Al-Tolerant Barley Mutant hvatr.g Shows the ATR-Regulated DNA Damage Response to Maleic Acid Hydrazide

ATR, a DNA damage signaling kinase, is required for cell cycle checkpoint regulation and detecting DNA damage caused by genotoxic factors including Al³⁺ ions. We analyzed the function of the HvATR gene in response to chemical clastogen-maleic acid hydrazide (MH). For this purpose, the Al-tolerant barley TILLING mutant hvatr.g was used. We described the effects of MH on the nuclear genome of hvatr.g mutant and its WT parent cv. “Sebastian”, showing that the genotoxic effect measured by TUNEL test and frequency of cells with micronuclei was much stronger in hvatr.g than in WT. MH caused a significant decrease in the mitotic activity of root cells in both genotypes, however this effect was significantly stronger in “Sebastian”. The impact of MH on the roots cell cycle, analyzed using flow cytometry, showed no differences between the mutant and WT.

Genome-wide identification of low phosphorus responsive microRNAs in two soybean genotypes by high-throughput sequencing

MicroRNAs (miRNAs) have been reported to be correlated with various stress responses in soybean, but only a few miRNAs have been demonstrated to respond to low phosphorus (LP) stress. To unravel the response mechanisms of miRNAs to low-P stress, the roots of two representative soybean genotypes with different P efficiency, Nannong94-156 (a LP-tolerant genotype) and Bogao (a LP-sensitive genotype), were used for the construction of RNA sequencing (RNA-seq) libraries under low/normal-P treatment by high-throughput sequencing. In total, 603 existing miRNAs and 1699 novel miRNAs belonging to 248 and 1582 families in all samples were identified, respectively. Among these miRNAs, 777 miRNAs were differentially expressed (DE) across different P levels and genotypes. Furthermore, putative targets of DE miRNAs were predicted, and these miRNAs mainly targeted ERF (ethylene responsive factor), auxin response factors (ARF), zinc finger protein, MYB, and NAC domain transcription factors. Gene ontology (GO) analysis showed that targets of DE miRNAs were significantly enriched in binding, metabolic processes, biological regulation, response to stress, and phosphorus metabolic processes. In addition, the expression profiles of chosen P-responsive miRNAs and target genes were validated by quantitative real-time PCR (qRT-PCR). Our study focused on genome-wide miRNA identification in two representative soybean genotypes under low-P stress. Overall, the DE miRNAs across different P levels and genotypes and their putative target genes will provide useful information for further study of miRNAs mediating low-P response and facilitate improvements in soybean breeding.

Genome-wide transcriptional profiling for elucidating the effects of brassinosteroids on Glycine max during early vegetative development

Soybean is a widely grown grain legume and one of the most important economic crop species. Brassinosteroids play a crucial role in plant vegetative growth and reproductive development. However, it remains unclear how BRs regulate the developmental processes in soybean, and the molecular mechanism underlying soybean early development is largely unexplored. In this study, we first characterized how soybean early vegetative growth was specifically regulated by the BR biosynthesis inhibitor propiconazole; this characterization included shortened root and shoot lengths, reduced leaf area, and decreased chlorophyll content. In addition, the growth inhibition induced by Pcz could be rescued by exogenous brassinolide application. The RNA-seq technique was employed to investigate the BR regulatory networks during soybean early vegetative development. Identification and analysis of differentially expressed genes indicated that BRs orchestrate a wide range of cellular activities and biological processes in soybean under various BR concentrations. The regulatory networks between BRs and multiple hormones or stress-related pathways were investigated. The results provide a comprehensive view of the physiological functions of BRs and new insights into the molecular mechanisms at the transcriptional level of BR regulation of soybean early development.

Increased tolerance to organic xenobiotics following recent allopolyploidy in Spartina (Poaceae)

Genome doubling or polyploidy is a widespread phenomenon in plants where it has important evolutionary consequences affecting the species distribution and ecology. PAHs are ubiquitous organic pollutants, which represent a major environmental concern. Recent data showed that tolerance to organic xenobiotics involve specific signaling pathways, and detoxifying gene sets referred as 'the xenome'. However, no data are available about how polyploidy impacts tolerance to organic xenobiotics. In the present paper, we investigated PAH tolerance following allopolyploidization in Spartina alterniflora, S. maritima and their derived allopolyploid species S. anglica. We performed comparative analyses of cellular compartmentalization, photosynthetic indices, and oxidative stress markers under phenanthrene-induced stress, and found that S. anglica exhibit increased tolerance compared to its parents. Based on 52 genes potentially involved in phenanthrene detoxification previously identified in A. thaliana, we investigated the Spartina xenome using genomic and transcriptomic available resources. Subsequently, we focused on GSTs, a ubiquitous enzymes class involved in organic xenobiotic detoxification. We examined expression profiles of selected genes by RT-qPCR, and revealed various patterns of parental expression alteration in the allopolyploid. The impacts of allopolyploidization on phenanthrene-induced stress and their potential ecological implications are discussed. The neo-allopolyploid S. anglica appears as a potential candidate for phytoremediation in PAH-polluted marshes.

Development of a Pedigreed Sorghum Mutant Library

Induced mutagenesis is a powerful approach to generate variations for elucidation of gene function and to create new traits for breeding. Here, we described a procedure to develop a pedigreed mutant library through chemical mutagenesis with ethylmethane sulfonate (EMS) treated seeds in sorghum and discussed its potential to generate new traits for sorghum improvement. Unlike random mutagenesis, a pedigreed mutant library, once properly established, can serve as a powerful resource to isolate and recover mutations of both agronomical and biological importance. With the development of affordable and high-throughput next-generation sequencing technologies, identification of causal mutations from a mutant library with a uniform genetic background becomes increasingly efficient and cost-effective. Fast causal gene discovery from mutant libraries combined with precise genome editing techniques will accelerate incorporation of new traits and revolutionize crop breeding.

Analysis of aluminum toxicity in Hordeum vulgare roots with an emphasis on DNA integrity and cell cycle

Barley is one of the cereals that are most sensitive to aluminum (Al). Al in acid soils limits barley growth and development and, as a result, its productivity. The inhibition of root growth is a widely accepted indicator of Al stress. Al toxicity is affected by many factors including the culture medium, pH, Al concentration and the duration of the treatment. However, Al can act differently in different species and still Al toxicity in barley deserves study. Since the mechanism of Al toxicity is discussed we cytogenetically describe the effects of different doses of bioavailable Al on the barley nuclear genome-mitotic activity, cell cycle profile and DNA integrity. At the same time, we tested an established deep-water culture (DWC) hydroponics system and analyzed the effects of Al on the root system parameters using WinRHIZO software. We demonstrated the cytotoxic and genotoxic effect of Al in barley root cells. We showed that Al treatment significantly reduced the mitotic activity of the root tip cells and it also induced micronuclei and damaged nuclei. The DNA-damaging effect of Al was observed using the TUNEL test. We define the inhibitory influence of Al on DNA replication in barley. Analysis with the labelling and detection of 5-ethynyl-2'-deoxyuridin (EdU) showed that the treatment with Al significantly decreased the frequency of S phase cells. We also demonstrated that Al exposure led to changes in the cell cycle profile of barley root tips. The delay of cell divisions observed as increased frequency of cells in G2/M phase after Al treatment was reported using flow cytometry.

Assessment of the antioxidant, cytotoxic, and genotoxic potential of the Annona muricata leaves and their influence on genomic stability

The popular use of Annona muricata L. is based upon a range of medicinal purposes, and the plant exhibits biological activities including antihyperglycemic, antiparasitic, and antitumor activities. The objectives of this study were to examine the antioxidant, cytotoxic, and genotoxic potential of the hydroalcoholic extract of A. muricata leaves (AMEs), as well as its effects on genotoxicity induced by methyl methanesulfonate (MMS) and hydrogen peroxide (H₂O₂). The results using 2,2-diphenyl-1-picrylhydrazyl assay showed that AME was able to scavenge 44.71% of free radicals. The extract significantly reduced the viability of V79 cells in the clonogenic assay at concentrations ≥8 µg/ml. No significant differences in micronucleus (MN) frequency were observed between V79 cell cultures treated with different concentrations of the extract (0.125, 0.25, 0.5, and 1 µg/ml) and negative control. When AME concentrations were combined with MMS, data revealed no marked differences from mutagen alone. In contrast, significant reductions in the frequencies of MN were noted in cultures treated with AME combined with H₂O₂ compared to H₂O₂ alone. In vivo studies found no significant differences in the frequencies of micronucleated polychromatic erythrocytes (MNPCEs) between animals treated with different AME doses compared to control. Animals treated with AME doses of 125 and 250 mg/kg and MMS exhibited significantly higher frequencies of MNPCE compared to mutagen alone. In conclusion, under current experimental conditions, AME was not genotoxic and exerted a modulatory effect on DNA damage depending upon the experimental conditions. The extract did not influence markedly MMS-induced genotoxicity in in vitro test system. However, the extract increased DNA damage induced by mutagen in mice. In V79 cells, AME reduced the genotoxicity produced by H₂O₂, and this protective effect was attributed in part to the antioxidant activity of AME.

Proteogenomic analysis reveals alternative splicing and translation as part of the abscisic acid response in Arabidopsis seedlings

In eukaryotes, mechanisms such as alternative splicing (AS) and alternative translation initiation (ATI) contribute to organismal protein diversity. Specifically, splicing factors play crucial roles in responses to environment and development cues; however, the underlying mechanisms are not well investigated in plants. Here, we report the parallel employment of short-read RNA sequencing, single molecule long-read sequencing and proteomic identification to unravel AS isoforms and previously unannotated proteins in response to abscisic acid (ABA) treatment. Combining the data from the two sequencing methods, approximately 83.4% of intron-containing genes were alternatively spliced. Two AS types, which are referred to as alternative first exon (AFE) and alternative last exon (ALE), were more abundant than intron retention (IR); however, by contrast to AS events detected under normal conditions, differentially expressed AS isoforms were more likely to be translated. ABA extensively affects the AS pattern, indicated by the increasing number of non-conventional splicing sites. This work also identified thousands of unannotated peptides and proteins by ATI based on mass spectrometry and a virtual peptide library deduced from both strands of coding regions within the Arabidopsis genome. The results enhance our understanding of AS and alternative translation mechanisms under normal conditions, and in response to ABA treatment.

DNA METHYLATION ANALYSIS DURING THE OPTIMIZATION OF Agrobacterium-MEDIATED TRANSFORMATION OF SOYBEAN

Soybean is recognized as one of the plants which are very difficult to be transformed. Considering the low transformation efficiency of soybean, we aimed to determine the effect of 6-benzylaminopurine (6-BA), shoot induction time, and infection time of Agrobacterium on the clonal propagation of Glycine max. Results showed that 1.6 mg/L 6-BA could be optimal to promote the induction of adventitious shoots. An induction time of 15 d was considered optimal for the actual experiment involving soybean shoot induction. Agrobacterium was cultured until an OD600 = 0.8 was reached for an infection time of 30 min; this infection time may be optimal to promote soybean transformation. Whole genome DNA methylation was analyzed by high-performance liquid chromatography (HPLC)-assisted quantification, and DNA methylation result is consistent with the phenotypic data of shoot development. In addition, two methylation-related genes (Decrease in DNA methylation 1 and DNA methyltransferases chromomethylase 2) were analyzed to determine expression differences by qRT-PCR in the shoots that were developed under different experimental conditions. In general, the expression values of these genes were normally downregulated under the recommended experimental conditions of soybean regeneration. This study showed the overall methylation changes in the in vitro culture of soybean, as affected by several variable parameters, which is useful to promote the transformation efficiency of soybean.

Measuring the damage of heavy metal cadmium in rice seedlings by SRAP analysis combined with physiological and biochemical parameters

BACKGROUND

Cadmium (Cd) is one of the most poisonous pollutants, and Cd pollution has become the limiting factor of rice production and quality improvement. Therefore it is of significant importance to monitor Cd toxicity by the detection of Cd contamination in rice with biomarkers. In the present study, sequence-related amplified polymorphism (SRAP) and physiological and biochemical methods were applied to determine the toxicological effects of Cd stress on rice.

RESULTS

With increasing Cd concentration and duration, the content of chlorophyll in the two rice varieties W7 and M63 decreased and that of malondialdehyde increased. This tendency was more apparent in M63. The antioxidant enzymes superoxide dismutase and peroxidase both increased significantly compared with controls. SRAP polymerase chain reaction results indicated significant differences between Cd treatments and controls in terms of SRAP profile, as well as genotypic differences. The genomic template stability (GTS) decreased with increasing Cd concentration and duration. Under the same treatment conditions, the GTS of W7 was higher than that of M63. Comparison analysis revealed that the changes in physiological and biochemical parameters of rice seedlings under Cd stress had a good correlation with the changes in SRAP profile. Furthermore, the changes in SRAP profile showed enhanced sensitivity in the roots of rice seedlings.

CONCLUSION

The SRAP profile and physiological and biochemical parameters could act as appropriate biomarkers for the measurement of Cd contamination during rice production.

The Use of Maleic Hydrazide for Effective Hybridization of Setaria viridis

An efficient method for crossing green foxtail (Setaria viridis) is currently lacking. S. viridis is considered to be the new model plant for the study of C4 system in monocots and so an effective crossing protocol is urgently needed. S. viridis is a small grass with C4-NADP (ME) type of photosynthesis and has the advantage of having small genome of about 515 Mb, small plant stature, short life cycle, multiple tillers, and profuse seed set, and hence is an ideal model species for research. The objectives of this project were to develop efficient methods of emasculation and pollination, and to speed up generation advancement. We assessed the response of S. viridis flowers to hot water treatment (48°C) and to different concentrations of gibberellic acid, abscisic acid, maleic hydrazide (MH), and kinetin. We found that 500 μM of MH was effective in the emasculation of S. viridis, whilst still retaining the receptivity of the stigma to pollination. We also report effective ways to accelerate the breeding cycle of S. viridis for research through the germination of mature as well as immature seeds in optimized culture media. We believe these findings will be of great interest to researchers using Setaria.

Relationship between RNA/DNA ratio, growth rate and accumulation of selenium in the cells of wheat leaves under the influence of minerals analcime and trepel

We studied specific effects of different doses of natural minerals--analcime (An) and trepel (Tr)--on the growth rate, selenium (Se) content and functional activity of the genome of wheat leaves measured by the RNA/DNA ratio. Our results show that under the influence of An and Tr, especially at low doses (25 mg/100 g sand), there is a significant increase in the content of Se, increased growth rate of leaves of wheat seedlings and decreased RNA/DNA ratio. We have found significant correlations between studied parameters. Our findings suggest that the RNA/DNA ratio can be used as a convenient, reliable indicator of the biological activity of minerals An and Tr, and for quantitative express-estimation of their impact on plant organisms.

Bioinformatic analysis of epigenetic and microRNA mediated regulation of drought responsive genes in rice

Drought stress response is a complex trait regulated at multiple levels. Changes in the epigenetic and miRNA regulatory landscape can dramatically alter the outcome of a stress response. However, little is known about the scope and extent of these regulatory factors on drought related cellular processes and functions. To this end, we selected a list of 5468 drought responsive genes (DRGs) of rice identified in multiple microarray studies and mapped the DNA methylation regions found in a genome wide methylcytosine immunoprecipitation and sequencing (mCIP-Seq) study to their genic and promoter regions, identified the chromatin remodeling genes and the genes that are targets of miRNAs. We found statistically significant enrichment of DNA methylation reads and miRNA target sequences in DRGs compared to a random set of genes. About 75% of the DRGs annotated to be involved in chromatin remodeling were downregulated. We found one-third of the DRGs are targeted by two-thirds of all known/predicted miRNAs in rice which include many transcription factors targeted by more than five miRNAs. Clustering analysis of the DRGs with epigenetic and miRNA features revealed, upregulated cluster was enriched in drought tolerance mechanisms while the downregulated cluster was enriched in drought resistance mechanisms evident by their unique gene ontologies (GOs), protein-protein interactions (PPIs), specific transcription factors, protein domains and metabolic pathways. Further, we analyzed the proteome of two weeks old young rice plants treated with a global demethylating agent, 5-azacytidine (5-azaC), subjected to drought stress and identified 56 protein spots that are differentially expressed. Out of the 56 spots, 35 were differently expressed in the sample with both demethylation and drought stress treatments and 28 (50%) were part of DRGs considered in the bioinformatic analysis.

Genome-wide identification of Brassica napus microRNAs and their targets in response to cadmium

MicroRNAs (miRNAs) are a distinct class of small RNAs in plants that not only regulate biological processes but also regulate response to environmental stresses. The toxic heavy metal cadmium (Cd) induces expression of several miRNAs in rapeseed (Brassica napus), but it is not known on a genome-wide scale how the expression of miRNAs and their target genes, is regulated by Cd. In this study, four small RNA libraries and four degradome libraries were constructed from Cd-treated and non-Cd-treated roots and shoots of B. napus seedlings. Using high-throughput sequencing, the study identified 84 conserved and non-conserved miRNAs (belonging to 37 miRNA families) from Cd-treated and non-treated B. napus, including 19 miRNA members that were not identified before. Some of the miRNAs were validated by RNA gel blotting. Most of the identified miRNAs were found to be differentially expressed in roots/shoots or regulated by Cd exposure. The study simultaneously identified 802 targets for the 37 (24 conserved and 13 non-conserved) miRNA families, from which there are 200, 537, and 65 targets, belonging to categories I, II, and III, respectively. In category I alone, many novel targets for miRNAs were identified and shown to be involved in plant response to Cd.

Plant 45S rDNA clusters are fragile sites and their instability is associated with epigenetic alterations

Our previous study demonstrated that 45S ribosomal DNA (45S rDNA) clusters were chromosome fragile sites expressed spontaneously in Lolium. In this study, fragile phenotypes of 45S rDNA were observed under aphidicolin (APH) incubation in several plant species. Further actinomycin D (ActD) treatment showed that transcriptional stress might interfere with chromatin packaging, resulting in 45S rDNA fragile expression. These data identified 45S rDNA sites as replication-dependent as well as transcription-dependent fragile sites in plants. In the presence of ActD, a dramatic switch to an open chromatin conformation and accumulated incomplete 5′ end of the external transcribed spacer (5′ETS) transcripts were observed, accompanied by decreased DNA methylation, decreased levels of histone H3, and increased histone acetylation and levels of H3K4me2, suggesting that these epigenetic alterations are associated with failure of 45S rDNA condensation. Furthermore, the finding that γ-H2AX was accumulated at 45S rDNA sites following ActD treatment suggested that the DNA damage signaling pathway was associated with the appearance of 45S rDNA fragile phenotypes. Our data provide a link between 45S rDNA transcription and chromatin-packaging defects and open the door for further identifying the molecular mechanism involved.

Identification of EMS-induced causal mutations in a non-reference Arabidopsis thaliana accession by whole genome sequencing

The most frequently used method to identify mutations induced by a commonly used mutagen, EMS (ethyl methane sulfonate), in Arabidopsis thaliana has been map-based cloning. The first step of this method is crossing a mutant with a plant of another accession as it requires polymorphisms between accessions for linkage analysis. Therefore, to perform the method routinely, it is greatly preferred to use accession combinations between which enough polymorphisms are already known. Further, it requires laborious examination of a large number of F₂ recombinants using many markers to detect each polymorphism. After linkage analysis narrows down the chromosomal region containing the causal mutation, sequencing candidate genes one by one within the region is necessary until the mutation is finally identified. Overall, this method is generally time-consuming and labor intensive, and it becomes harder when multiple loci are involved in phenotypes. A few recent reports showed that causal mutations induced by EMS could be identified by deep-sequencing technologies with less labor compared with the conventional method when mutants were generated in the Arabidopsis reference Columbia background whose genome organization is well known. Here we report that we succeeded in rapid identification of EMS-induced causal mutations in a non-reference accession background, whose whole genome sequence is not publicly available, using one round of whole genome sequencing. Moreover, in our case, we could monitor the causal locus and the transgenic reporter locus simultaneously, implying that this methodology could theoretically be applicable to analyzing even complex traits. We describe the pipeline of this methodology and discuss its characteristics.

Mapping QTLs for seed yield and drought susceptibility index in soybean (Glycine max L.) across different environments

Drought stress has long been a major constraint in maintaining yield stability of soybean (Glycine max (L.) Merr.) in rainfed ecosystems. The identification of consistent quantitative trait loci (QTL) involving seed yield per plant (YP) and drought susceptibility index (DSI) in a population across different environments would therefore be important in molecular marker-assisted breeding of soybean cultivars suitable for rainfed regions. The YP of a recombinant line population of 184 F(2:7:11) lines from a cross of Kefeng1 and Nannong1138-2 was studied under water-stressed (WS) and well-watered (WW) conditions in field (F) and greenhouse (G) trials, and DSI for yield was calculated in two trials. Nineteen QTLs associated with YP-WS and YP-WW, and 10 QTLs associated with DSI, were identified. Comparison of these QTL locations with previous findings showed that the majority of these regions control one or more traits related to yield and other agronomic traits. One QTL on molecular linkage group (MLG) K for YP-F, and two QTLs on MLG C2 for YP-G, remained constant across different water regimes. The regions on MLG C2 for YP-WW-F and MLG H for YP-WS-F had a pleiotropic effect on DSI-F, and MLG A1 for YP-WS-G had a pleiotropic effect on DSI-G. The identification of consistent QTLs for YP and DSI across different environments will significantly improve the efficiency of selecting for drought tolerance in soybean.

[Cytological and SSR analysis of irradiation-induced progenies of Trititrigia substitution line SN0095]

Pollens of Trititrigia substitution line SN0095 were radiated with 60Co-gamma ray and cytological characters of the progenies M1 and M2 were studied. The results showed that variations with different frequencies and chromosome numbers (2n=41, 2n=40 and 2n=39) were observed in both M1 and M2. Abnormal phenomena, such as univalents, multivalents, chromosome fragments, laggard chromosomes, chromosome bridges and micronucleus, appeared in high frequencies during the meiosis. It suggested that irradiation could promote changes of chromosome number and configuration efficiently, and could lead to rearrangements or translocations between chromosomes. The M2 progenies were examined using BARC159(240), a Thinopyrum intermedium-specific SSR marker of SN0095. Most M2 plants carried the locus BARC159(240), which indicated that the specific segment involving the locus BARC159(240) of Thinopyrum intermedium existed in these plants. However, a band of common wheat YN15 disappeared in a few plants although the locus BARC159(240) existed, which implied that chromosome rearrangements may have occurred in these plants.

Rice-arsenate interactions in hydroponics: whole genome transcriptional analysis

Rice (Oryza sativa) varieties that are arsenate-tolerant (Bala) and -sensitive (Azucena) were used to conduct a transcriptome analysis of the response of rice seedlings to sodium arsenate (AsV) in hydroponic solution. RNA extracted from the roots of three replicate experiments of plants grown for 1 week in phosphate-free nutrient with or without 13.3 muM AsV was used to challenge the Affymetrix (52K) GeneChip Rice Genome array. A total of 576 probe sets were significantly up-regulated at least 2-fold in both varieties, whereas 622 were down-regulated. Ontological classification is presented. As expected, a large number of transcription factors, stress proteins, and transporters demonstrated differential expression. Striking is the lack of response of classic oxidative stress-responsive genes or phytochelatin synthases/synthatases. However, the large number of responses from genes involved in glutathione synthesis, metabolism, and transport suggests that glutathione conjugation and arsenate methylation may be important biochemical responses to arsenate challenge. In this report, no attempt is made to dissect differences in the response of the tolerant and sensitive variety, but analysis in a companion article will link gene expression to the known tolerance loci available in the BalaxAzucena mapping population.

Expression of EuNOD-ARP1 encoding auxin-repressed protein homolog is upregulated by auxin and localized to the fixation zone in root nodules of Elaeagnus umbellata

Root nodule formation is controlled by plant hormones such as auxin. Auxin-repressed protein (ARP) genes have been identified in various plant species but their functions are not clear. We have isolated a full-length cDNA clone (EuNOD-ARP1) showing high sequence homology to previously identified ARP genes from root nodules of Elaeagnus umbellata. Genomic Southern hybridization showed that there are at least four ARP-related genes in the genome of E. umbellata. The cDNA clone encodes a polypeptide of 120 amino acid residues with no signal peptide or organelle-targeting signals, indicating that it is a cytosolic protein. Its cytosolic location was confirmed using Arabidopsis protoplasts expressing a EuNOD-ARP1:smGFP fusion protein. Northern hybridization showed that EuNOD-ARP1 expression was higher in root nodules than in leaves or uninoculated roots. Unlike the ARP genes of strawberry and black locust, which are negatively regulated by exogenous auxin, EuNOD-ARP1 expression is induced by auxin in leaf tissue of E. umbellata. In situ hybridization revealed that EuNOD-ARP1 is mainly expressed in the fixation zone of root nodules.

Arabidopsis–rice–wheat gene orthologues for Na+ transport and transcript analysis in wheat–L. elongatum aneuploids under salt stress

Lophopyrum elongatum is a wild relative of wheat that provides a source of novel genes for improvement of the salt tolerance of bread wheat. Improved Na(+) 'exclusion' is associated with salt tolerance in a wheat-L. elongatum amphiploid, in which a large proportion (ca. 50%) of the improved regulation of leaf Na(+) concentrations is controlled by chromosome 3E. In this study, genes that might control Na(+) accumulation, such as for transporters responsible for Na(+) entry (HKT1) and exit (SOS1) from cells, or compartmentalisation within vacuoles (NHX1, NHX5, AVP1, AVP2) in the model plant, Arabidopsis thaliana, were targeted for comparative analyses in wheat. Putative rice orthologues were identified and characterised as a means to bridge the large evolutionary distance between genomes from the model dicot and the more complex grass species. Wheat orthologues were identified through BLAST searching to identify either FL-cDNAs or ESTs and were subsequently used to design primers to amplify genomic DNA. The probable orthologous status of the wheat genes was confirmed through demonstration of similar intron-exon structure with their counterparts in Arabidopsis and rice. The majority of exons for Arabidopsis, rice and wheat orthologues of NHX1, NHX5 and SOS1 were conserved except for those at the amino and carboxy terminal ends. However, additional exons were identified in the predicted NHX1 and SOS1 genes of rice and wheat, as compared with Arabidopsis, indicating gene rearrangement events during evolution from a common ancestor. Nullisomic-tetrasomic, deletion and addition lines in wheat were used to assign gene sequences to chromosome regions in wheat and L. elongatum. Most sequences were assigned to homoeologous chromosomes, however, in some instances, such as for SOS1, genes were mapped to other unpredicted locations. Differential transcript abundance under salt stress indicated a complex pattern of expression for wheat orthologues that may regulate Na(+) accumulation in wheat lines containing chromosomes from L. elongatum. The identification of wheat orthologues to well characterized Arabidopsis genes, map locations and gene expression profiles increases our knowledge on the complex mechanisms regulating Na(+) transport in wheat and wheat-L. elongatum lines under salt stress.

Genome-wide expression profiling of ARABIDOPSIS RESPONSE REGULATOR 7(ARR7) overexpression in cytokinin response

The type-A ARRs of cytokinin two-component signaling system act as negative regulators for cytokinin signaling except for ARR4, but the molecular mechanism by which the A-type ARRs regulate cytokinin signaling remain elusive. To get insights into the molecular function of A-type ARR in cytokinin response, we sought to find the components that function downstream of A-type ARR protein by investigating the effects of ARR7 overexpression on cytokinin-regulated gene expression with the Affymetrix full genome array. To examine early cytokinin response, plants were treated with cytokinin for 30 min or 2 h, followed by GeneChip analysis. The hierarchical clustering analysis of our GeneChip data showed that ARR7 overexpression had distinctively repressive impacts on various groups of the cytokinin-regulated genes. In particular, the induction of all A-type ARRs except for ARR22, and AHK(ARABIDOPSIS HISTIDINE KINASE)1 and AHK4 was suppressed by ARR7. Cytokinin-induced expression of most of 12 expansin genes were repressed by ARR7, indicating potential involvement of ARR7 in cell expansion and plant development. Up-regulation of five cytokinin oxidase genes by cytokinins was negatively affected by ARR7. Our GeneChip analysis suggest that ARR7 mainly acts as a transcriptional repressor for a variety of early cytokinin-regulated genes encoding transcription factors, signal transmitters, plant development, and cellular metabolism, which may be responsible for reduced sensitivity of Arabidopsis transgenic plants overexpressing ARR7 to exogenous cytokinins.

High throughput screening in agrochemical research

The demand for new herbicides, insecticides and fungicides led to a steady increase in the number of compounds being tested to find novel market products. To keep pace with the rising workload, high throughput screening (HTS) technologies have been introduced. In agrochemical research miniaturised in vivo tests on whole real target organisms are now possible and are an integral part of the screening cascade. A complementary target based in vitro HTS has also been established in agrochemical research. Target based HTS allows a directed approach towards untouched market shares by novel modes of action. Selection of the best suited targets is the most crucial issue in this approach. Genomic methods thereby deliver many essential genes as candidate targets. Consideration of further criteria such as druggability notably narrows down the number of promising targets. Though target to hit to lead progression still is as in pharmaceutical research a complex and therefore risky process, the implementation of novel bioscience technologies has entailed the transition to an integrated innovative agrochemical research perspective.