A snapshot of the low temperature stress transcriptome of developing rice seedlings (Oryza sativa L.) via ESTs from subtracted cDNA library

Abstract

Rice (Oryza sativa L.) is sensitive to chilling particularly during early seedling development. Given the biochemical complexity of tolerance mechanisms, genetic potential for this trait depends on highly coordinated expression of many genes. We used a simple cDNA subtraction strategy to develop Expressed Sequence Tags (ESTs) that represent an important subset of cold stress-upregulated genes. The 3,084 subtracted cDNA clones represent a total of 1,967 unigenes from 1,354 singletons and 613 contigs. As expected in the developing seedlings, genes involved in basic cellular processes, i.e., metabolism, growth and development, protein synthesis, folding and destination, cellular transport, cell division and DNA replication were widely represented. Genes with stress-related and regulatory functions comprised 23.17% of the total ESTs. These categories included proteins with known function in cellular defenses against abiotic (drought, cold and salinity) and biotic (pathogen) stresses, and proteins involved in developmental and stress response signalling and transcription. Based on the types of genes represented, tolerance mechanisms rely on precise integration of developmental processes with stress-related responses. A large fraction of the ESTs (38.7%) represents unknown proteins. This EST library is a rich source of cold stress-related genes, and supplements for other publicly available libraries for comprehensive analysis of the stress-response transcriptome.

Identification and physiological characterization of two sister lines ofindicarice (Oryza sativaL.) with contrasting levels of cold tolerance

“…6), which indicates that this gene may maintain a higher basal expression level in this genotype than in the sensitive one. Surprisingly, neither of the tested genotypes presented increased levels of OsWCOR413 expression after 6 h of cold treatment, as would be expected based on the literature (de Los Reyes et al 2003). A plausible explanation for such difference in OsWCOR413 expression could be the different subspecies used (japonica versus indica in our work) and also the different developmental stages analyzed (5, 8, and 12 days postimbibition versus three leaf stage in our work, with plants being under cold treatment from 20 to 30 days post-imbibition).…”

“…Several other gene families are involved in responses to cold stress in rice, and overexpression of some of the genes resulted in cold tolerance: OsLIP5 and OsLIP9 (lowtemperature-induced dehydrin proteins) (Aguan et al 1991); OsCDPK7 (Ca 2+ -dependent protein kinase) (Saijo et al 2000); OsMEK1 and OsMAP1 (mitogen-activated protein signaling components) (Wen et al 2002); OsWCOR413 (unknown function membrane protein) (de Los Reyes et al 2003); and OsAsr1 (hydrophilin) (Kim et al 2009). …”

GGE biplot analysis of multi-environment yield trials of rice produced in a temperate climate

“…The effects of cold on the crop depend on the growth stage, intensity, and exposure time (Díaz et al, 2006). Low temperatures can cause physiological alterations in rice (de Los Reyes et al, 2003;Aghaee et al, 2011); for example, reduced chlorophyll content (Aghaee et al, 2011), decreased photosynthetic activity (Allen and Ort, 2001;Díaz et al, 2006;Suzuki et al, 2008), and increased reactive oxygen species. Low temperatures during reproductive stages can decrease fertility, thus reducing rice grain yield (Shimono et al, 2002;Sato et al, 2011).…”

Identification of sugar beet germplasm EL51 as a source of resistance to post-emergence Rhizoctonia damping-off

“…60% of planted seed ultimately develops into beets for sucrose production (Anonymous 2007). In contrast to poor emergence, which in Michigan is a more serious concern and largely results from various abiotic stresses (De los Reyes and McGrath 2003;McGrath et al 2000), stand loss in fields with otherwise good emergence appears largely due to biotic stresses that almost certainly include interactions of beets with species of Aphanomyces, Pythium, Fusarium, nematodes, and Rhizoctonia. Our observations over the past 10 years suggest that early-season crop failures result in large part from Rhizoctonia damping-off.…”