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Development of EST-SSR molecular markers in rice (Oryza sativa L.) under salinity stress and identification of key genes | ||
| Journal of Plant Physiology and Breeding | ||
| دوره 13، شماره 2، اسفند 2023، صفحه 61-80 اصل مقاله (1.38 M) | ||
| نوع مقاله: Research Paper | ||
| شناسه دیجیتال (DOI): 10.22034/jppb.2023.54527.1290 | ||
| نویسندگان | ||
| Alireza Tarinejad* 1؛ Mohammad Reza Hossinzadeh2؛ Sedigheh Soltabnpour3؛ Mohammad Majidi2 | ||
| 1Department of Biotechnology, Faculty of Agriculture, Azarbaijan Shahid Madani University, Tabriz, Iran | ||
| 2Azarbaijan Shahid Madani University | ||
| 3a staff member of the Agriculture | ||
| چکیده | ||
| Expressed sequence tags of simple sequence repeats (EST-SSRs) are used to investigate genetic diversity and develop molecular markers for plants under biotic and abiotic stresses. However, there are a limited number of molecular markers based on the ESTs in rice to cope with the abiotic stresses including salinity, for use in breeding programs. Among 8299 ESTs, available in the NCBI database for salinity stress, 525 contigs, and 1139 singleton sequences were obtained. Twenty EST-SSR markers could be introduced for the selection of tolerant varieties to salt stress in rice by analysis of contigs and singletons. In contigs and singletons, significant common gene ontology terms are mainly related to the single-organism cellular process and response to abiotic stresses. The highest percentage of transcription factors for contigs and singletons was related to ERF, Dof, MYB, C2H2, BBR-BPC, bZIP, and WRKY. Moreover, the HSP81-2 (heat shock protein 81-2) and regulators of complement activation were identified as proteins of hub genes that were related to the salt stress tolerance mechanisms. Three uncharacterized hub genes (OS02T0161900-01, OsJ_19443, and OsJ_04035) including EST-SSRs for function identification were investigated by the 3D protein structure homology-modeling. OS02T0161900-01 as tetra ubiquitin, OSj-19443 as a serine/threonine-protein kinase/endoribonuclease, and OSj-04035 as a triosephosphate isomerase were identified. Most of the hub genes were related to environmental stresses and our findings provided candidate genes and transcription factors involved in salinity stress. The development of functional markers associated with abiotic stress tolerance will be helpful to facilitate rice breeding programs. However, before using these markers, laboratory confirmation is necessary. | ||
| کلیدواژهها | ||
| abiotic stress؛ contig؛ gene discovery؛ Oryza sativa L؛ salt؛ singleton؛ yield | ||
| مراجع | ||
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Al Azzawi TNI, Khan M, Hussain A, Shahid M, Imran QM, Mun BG, Lee SU, Yun BW. 2020. Evaluation of Iraqi rice cultivars for their tolerance to drought stress. Agronomy. 10(11): 1782-1802.
Bhargava A, Clabaugh I, To JP, Maxwell BB, Chiang Y-H, Schaller GE, Loraine A, Kieber JJ. 2013. Identification of cytokinin-responsive genes using microarray meta-analysis and RNA-Seq in Arabidopsis. Plant Physiol. 162: 272-294.
Chen Y, Wang M, Ouwerkerk PB. 2012. Molecular and environmental factors determining grain quality in rice. Food Energy Secur. 1: 111-132.
Cohen SP, Leach JE. 2019. Abiotic and biotic stresses induce a core transcriptome response in rice. Sci Rep. 9: 6273.
Ellis J, Burke J. 2007. EST-SSRs as a resource for population genetic analyses. Heredity. 99: 125-132.
Emon RM, Gregorio GB, Nevame AY, Islam MM, Islam M, Ye-Yang F. 2015. Morpho-genetic screening of the promising rice genotypes under salinity stress. J Agric Sci. 7: 94.
Guo J, Sun B, He H, Zhang Y, Tian H, Wang B. 2021. Current understanding of bHLH transcription factors in plant abiotic stress tolerance. Int J Mol Sci. 22(9): 4921-4933.
Hosseini M, Rabiei B, Ebadi A, Kordrostami M. 2018. The response of rice mutant lines to salinity stress at seedling stage using morphological traits and microsatellite markers. Cereal Res. 8: 15-31 (In Persian with English abstract).
Kim JH, Kim WT. 2013. The Arabidopsis RING E3 ubiquitin ligase AtAIRP3/LOG2 participates in positive regulation of high-salt and drought stress responses. Plant Physiol.162: 1733-1749.
Kumar KVK, Reddy M, Kloepper J, Lawrence K, Groth D, Miller M. 2016. Sheath blight disease of rice (Oryza sativa L.)– an overview. Biosci Biotechnol Res Asia 6: 465-480.
Kumari S, Verma VK. 2020. Rubisco degradation, glutathione reductase induction, proline and valine accumulation in contrasting wheats under sodium chloride (NaCl) induced oxidative stress conditions. Int J Curr Microbiol App Sci. 9(10): 3192-3204.
Kwon S, Kang NK, Koh HG, Shin SE, Lee B, Jeong BR, Chang YK. 2018. Enhancement of biomass and lipid productivity by overexpression of a bZIP transcription factor in Nannochloropsis salina. Biotechnol Bioeng. 115(2): 331-340.
Masoudi-Nejad A, Tonomura K, Kawashima S, Moriya Y, Suzuki M, Itoh M, Kanehisa M, Endo T, Goto S. 2006. EGassembler: online bioinformatics service for large-scale processing, clustering and assembling ESTs and genomic DNA fragments. Nucleic Acids Res. 34(2): W459-W462.
McCouch SR, Teytelman L, Xu Y, Lobos KB, Clare K, Walton M, Fu B, Maghirang R, Li Z, Xing Y, et al. 2002. Development and mapping of 2240 new SSR markers for rice (Oryza sativa L.). DNA Res. 9(6): 199-207.
Mohammadinezhad G, Singh R, Arzani A, Rezaei A, Sabouri H, Gregorio G. 2010. Evaluation of salinity tolerance in rice genotypes. Int J Plant Prod. 4(3): 199-208.
Negrão S, Courtois B, Ahmadi N, Abreu I, Saibo N, Oliveira MM. 2011. Recent updates on salinity stress in rice: from physiological to molecular responses. Crit Rev Plant Sci. 30(4): 329-377.
Powell W, Machray GC, Provan J. 1996. Polymorphism revealed by simple sequence repeats. Trends Plant Sci. 1: 215-222.
Ram S. 2013. Metachromatic leukodystrophy: a bioinformatics approach through protein-protein interaction network analysis. Department of Biotechnology, Delhi Technological University, Delhi, India. p. 1-112.
Sabouri H, Rezai AM, Moumeni A, Kavousi A, Katouzi M, Sabouri A. 2009. QTLs mapping of physiological traits related to salt tolerance in young rice seedlings. Biol Plant. 53: 657-662.
Sarkar RK, Chakraborty K, Chattopadhyay K, Ray S, Panda D, Ismail AM. 2019. Responses of rice to individual and combined stresses of flooding and salinity. In: Hasanuzzaman M, Fujita M, Nahar K, Biswas, J , editors. Advances in rice research for abiotic stress tolerance. Cambridge, UK: Woodhead Publishing. p. 281-297.
Shah WH, Rasool A, Saleem S, Mushtaq NU, Tahir I, Hakeem KR, Rehman RU. 2021. Understanding the integrated pathways and mechanisms of transporters, protein kinases, and transcription factors in plants under salt stress. Int J Genomics. ID: 5578727.
Siebenmorgen TJ, Grigg BC, Lanning SB. 2013. Impacts of preharvest factors during kernel development on rice quality and functionality. Annu Rev Food Sci Technol. 4: 101-115.
Stone SL. 2022. Ubiquitin ligases at the nexus of plant responses to biotic and abiotic stresses.
Essays Biochem. 66: 123-133.
Takehisa H, Shimodate T, Fukuta Y, Ueda T, Yano M, Yamaya T, Kameya T, Sato T. 2004. Identification of quantitative trait loci for plant growth of rice in paddy field flooded with salt water. Field Crops Res. 89: 85-95.
Tang Y, Bao X, Zhi Y, Wu Q, Guo Y, Yin X, Zeng L, Li J, Zhang J, He W, et al. 2019. Overexpression of a MYB family gene, OsMYB6, increases drought and salinity stress tolerance in transgenic rice. Front Plant Sci. 10: 168.
Temnykh S, Park WD, Ayres N, Cartinhour S, Hauck N, Lipovich L, Cho YG, Ishii T, McCouch SR. 2000. Mapping and genome organization of microsatellite sequences in rice (Oryza sativa L.). Theor Appl Genet. 100: 697-712.
Thiel T, Michalek W, Varshney R, Graner A. 2003. Exploiting EST databases for the development and characterization of gene-derived SSR-markers in barley (Hordeum vulgare L.). Theor Appl Genet. 106: 411-422.
Wu G, Tian N, She F, Cao A, Wu W, Zheng S, Yang N. 2022. Characteristics analysis of early responsive to dehydration genes in Arabidopsis thaliana (AtERD). Plant Signal Behav. 18(1): 2105021.
Yang Y, Xie J, Li J, Zhang J, Zhang X, Yao Y, Wang C, Niu T, Bakpa EP. 2022. Trehalose alleviates salt tolerance by improving photosynthetic performance and maintaining mineral ion homeostasis in tomato plants. Front Plant Sci. 13: 974507.
Yu J-K, La Rota M, Kantety R, Sorrells M. 2004. EST derived SSR markers for comparative mapping in wheat and rice. Mol Genet Genom.271: 742-751. | ||
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