Transcriptome based identification of genes imparting bacterial leaf blight (Xanthomonas oryzae) resistance in rice (Oryza sativa L.)
| dc.contributor.advisor | Dr. Subhash N. | |
| dc.contributor.author | DESAI AMRUTA S. | |
| dc.date.accessioned | 2018-02-01T09:52:05Z | |
| dc.date.available | 2018-02-01T09:52:05Z | |
| dc.date.issued | 2017 | |
| dc.description.abstract | Rice is one of the most important staple foods for a larger part of the world’s population. It is a rich source of carbohydrates, energy, thiamine, pantothenic acid and folic acid. Because world-wide rice production has been severely affected by one of the major disease referred to as bacterial leaf blight caused by Xanthomonas oryzae pv. oryzae (Xoo), early efforts has been focusing on cloning and utilizing of disease resistance (R) genes in rice for resistance breeding. In the present study, thirty day old seedlings of BB resistant (IR 64) and susceptible (GR 11) genotypes were inoculated with and without BB (4 x l04 cells /ml). The seedlings were harvested 36 hours post inoculation for transcriptome sequencing employing the Miseq Illumina NGS sequencer after assaying the normal range for quantity and quality of total RNA, mRNA and cDNA. Transcriptome sequencing yielded 19311304 bp data with an average read length of 150 bp and constituted of 18440773 high quality reads which were assembled employing Trinity assembler for functional annotation. Trinity assembler gave assembly matrix (N50 of 2,453), proteome coverage and read alignment (90%) resulting in 30,000 contigs and 2,35,433 singletons/transcripts which were subjected to gene ontology (GO) following functional annotation. ii The maximum number of gene ontology was ascribed to cellular components, molecular function and biological processes showed that the maximum transcripts belonged to plastid, mitochondria and plasma membrane; nucleotide binding, kinase activity, DNA binding; cellular protein modification response to abiotic stress and biotic stress, respectively. Rice transcripts showed highest homology to Setaria italica and maximum blast hits with Hordeum vulgare. The maximum number of annotated transcripts was ascribed to transferase, hydrolase and oxidoreductase class of enzymes. The highly represented transcripts included disease resistance genes, pathogenesis related proteins, transcription factors (MYB, WRKY), signaling molecules (MAPK), enzymes of oxidative burst and LRR domain. These proteins were assumed to be involved in signaling networks induced in rice during BB infection. The transcripts were further subjected to confer their metabolic involvement through biochemical pathway through Kyoto encyclopedia of genes and genomes. Total 118 metabolic pathways were identified in rice transcriptome. Metabolic pathway enrichment ascribed the maximum number of transcripts in Glutathione metabolism leading to activation of defence responses called systemic acquired resistance (SAR). Metabolic pathway for purine metabolism, phenylalanine metabolism and starch and sucrose metabolism were prominently present. Transcriptomes of resistant and susceptible rice genotypes (with and without inoculum) were further screened for differential gene expression analysis by mapping individual reads to the assembly. Among the resistant and susceptible genotypes (with and without inoculum), 1314 transcripts were either up regulated or down regulated. The number of differentially expressed transcripts between the samples resistant inoculated and susceptible inoculated was 154. Further confirmation and validation was carried out through quantitative real time PCR. iii Relative quantification of defence related transcripts by quantitative real time PCR was performed using a-tubulin as endogeneous control. The relative expression of defence related genes associated with BB disease MYB, bZIP; defence related enzymes including lipoxygenase (LOX), phenylalanine ammonia lyase (PAL), respiratory burst oxidase (RBO), beta glucanase (BGLUC), Ribonuclease (RNase), Endo chitinase (CHI), signaling molecules, MAPK and CDPK showed up regulation in resistant inoculated than susceptible inoculated. Overall results of transcriptome study generated the information on involvement of MYB, WRKY, mitogen activated protein kinases, cellular ATPases, calcium dependent protein kinase and phenylalanine ammonia lyase transcription factors and the genes associated with resistance involved R genes homologous with the cell wall degrading enzymes like chitinase, 3-1,3 glucanases and metabolic pathway coding enymes polygalacturonase inhibiting proteins (PGIPs), cysteine proteases in the process of BB resistance. It could be inferred that defence responses associated with BB in rice were activated by hypersensitive response arising due to gene to gene interaction and systemic acquired resistance associated with pathogenesis related proteins, transcription factors, signaling molecules and enzyme related to glutathione pathway | en_US |
| dc.identifier.uri | http://krishikosh.egranth.ac.in/handle/1/5810040229 | |
| dc.keywords | Transcriptome based identification of genes imparting bacterial leaf blight (Xanthomonas oryzae) resistance in rice (Oryza sativa L.) | en_US |
| dc.language.iso | en | en_US |
| dc.publisher | AAU, Anand | en_US |
| dc.research.problem | Transcriptome based identification of genes imparting bacterial leaf blight (Xanthomonas oryzae) resistance in rice (Oryza sativa L.) | en_US |
| dc.sub | Agricultural Biotechnology | en_US |
| dc.subject | agriculture, biotechnology | en_US |
| dc.subject | identification | en_US |
| dc.theme | Transcriptome based identification of genes imparting bacterial leaf blight (Xanthomonas oryzae) resistance | en_US |
| dc.these.type | Ph.D | en_US |
| dc.title | Transcriptome based identification of genes imparting bacterial leaf blight (Xanthomonas oryzae) resistance in rice (Oryza sativa L.) | en_US |
| dc.type | Thesis | en_US |