TRANSCRIPTOMIC ANALYSIS FOR TWO EGYPTIAN RICE CULTIVARS (Oryza sativa) UNDER DROUGHT STRESS
Abstract
Rice (Oryza sativa L.) is a semiaquatic plant, grow well in tropical, subtropical and temperate regions and it is highly affected by water shortage. Differential display reverse transcription (DDRT) technique was used to investigate differential gene expression between two Egyptian Oryza sativa cultivars under drought treatment, in an attempt to identify stress genes whose expression is regulated by drought and define their function. Fifty-six and fourty-seven fragments were differentially expressed under drought in G179 and Sk101, respectively. These differentially display (DD-PCR) fragments were categorized into up- and down- regulated fragments. DNA sequences of 17 fragments out of the total DD-PCR fragments was subjected to a nucleotide and amino acid sequence homology search through BLAST analysis programs from the National Center for Biotechnology and Information (NCBI). Four of the DD-PCR fragments were found to have the same base sequences showed homology with chaperone proteins DnaJ15. Moreover, another three fragments with the same sequence illustrated a homology with re-trotransposon protein, putativeTy3-gypsy subclass. Narrowing down the number of DD-PCR fragments to 12 fragments. Sequence alignment analysis identified four fragment sequences with significant homology to ribosome biogenesis protein WDR12, transposon protein, putative, CACTA, En/Spm sub-class, cytokinin riboside 5'-monophosphate phosphoribo-hydrolase LOGL10 and peroxisome biogenesis protein 12 of Oryza sativa. Real time PCR for three genes cytokinin riboside 5'-monophosphate phosphoribohy-drolase LOGL10, peroxisome biogenesis protein 12 and retrotransposon protein, putativeTy3-gypsy subclass were done to confirm their concentration.References
Abd Allah A., Badawy S. and Eliba A. (2016). Response of some root and yield traits to water stress for some rice varieties. J. Agric. Res. Kafr El-Sheikh Univ., 42: 352-364.
Abou Ali R. M., Shanab G. M., Haider A. S., Eissa H. F. and Salem A. M. (2010). Characterization and Expression of Abscisic Acid Inducible Gene(s) In Wild Legumes. Egypt. J. Genet. Cytol., 39: 57-72.
Abou Ali R. M., Hashim Warda. A., Ibrahim E. M., Fahmy I., Iman. F., Hassanein S. E. and Nada A. M. K. (2019). Enhancement of drought tolerance in rice (Oryza sativa L.) using Oxo-phytodienoate reductase 7 (OPR7) gene Egypt. J. Genet. Cytol., 48:155-177.
Ahn C. S., Cho H. K., Lee D. H., Sim H. J., Kim S. G. and Pai H. S. (2016). Functional characterization of the ribosome biogenesis factors PES, BOP1, and WDR12 (PeBoW), and mechanisms of defective cell growth and proliferation caused by PeBoW deficiency in Arabidopsis. J. Exp. Bot., 67: 5217-5232.
Altschul S. F., Madden T. L., Schäffer A. A., Zhang J., Zhang Z., Miller W. and Lipman D. J. (1997). Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res., 25: 3389-3402.
Borah P., Sharma E., Kaur A., Chandel G., Mohapatra T., Kapoor S. and Jitendra P. (2017). Analysis of drought-responsive signalling network in two contrasting rice cultivars using transcriptome-based approach. Sci. Rep., 7: 42131
Bourque G., Burns K. H., Gehring M., Gorbunova V., Seluanov A., Hammell M., Imbeault M., Izsvák Z., Levin H. L., Macfarlan T. S., Mager D. L. and Feschotte C. (2018). Ten things you should know about transposable elements. Genome Biol., 19: 199.
Campo S., Peris-Peris C., Montesinos L., Peñas G., Messeguer J., and San Segundo B. (2012). Expression of the maize ZmGF14-6 gene in rice confers tolerance to drought stress while enhancing susceptibility to pathogen infection. J. Exp. Bot., 63: 983-999.
Chandera S., Diego M., Tânia S., Douglas J., Pedro M., Tiago F., Duarte D., Marcia M., Joaquim M., Margarida M. and Nelson J. (2018). OsICE1 transcription factor improves photosynthetic performance and reduces grain losses in rice plants subjected to drought. Environ. Exper. Bot., 150: 88-98.
Chomczynski P. (1993). A reagent for single-step simultaneous isolation of RNA, DNA and proteins from cell and tissue samples. Biotechniques, 15: 532-536.
Dang Z., Qi Q., Zhang H., Li H., Wu S. and Wang Y. (2014). Identification of salt-stress-induced genes from the RNA-seq data of Reaumuria trigyna using differential-display reverse transcription PCR. Int. J. Genomics, 1-7
Das K. and Roychoudhury A. (2014). Reactive oxygen species (ROS) and response of antioxidants as ROS-scavengers during environmental stress in plants. Frontiers in Environmental Science., 2:1-13.
Ebeed H. T., Stevenson S. R., Cuming A. C. and Baker A. (2018). Conserved and differential transcriptional responses of peroxisome associated pathways to drought, dehydration and ABA. J. Exp. Bot., 69: 4971-4985.
Gojobori T., Sasaki T., Matsumoto T., Yamamoto K., Sakata K., Baba T., Y. Katayose, Wu J., Niimura Y., Cheng Z., Nagamura Y., Antonio B. A., Kanamori H., Hosokawa S., Masukawa M., and Arikawa K. (2002). The genome sequence and structure of rice chromosome 1. Nature, 420: 312-316.
Hassan H., El-Khoby W. and El-Hissewy A. (2013). Performance of some rice genotypes under both salinity and water stress conditions in Egypt. J. Plant Production, Mansoura Univ., 4: 1235-1257.
Hu J., Baker A., Bartel B., Linka N., Mullen R. T., Reumann S. and Zolman B. K. (2012). Plant peroxisomes: biogenesis and function. Plant Cell, 24: 2279-2303.
Hu X., Wu L., Zhao F., Zhang D., Li N., Zhu G., Li C. and Wang W. (2015). Phosphoproteomic analysis of the response of maize leaves to drought, heat and their combination stress. Front. Plant Sci., 6: 1-21.
Huang C. K., Shen Y. L., Huang L. F., Wu S. J.., Yeh C. H. and Lu C. A. (2016). The DEAD-Box RNA helicase AtRH7/PRH75 Participates in Pre-rRNA Processing, plant development and cold tolerance in Ara-bidopsis. Plant Cell Physiol., 57: 1741-1791.
Ibrahim E. K., Hashem H. A., Abou Ali R. M. and Hassanein A. A. (2019). Comparative Physiological Study on Six Egyptian Rice Cultivars Differing in their Drought Stress Tolerance. Acta Scientific Agriculture., 3: 44-52.
Katayose Y., Sasaki T., Matsumoto T., Hattori M. and Sakaki Y. (2002). Oryza sativa nipponbare (GA3) genomic DNA, chromosome 9, BAC clone: OJ1740_D06. https://www.ncbi.nlm.nih.gov/nucleotide/50726104?report=genbank&log$=nucltop&blast_rank=2&RID=ZNDUJK95015
Larkunthod P., Noppawan N., Jonaliza L., Theerayut T., Jirawat S., Boonrat J. and Piyada T. (2018). Physiological responses under drought stress of improved drought tolerant rice lines and their parents. Not. Bot. Horti. Agrobo., 46: 679-687.
Liu J. and Whitham S. A. (2013). Overexpression of a soybean nuclear localized type-III DnaJ domain-containing HSP40 reveals its roles in cell death and disease resistance. Plant J., 74: 110-121.
Liu J., Shen J., Xu Y., Li X., Xiao J., and Xiong L. (2016). Ghd2, a CONSTANS-like gene, confers drought sensitivity through regulation of senescence in rice. J. Exp. Bot., 67: 5785-5798.
Lum M., Hanafi M., Rafii Y., and Akmar A. (2014). Effect of drought stress on growth, proline and anti-oxidant enzyme activities of upland rice. J. Anim. Plant Sci., 24: 1487-1493.
Maekawa S., Ishida T. and Yanagisawa S. (2018). Reduced expression of APUM24, encoding a novel rRNA processing factor, induces sugar-dependent nucleolar stress and altered sugar responses in Arabidopsis thaliana. Plant Cell, 30: 209-227.
Manjesh S., Thirthikar M. B., Abida P. S., Rose M. F., Valasala P. A., George T. and Sajeevan R. S. (2017). Identification and characterization of genes responsible for drought tolerance in rice mediated by Pseudomonas fluorescens. Rice Sci., 24: 291-298.
Meyers B. C., Tingey S. V. and Morgante M. (2001). Abundance, distribution, and transcriptional activity of repetitive elements in the maize genome. Genome Res., 11:1660-1676.
Moonmoon S., Fakir M. and Islam M. (2017). Effect of drought stress on grain dry weight, photosynthesis and chlorophyll in six rice genotypes. Sch. J. Agric. Vet. Sci., 4:13-17.
Omar M. and Moussa A. (2016). Water management in Egypt for facing the future challenges. J. Adv. Res., 7: 403-412.
Pabuayon I. M., Yamamoto N., Trinidad J. L., Longkumer T., Raorane M. L. and Kohli A. (2016). Reference genes for accurate gene expression analyses across different tissues , developmental stages and genotypes in rice for drought tolerance. Rice, 9: 1-8.
Piégu B., Guyot R., Picault N., Roulin A., Sanyal A., Saniyal A., Kim H., Collura K., Brar D., Jackson S., Wing R. and Panaud O. (2006). Doubling genome size without polyploidization: Dynamics of re-trotransposition-driven genomic expansions in Oryza australiensis, a wild relative of rice. Genome research., 16:1262-1269.
Radwan A., Abou Ali R. M. I., Nada A., Hashem W., Assem S. and Husein E. (2015). Isolation and characterization of some drought related ESTs from barley. Afric. J. of Biotech., 14 :794-810.
Rivero R. M., Kojima M., Gepstein A., Sakakibara H., Mittler R., Gepstein S. and Blumwald E. (2007). Delayed leaf senescence induces extreme drought tolerance in a flowering plant. Proc. Natl Acad. Sci. USA, 104: 19631-19636.
RRTC (2014). Rice Research and Training Center. Technology transfer report of rice program. Agric. Res. Cen., Ministry of Agriculture and Land Reclamation. Salasmunoz S., Rodriguezhernandez A. A., Ortegaamaro M. A., Salazarbadillo F. B. and Jimenezbremont J. F. (2016). Arabidopsis AtDjA3 null mutant shows increased sensitivity to abscisic acid, salt, and osmotic stress in germination and post-germination stages. Front. Plant Sci., 7: 1-11.
Sambrook J., Fritsch E. and Maniatis T. (1989). Molecular cloning: A laboratory manual, 2nd ed. Cold Spring Harbor laboratoty, Cold Spring Harbor, NY.
Sanger F., Nicklen S. and Coulson A. R. (1977). DNA sequencing with chain-terminating inhibitors. Proc. Natl Acad. Sci., USA. 74: 5463-5467.
Sato, Shusei, Zamir, Dani, Giuliano, Giovanni, Tyagi, K. Akhilesh, Chatto-padhyay and Debasis (2012). The tomato genome sequence provides insights into fleshy fruit evolution. Nature, 485: 635-641.
Tomokazu K., Kaoru T., Hisakazu H., Atsuko G., Setsuko K., Takashi O., Kazunori O. and Teruhiko T. (2016). Overexpression of RSOsPR10, a root-specific rice PR10 gene ,confers tolerance against drought stress in rice, drought and salt stresses in bentgrass. Plant Cell Tiss. Organ Cult., 127: 35-46
Verde I., Abbott A. G., Scalabrin S., Jung S., Shu S., Marroni F., Zhebentya- yeva T., Dettori M. T., Grimwood J., Cattonaro F. and Zuccolo A. (2013). The high-quality draft genome of peach (Prunus persica) identifies unique patterns of genetic diversity, domestication and genome evolution. Nature Genet., 45: 487-494.
Vitte C., Panaud O. and Quesneville H. (2007). LTR retrotransposons in rice (Oryza sativa L.): recent burst amplifications followed by rapid DNA loss. BMC genomics, 8: 218-232.
Wang G., Cai G., Kong F., Deng Y., Ma N. and Meng Q. (2014). Overexpression of tomato chloroplast-targeted DnaJ protein enhances tolerance to drought stress and resistance to Pseudomonas solanacearum in transgenic tobacco. Plant Physiol. Biochem., 82: 95-104.
Xiong H., Jianping Y., Jinli M., Jinjie L., Hongliang Z., Xin W., Pengli L., Yan Z., Chonghui J., Zhigang Y., Yang L., Yan G., Binying F., Wensheng W., Zhikang L., Jauhar A. and Zichao L. (2018). Natural variation in OsLG3 increases drought tolerance in rice by inducing ROS scavenging. Plant Physiol., 178: 451-467.
Xu X., Pan S., Cheng S., Zhang B., Mu D., Ni P., Zhang G., Yang S., Li R., Wang J., Orjeda G., Guzman F., Torres M., Lozano R., Ponce O., Martinez D., Cruz G. De la, Chakrabarti S. K., Patil V. U., Skryabin K. G., Kuznetsov B. B., Ravin N. V., Kolganova T. V., Beletsky A. V. and Mardanov A. V. (2011). Genome sequence and analysis of the tuber crop potato. Nature, 475: 189-195.
Yamamoto K., Sasaki T. and Matsumoto T. (2001). Oryza sativa nipponbare (GA3) genomic DNA, chromosome 7, BAC clone:OJ1634_B10. https://www.ncbi.nlm.nih.gov/nucleotide/21623775?report=genbank&log$=nucltop&blast_rank=4&RID=0JEMREU7015
Yamamoto T., Mori Y., Ishibashi T., Uchiyama Y., Ueda T., Ando T., Hashimoto J., Kimura S. and Sakaguchi K. (2005). Interaction between proliferating cell nuclear antigen (PCNA) and a DnaJ induced by DNA damage. J. Plant Res., 118: 91-97.
Zhao H., Lü S. and Xiong L. (2017). At-LSG1-2 regulates leaf growth by affecting cell proliferation and the onset of endoreduplication and synergistically interacts with AtNMD3 during cell proliferation process. Front. Plant Sci., 8: 1-10.
Zhu X., Liang S., Yin J., Yuan C., Wang J., Li W., He M., Wang J., Chen W. and Ma B. (2015). The DnaJ OsDjA7/8 is essential for chloroplast development in rice (Oryza sativa). Gene, 574: 11-19.
Zhu Z., Song T., Zhang Q., Wang H., Han J., Xu Z. and Yan S. (2018).
OsJMJ703, a rice Gojobori histone demethylase gene, plays key roles in plant development and responds to drought stress. Plant Physiol. Biochem., 132: 183-188.
