yu JW, Park SW. 2015. Effect of over and under expression of glyceraldehyde 3-phosphate dehydrogenase on tolerance of plants to water-deficit stress. Plant Cell Tiss Org 121(1): 97-107.
Kaur G, Asthir B. 2017. Molecular responses to drought stress in plants. Biol Plant 61(2): 201-209.
Kayum M, Park JI, Nath UK, Saha G, Biswas MK, Kim HT, Nou IS. 2017. Genomewide characterization and expression profile of PDI family gene reveals function as abiotic and biotic stress tolerance in Chinese cabbage. BMC Genomics 18(1): 1-20.
Koiwa H, Hausmann S, Bang WY, Ueda A, Kondo N, Hiraguri A, Shuman S. 2004. Arabidopsis C-terminal domain phosphatase-like 1 and 2 are essential Ser-5-specific C-terminal domain phosphatases. Proc Natl Acad Sci 101(40): 14539-14544.
Kozuleva M, Goss T, Twachtmann M, Rudi K, Trapka J, Selinski J, Hanke GT. 2016. Ferredoxin: NADP (H) oxidoreductase abundance and location influences redox poise and stress tolerance. Plant Physiol 172(3): 1480-1493.
Kudla J, Batistič O, Hashimoto K. 2010. Calcium signals: the lead currency of plant information processing. Plant Cell 22(3): 541-563.
Lehtimäki N, Lintala M, Allahverdiva Y, Aro EM, Mulo P. 2010. Drought stress induced regulation of component involved in feredoxindependent cyclic electron transfer. J Plant Physiol 167(12): 1018-1022.
Masoudi-Nejad A, Tonomura K, Kawashima S, Moriya Y, Suzuki M, Itoh M, Goto S. 2006. EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments. Nucleic Acids Res 34: 459-462.
Ortiz N, Armada E, Duque E, Roldán A, Azcón R. 2015. Contribution of arbuscular mycorrhizal fungi and/or bacteria to enhancing plant drought tolerance under natural soil conditions: Effectiveness of autochthonous or allochthonous strains. J Plant Physiol 174: 87-96.
Peiter E, Maathuis FJ, Mills LN, Knight H, Pelloux J, Hetherington AM, Sanders D. 2005. The vacuolar Ca2+-activated channel TPC1 regulates germination and stomatal movement. Nature 434: 404-408.
Rai AN, Mandliya T, Kulkarni P, Rao M, Suprasanna P. 2021. Evolution and Transcriptional Modulation of Lipoxygenase Genes Under Heat, Drought, Combined Stress in Brassica rapa. Plant Mol Biol Rep 39(1): 60-71.
Ramšak Ž, Baebler Š, Rotter A, Korbar M, Mozetič I, Usadel B, Gruden K. 2014. GoMapMan: integration, consolidation and visualization of plant gene annotations within the MapMan ontology. Nucleic Acids Res 42: 67-75.
Romualdi C, Bortoluzzi S, d’Alessi F, Danieli GA. 2003. IDEG6: a web tool for detection of differentially expressed genes in multiple tag sampling experiments. Physiol Genomics 12(2): 159-162.
Rosa M, Prado C, Podazza G, Interdonato R, Gonzalez JA, Hilal M, Prado FE. 2009. Soluble sugars- metabolism, sensing and abiotic stress. Plant Signal Behav 4(5): 388-393.
Sanan-Mishra N, Pham XH, Sopory SK, Tuteja N. 2005. Pea DNA helicase overexpression in tobacco confers high salinity tolerance without affecting yield. Proc Natl Acad Sci 102(2): 509-514.
Schäffer AA, Nawrocki EP, Choi Y, Kitts PA, Karsch-Mizrachi I, McVeigh R. 2018. VecScreen-plus-taxonomy: imposing a taxonomy increase on vector contamination screening. Bioinformtics 34(5): 755-759.
Song WY, Zhang ZB, Shao HB, Guo XL, Cao HX, Zhao HB, Hu XJ. 2008. Relationship between calcium decoding elements and plant abiotic-stress resistance. Int J Biol Sci 4(2): 116-125.
Sudhakar C, Thippeswamy M, Sivakumar M, Sudhakarbabu O, Dudhe MY. 2020. In silico Mining of EST-SSRs from the Drought Tolerant ESTs in Safflower. J Proteomics Bioinform 12(8).
Tang C, Deng L, Chang D, Chen S, Wang X, Kang Z. 2016. TaADF3, an actin-depolymerizing factor, negatively modulates wheat resistance against Puccinia striiformis. Front Plant Sci 6:1214. doi: 10.3389/fpls.2015.01214.
Tiňo P. 2009. Basic properties and information theory of Audic-Claverie statistic for analyzing cDNA arrays. BMC Bioinformatics 10(1): 1-9.
Tweneboah S, Oh S. 2017. Biological roles of NAC transcription factors in the regulation of biotic and abiotic stress responses in solanaceous crops. J Plant Biotechnol 44: 1-11.
SU Haq S, Khan A, Ali M, Khattak AM, Gai WX, Zhang HX, Gong ZH. 2019. Heat shock proteins: dynamic biomolecules to counter plant biotic and abiotic stresses. Int J mol Sci 20(21): 5321.
Webb AAR, McAinsh MR, Taylor JE, Hetherington AM. 1996. Calcium ions as intracellular second messengers in higher plants. Adv Bot Res 22: 45-96.
Xiong L, Lee H, Ishitani M, Tanaka Y, Stevenson B, Koiwa H, Zhu JK. 2002. Repression of stress-responsive genes by FIERY2, a novel TF in Arabidopsis. Proc Natl Acad Sci 99(16): 10899-10904.
Xu YH, Liu R, Yan L, Liu ZQ, Jiang SC, Shen YY, Zhang DP. 2012. Light-harvesting chlorophyll a/b-binding proteins are required for stomatal response to abscisic acid in Arabidopsis. J Exp Bot 63(3): 1095-1106.
Xu T, Lee K, Gu L, Kim J, Kang H. 2013. Functional characterization of plastid-specific ribosomal protein PSRP2 in A thaliana under stress conditions. Plant Physiol Biochem 73: 405-411.
Yang L, Zheng B, Mao C, Yi K, Liu F, Wu Y, Wu P. 2003. cDNA-AFLP analysis of inducible gene expression in rice seminal root tips under a water deficit. Gene 314: 141-148.
Yuan X, Wang H, Cai J, Bi Y, Li D, Song F. 2019. Rice NAC transcription factor ONAC functions as a positive regulator of drought and oxidative stress response. BMC Plant Biol 19: 278.
Zhou S, Li M, Guan Q, Liu F, Zhang S, Chen W, Ma F. 2015. Physiological and proteome analysis suggest critical roles for the photosynthetic system for high water-use efficiency under drought stress in malus. Plant Sci 236: 44-60. | ||
|
آمار تعداد مشاهده مقاله: 1,805 تعداد دریافت فایل اصل مقاله: 550 |
||