Combining in silico mapping and arraying: an approach to identifying common candidate genes for submergence tolerance and resistance to bacterial leaf blight in rice.
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.
Kottapalli
Kameswara Rao
KR
Plant Genome Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan. rkottapalli@lbk.ars.usda.gov
Satoh
Kouji
K
Rakwal
Randeep
R
Shibato
Junko
J
Doi
Koji
K
Nagata
Toshifumi
T
Kikuchi
Shoshi
S
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