A plastome primer set for comprehensive quantitative real time RT-PCR analysis of Zea mays: a starter primer set for other Poaceae species

Role of sodium ion transporters and osmotic adjustments in stress alleviation of Cynodon dactylon under NaCl treatment: a parallel investigation with rice

Comparative analyses of the responses to NaCl in Cynodon dactylon and a sensitive crop species like rice could effectively unravel the salt tolerance mechanism in the former. C. dactylon, a wild perennial chloridoid grass having a wide range of ecological distribution is generally adaptable to varying degrees of salinity stress. The role of salt exclusion mechanism present exclusively in the wild grass was one of the major factors contributing to its tolerance. Salt exclusion was found to be induced at 4 days when the plants were treated with a minimum conc. of 200 mM NaCl. The structural peculiarities of the salt exuding glands were elucidated by the SEM and TEM studies, which clearly revealed the presence of a bicellular salt gland actively functioning under NaCl stress to remove the excess amount of Na⁺ ion from the mesophyll tissues. Moreover, the intracellular effect of NaCl on the photosynthetic apparatus was found to be lower in C. dactylon in comparison to rice; at the same time, the vacuolization process increased in the former. Accumulation of osmolytes like proline and glycine betaine also increased significantly in C. dactylon with a concurrent check on the H₂O₂ levels, electrolyte leakage and membrane lipid peroxidation. This accounted for the proper functioning of the Na⁺ ion transporters in the salt glands and also in the vacuoles for the exudation and loading of excess salts, respectively, to maintain the osmotic balance of the protoplasm. In real-time PCR analyses, CdSOS1 expression was found to increase by 2.5- and 5-fold, respectively, and CdNHX expression increased by 1.5- and 2-fold, respectively, in plants subjected to 100 and 200 mM NaCl treatment for 72 h. Thus, the comparative analyses of the expression pattern of the plasma membrane and tonoplast Na⁺ ion transporters, SOS1 and NHX in both the plants revealed the significant role of these two ion transporters in conferring salinity tolerance in Cynodon.

Deep sequencing of the tobacco mitochondrial transcriptome reveals expressed ORFs and numerous editing sites outside coding regions

BACKGROUND

The purpose of this study was to sequence and assemble the tobacco mitochondrial transcriptome and obtain a genomic-level view of steady-state RNA abundance. Plant mitochondrial genomes have a small number of protein coding genes with large and variably sized intergenic spaces. In the tobacco mitogenome these intergenic spaces contain numerous open reading frames (ORFs) with no clear function.

RESULTS

The assembled transcriptome revealed distinct monocistronic and polycistronic transcripts along with large intergenic spaces with little to no detectable RNA. Eighteen of the 117 ORFs were found to have steady-state RNA amounts above background in both deep-sequencing and qRT-PCR experiments and ten of those were found to be polysome associated. In addition, the assembled transcriptome enabled a full mitogenome screen of RNA C→U editing sites. Six hundred and thirty five potential edits were found with 557 occurring within protein-coding genes, five in tRNA genes, and 73 in non-coding regions. These sites were found in every protein-coding transcript in the tobacco mitogenome.

CONCLUSION

These results suggest that a small number of the ORFs within the tobacco mitogenome may produce functional proteins and that RNA editing occurs in coding and non-coding regions of mitochondrial transcripts.

Developmental and cell type characterization of bundle sheath and mesophyll chloroplast transcript abundance in maize

The C4 grass Zea mays separates light and light-independent photosynthetic processes into two leaf cell types: bundle sheath (BS) and mesophyll (M). When mature, BS and M cells have anatomically and biochemically distinct chloroplasts that must cooperate to complete the process of photosynthesis. This report compares changes in transcript abundance between young and mature maize BS and M chloroplasts from specific segments of the leaf developmental gradient. Representative transcripts encoding components of Photosystem I, Photosystem II, Cytochrome b (6) f, thylakoidal NADH dehydrogenase; and the large subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase as well as nine nuclear-coded transcripts encoding chloroplast proteins were measured using quantitative RT-PCR. In addition, 887 nuclear genes encoding plastid-localized proteins, as well as 64 chloroplast and 34 mitochondrial genes were assayed utilizing a cDNA microarray. In 9 out of the 18 chloroplast-encoded genes and 84 genes from the 985 element microarray revealed greater than twofold transcript abundance differences between developmental stages and/or cell types. Patterns for transcripts associated with operons and gene clusters suggest differing regulatory mechanisms for particular polycistronic stretches. In summary, this report provides evidence that cell type-specific transcript abundance varies more in the young developing chloroplast, and differences plateau or subside as chloroplasts mature.

High-throughput shoot imaging to study drought responses

Drought is a complex stress which elicits a wide variety of plant responses. As such, genetic studies of drought are particularly difficult. Elucidation of the genetic basis of components contributing to drought tolerance is likely to be more tractable than that of overall drought tolerance. Certain of the traits which contribute to drought tolerance in plants and the high-throughput phenotyping techniques available to measure those traits are described in this paper. On the basis of the dynamic nature of drought, plant development, and the resulting stress response, the focus is on non-destructive imaging techniques which allow a temporal resolution and monitoring of the same plants throughout the experiment. Information on the physiological changes in response to drought over time is vital in order to identify and characterize different drought-tolerance mechanisms. High-throughput imaging provides a valuable new tool which allows the dissection of plant responses to drought into a series of component traits.

Quantitative real time PCR in plant developmental biology

Gene expression patterns are important determinants of a cell's state, and changes in the expression profile indicate adaptation processes as a response to developmental transitions or environmental changes. Assaying gene expression can, therefore, help to elucidate mechanisms of determination and differentiation, as well as signaling networks. Several methods have been employed to determine transcript levels. The most quantitative and widely used technique is reverse transcription coupled to quantitative real time polymerase chain reaction (RT-qPCR). Live observation of fluorescence and, therefore, product increase during RT-qPCR allows the accurate determination of differences between initial template amounts. This is in contrast to the end-point analysis of conventional PCR, where initial differences in template amounts are usually masked because the analysis is done at the plateau phase. In the plateau phase, differences can no longer be distinguished due to inherent characteristics of PCR (e.g., loss of activity of the polymerase or because reaction components become limiting) that cause a drop in amplification efficiency, so that product accumulation levels out. Real time PCR circumvents this problem by shifting the analysis to an earlier stage of the amplification reaction.