title: Combining in silico mapping and arraying: an approach to identifying common candidate genes for submergence tolerance and resistance to bacterial leaf blight in rice.
abstract: Several genes/QTLs governing resistance/tolerance to abiotic and biotic stresses have been reported and mapped in rice. A QTL for submergence tolerance was found to be co-located with a major QTL for broad-spectrum bacterial leaf blight (bs-blb) resistance on the long arm of chromosome 5 in indica cultivars FR13A and IET8585. Using the Nipponbare (japonica) and 93-11 (indica) genome sequences, we identified, in silico, candidate genes in the chromosomal region [Kottapalli et al. (2006)]. Transcriptional profiling of FR13A and IET8585 using a rice 22K oligo array validated the above findings. Based on in silico analysis and arraying we observed that both cultivars respond to the above stresses through a common signaling system involving protein kinases, adenosine mono phosphate kinase, leucine rich repeat, PDZ/DHR/GLGF, and response regulator receiver protein. The combined approaches suggest that transcription factor EREBP on long arm of chromosome 5 regulates both submergence tolerance and blb resistance. Pyruvate decarboxylase and alcohol dehydrogenase, co-located in the same region, are candidate downstream genes for submergence tolerance at the seedling stage, and t-snare for bs-blb resistance. We also detected up-regulation of novel defense/stress-related genes including those encoding fumaryl aceto acetate (FAA) hydrolase, scramblase, and galactose oxidase, in response to the imposed stresses.
authors.affiliation: Plant Genome Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan. rkottapalli@lbk.ars.usda.gov
authors.forename: Kameswara Rao
authors.initials: KR
authors.lastname: Kottapalli
authors.forename: Kouji
authors.initials: K
authors.lastname: Satoh
authors.forename: Randeep
authors.initials: R
authors.lastname: Rakwal
authors.forename: Junko
authors.initials: J
authors.lastname: Shibato
authors.forename: Koji
authors.initials: K
authors.lastname: Doi
authors.forename: Toshifumi
authors.initials: T
authors.lastname: Nagata
authors.forename: Shoshi
authors.initials: S
authors.lastname: Kikuchi
mesh_terms: D002874:Chromosome Mapping; D019295:Computational Biology; D018506:Gene Expression Regulation, Plant; D017343:Genes, Plant; D020411:Oligonucleotide Array Sequence Analysis; D012275:Oryza / Q000235:genetics* / Q000382:microbiology; D010935:Plant Diseases / Q000235:genetics* / Q000382:microbiology; D040641:Quantitative Trait Loci / Q000235:genetics*; D014974:Xanthomonas / Q000472:pathogenicity