Genome wide expression analysis of Multidrug and toxin compound extrusion(MATE) gene in rice for understanding its role in resistance/susceptibility to Rhizoctonia solani AG1-IA

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dc.contributor.advisorVikal, Yogesh
dc.contributor.authorRupnaz Kaur
dc.date.accessioned2022-12-04T04:45:27Z
dc.date.available2022-12-04T04:45:27Z
dc.date.issued2021
dc.description.abstractRice (Oryza sativa) is one of the most important staple food crop for approximately 50% of human population across the world and is constantly hampered by sheath blight disease caused by Rhizoctonia solani AG1-IA pathogen. Several cultural, chemical and breeding approaches were applied to combat this disease but till date no major success was achieved. Study of hostpathogens interactions may find a new possible way to understand its molecular mechanism to overcome this disease. Various transporters are well characterized that plays significant role in various stress conditions. MATE gene family is one of them that belongs to secondary transporters group and help in extrusion, transportation of products across membrane via electrochemical gradient way. The current study is aimed to understand role of MATE transporter family towards the resistance/susceptibility in rice caused by R. solani AG1-IA. The commonly grown PR114 (susceptible) variety and ShB-8 (IET-21299) (moderate resistant) line were selected for present study. The R. solani fungus strain was cultured on PDA media and infection was done on targeted rice lines. The RNA was extracted from both infective lines at 0 hr, 24 and 48 hpi and preceded for transcriptome analysis (RNA Seq). The data of RNA Seq dissipated that a set of six differentially expressed MATE genes were identified on the basis of their log2 fold change value. The selected six genes were further validated through RT-PCR. Differential gene expression at different treatments showed that LOC_Os02g45380.1 MATE gene is one of the potential candidate gene involved in ShB resistance/susceptibility. Further in-silico analysis was performed for candidate MATE gene LOC_Os02g45380.1. The evolutionary phylogenetic analysis depicted that candidate MATE gene showed homology to various dicots and monocots. However, in monocots it is highly similar to Oryza nivara which means this gene might be transferred from wild species during natural selection. Various MATE genes are reported in different plant species genome, clustering analysis also suggested that a set of 52 MATE genes were present in rice genome that is supported by previous studies. Clustering of these 52 MATE genes showed that they can be further sub-grouped into four clades on the basis of function as previously reported. The LOC_Os02g45380.1 was present in clade III which may have role in citrate and metal transport. Cis regulating (promoter) analysis of LOC_Os02g45380.1 depicted various cis regulatory elements that are present in UTR which may play significant role in various abiotic and biotic stresses. Protein modelling of LOC_Os02g45380.1 revealed the presence of 11 transmembrane helix which helps to understand its topology. The PPI interaction analysis showed that various interaction molecules and proteins are present that aid in regulation of candidate MATE gene. To identify the variation in genic region of LOC_Os02g45380.1, the gene was amplified and cloned. For functional validation and raising of cis-genic lines, the tissue culture media was standardized for ShB-8 variety.en_US
dc.identifier.citationRupnaz Kaur (2021). Genome wide expression analysis of Multidrug and toxin compound extrusion(MATE) gene in rice for understanding its role in resistance/susceptibility to Rhizoctonia solani AG1-IA (Unpublished M.Sc. thesis). Punjab Agricultural University, Ludhiana, Punjab, India.en_US
dc.identifier.urihttps://krishikosh.egranth.ac.in/handle/1/5810190304
dc.keywordsOryza sativa, R. solani AG1-IA, ShB (IET-21299), PR114, MATE, PPI, hpi, hr, log2, R. solani, ABC, UTRen_US
dc.language.isoEnglishen_US
dc.pages76en_US
dc.publisherPunjab Agricultural University, Ludhianaen_US
dc.research.problemGenome wide expression analysis of Multidrug and toxin compound extrusion(MATE) gene in rice for understanding its role in resistance/susceptibility to Rhizoctonia solani AG1-IAen_US
dc.subAgricultural Biotechnologyen_US
dc.themeGenome wide expression analysis of Multidrug and toxin compound extrusion(MATE) gene in rice for understanding its role in resistance/susceptibility to Rhizoctonia solani AG1-IAen_US
dc.these.typeM.Scen_US
dc.titleGenome wide expression analysis of Multidrug and toxin compound extrusion(MATE) gene in rice for understanding its role in resistance/susceptibility to Rhizoctonia solani AG1-IAen_US
dc.typeThesisen_US
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