[Show abstract][Hide abstract] ABSTRACT: Elevated salinity imposes osmotic and ion toxicity stresses on living cells and requires a multitude of responses in order to enable plant survival. Building on earlier work profiling transcript levels in rice (Oryza sativa) shoots of FL478, a salt-tolerant indica recombinant inbred line, and IR29, a salt-sensitive cultivar, transcript levels were compared in roots of these two accessions as well as in the roots of two additional salt-tolerant indica genotypes, the landrace Pokkali and the recombinant inbred line IR63731. The aim of this study was to compare transcripts in the sensitive and the tolerant lines in order to identify genes likely to be involved in plant salinity tolerance, rather than in responses to salinity per se. Transcript profiles of several gene families with known links to salinity tolerance are described (e.g. HKTs, NHXs). The putative function of a set of genes identified through their salt responsiveness, transcript levels, and/or chromosomal location (i.e. underneath QTLs for salinity tolerance) is also discussed. Finally, the parental origin of the Saltol region in FL478 is further investigated. Overall, the dataset presented appears to be robust and it seems likely that this system could provide a reliable strategy for the discovery of novel genes involved in salinity tolerance.
[Show abstract][Hide abstract] ABSTRACT: Rice and barley are both members of Poaceae (grass family) but have a marked difference in salt tolerance. The molecular mechanism underlying this difference was previously unexplored. This study employs a comparative genomics approach to identify analogous and contrasting gene expression patterns between rice and barley.
A hierarchical clustering approach identified several interesting expression trajectories among rice and barley genotypes. There were no major conserved expression patterns between the two species in response to salt stress. A wheat salt-stress dataset was queried for comparison with rice and barley. Roughly one-third of the salt-stress responses of barley were conserved with wheat while overlap between wheat and rice was minimal. These results demonstrate that, at transcriptome level, rice is strikingly different compared to the more closely related barley and wheat. This apparent lack of analogous transcriptional programs in response to salt stress is further highlighted through close examination of genes associated with root growth and development.
The analysis provides support for the hypothesis that conservation of transcriptional signatures in response to environmental cues depends on the genetic similarity among the genotypes within a species, and on the phylogenetic distance between the species.
[Show abstract][Hide abstract] ABSTRACT: A large number of genetic variations have been identified in rice. Such variations must in many cases control phenotypic differences in abiotic stress tolerance and other traits. A single feature polymorphism (SFP) is an oligonucleotide array-based polymorphism which can be used for identification of SNPs or insertion/deletions (INDELs) for high throughput genotyping and high density mapping. Here we applied SFP markers to a lingering question about the source of salt tolerance in a particular rice recombinant inbred line (RIL) derived from a salt tolerant and salt sensitive parent.
Expression data obtained by hybridizing RNA to an oligonucleotide array were analyzed using a statistical method called robustified projection pursuit (RPP). By applying the RPP method, a total of 1208 SFP probes were detected between two presumed parental genotypes (Pokkali and IR29) of a RIL population segregating for salt tolerance. We focused on the Saltol region, a major salt tolerance QTL. Analysis of FL478, a salt tolerant RIL, revealed a small (< 1 Mb) region carrying alleles from the presumed salt tolerant parent, flanked by alleles matching the salt sensitive parent IR29. Sequencing of putative SFP-containing amplicons from this region and other positions in the genome yielded a validation rate more than 95%.
Recombinant inbred line FL478 contains a small (< 1 Mb) segment from the salt tolerant parent in the Saltol region. The Affymetrix rice genome array provides a satisfactory platform for high resolution mapping in rice using RNA hybridization and the RPP method of SFP analysis.
Full-text · Article · May 2009 · BMC Plant Biology
[Show abstract][Hide abstract] ABSTRACT: Barley (Hordeum vulgare L.) is a salt-tolerant member of the Triticeae. Recent transcriptome studies on salinity stress response in barley revealed regulation of jasmonic acid (JA) biosynthesis and JA-responsive genes by salt stress. From that observation and several other physiological reports, it was hypothesized that JA is involved in the adaptation of barley to salt stress. Here we tested that hypothesis by applying JA to barley plants and observing the physiological responses and transcriptome changes. Photosynthetic and sodium ion accumulation responses were compared after (1) salinity stress, (2) JA treatment and (3) JA pre-treatment followed by salinity stress. The JA-pre-treated salt-stressed plants accumulated strikingly low levels of Na(+) in the shoot tissue compared with untreated salt-stressed plants after several days of exposure to stress. In addition, pre-treatment with JA partially alleviated photosynthetic inhibition caused by salinity stress. Expression profiling after a short-term exposure to salinity stress indicated a considerable overlap between genes regulated by salinity stress and JA application. Three JA-regulated genes, arginine decarboxylase, ribulose 1.5-bisphosphate carboxylase/oxygenase (Rubisco) activase and apoplastic invertase are possibly involved in salinity tolerance mediated by JA. This work provides a reference data set for further study of the role of JA in salinity tolerance in barley and other plants species.
Preview · Article · May 2007 · Plant Cell and Environment
[Show abstract][Hide abstract] ABSTRACT: Rice yield is most sensitive to salinity stress imposed during the panicle initiation (PI) stage. In this study, we have focused on physiological and transcriptional responses of four rice genotypes exposed to salinity stress during PI. The genotypes selected included a pair of indicas (IR63731 and IR29) and a pair of japonica (Agami and M103) rice subspecies with contrasting salt tolerance. Physiological characterization showed that tolerant genotypes maintained a much lower shoot Na+ concentration relative to sensitive genotypes under salinity stress. Global gene expression analysis revealed a strikingly large number of genes which are induced by salinity stress in sensitive genotypes, IR29 and M103 relative to tolerant lines. We found 19 probe sets to be commonly induced in all four genotypes. We found several salinity modulated, ion homeostasis related genes from our analysis. We also studied the expression of SKC1, a cation transporter reported by others as a major source of variation in salt tolerance in rice. The transcript abundance of SKC1 did not change in response to salinity stress at PI stage in the shoot tissue of all four genotypes. However, we found the transcript abundance of SKC1 to be significantly higher in tolerant japonica Agami relative to sensitive japonica M103 under control and stressed conditions during PI stage.
Electronic supplementary material
Supplementary material is available in the online version of this article at http://dx.doi.org/10.1007/s11103-006-9112-0 and is accessible for authorized users.
[Show abstract][Hide abstract] ABSTRACT: Golden Promise is a salt-tolerant spring barley closely related to Maythorpe. Salt tolerance in Golden Promise has been attributed to a single mutation at the Ari-e locus (on 5H) resulting from irradiation of Maythorpe. Golden Promise accumulates lower shoot Na+ compared to Maythorpe when growing under saline conditions. This study focused on elucidating the genetic basis and mechanisms involved in this difference.
The level of polymorphism between the two genotypes was explored using the Barley1 GeneChip for single feature polymorphisms (SFPs) and an oligonucleotide pool assay for single nucleotide polymorphisms (SNPs). Polymorphism analyses revealed three haplotype blocks spanning 6.4 cM on chromosome 1H, 23.7 cM on chromosome 4H and 3.0 cM on 5H. The Barley1 GeneChip was used to examine transcript abundance in different tissues and stages during development. Several genes within the polymorphic haplotype blocks were differentially regulated. Additionally, a more global difference in the jasmonic acid pathway regulation was detected between the two genotypes.
The results confirm that Golden Promise and Maythorpe are genetically very closely related but establish that they are not isogenic, as previously reported, due to three polymorphic haplotype blocks. Transcriptome analysis indicates that the response of the two genotypes to salinity stress is quite different. Additionally, the response to salinity stress in the roots and shoot tissue is strikingly different.
[Show abstract][Hide abstract] ABSTRACT: In an effort to elucidate the physiological processes involved in cowpea differential growth response of four major USA cowpea cultivars (CB5, CB27, 8517 and 7964) to increasing salinity, we investigated the effect of salinity on leaf gas exchange of net photosynthetic rate per unit leaf mass (Pnm) and per unit leaf area (Pna), and stomatal conductance (gs) of the four cowpea cultivars. The experiment was set up as a standard split-plot design in which cowpea plants were grown in greenhouse sand tanks irrigated with nutrient solutions. Seven salinities ranging from 2.6 to 20.5dSm−1 were constructed based on Colorado River water salt composition with NaCl, CaCl2 and MgSO4 as the salinization salts. Light-saturated Pnm, Pna and gs of fully expanded trifoliage were examined at the vegetative growth and flowering stages, and the data were analyzed using a split-plot analysis of variance (ANOVA) model. We found a highly significant (P≤0.0001) reduction of Pnm, Pna and gs due to salinity. The responses of Pnm, Pna and gs to salinity could be further described by a general model of log(y)=a1+a2x+a3x2, where y represents either Pnm, Pna, or gs; a1, a2 and a3, empirical constants; x, salinity. We found that Pnm was more sensitive to salinity than Pna. Additionally, we found that increasing stomatal closure with increasing salinity might limit Pnm or Pna. While we did not find any significant difference (P>0.05) of Pnm and Pna among the four cultivars, we did find a significant difference (P≤0.05) in gs. No significant salt×cultivar interaction effect (P>0.05) was found with Pnm, Pna and gs indicating that the four cowpea cultivars have the same response pattern of their leaf gas exchange to salinity.
[Show abstract][Hide abstract] ABSTRACT: Barley (Hordeum vulgare L.) is a salt-tolerant crop species with considerable economic importance in salinity-affected arid and semiarid regions of the world. In this work, barley cultivar Morex was used for transcriptional profiling during salinity stress using a microarray containing approximately 22,750 probe sets. The experiment was designed to target the early responses of genes to a salinity stress at seedling stage. We found a comparable number of probe sets up-regulated and down-regulated in response to salinity. The differentially expressed genes were broadly characterized using gene ontology and through expression-based hierarchical clustering to identify interesting features in the data. A prominent feature of the response to salinity was the induction of genes involved in jasmonic acid biosynthesis and genes known to respond to jasmonic acid treatment. A large number of abiotic stress (heat, drought, and low temperature) related genes were also found to be responsive to salinity stress. Our results also indicate osmoprotection to be an early response of barley under salinity stress. Additionally, we compared the results of our studies with two other reports characterizing gene expression of barley under salinity stress and found very few genes in common.
Full-text · Article · May 2006 · Functional and Integrative Genomics
[Show abstract][Hide abstract] ABSTRACT: We investigated the effect of salt stress on the electrostatic properties of plasma membrane vesicles obtained from both the glycophytic, cultivated tomato, Lycopersicon esculentum (Mill, cvs. Heinz-1350 and VF 36) and the halophytic, wild species, L. cheesmanii (Hook, C.H. Mull, ecotype 1401) grown under control and saline conditions to determine if there exists a difference in the modulation of the membrane surface charge between the glycophytic and halophytic tomato. In agreement with earlier findings, fluorescence titration of vesicles indicated that salinity stress resulted in the modulation of the plasma membrane surface potential to more positive values in the glycophytic tomato species. However, a much smaller shift was measured in the halophytic tomato. Membrane surface potentials (Ψ0) of −20.0 and −7.6 mv were calculated for control and salt-stressed vesicles from the glycophytic Heinz-1350 cultivar, respectively, and −22.0 and −3.3 mv, respectively, from the glycophytic VF 36 cultivar. For the halophytic species, Lc-1401, we measured membrane surface potentials (Ψ0) of −24.8 and −19.7 mv for control and salt-stressed vesicles, respectively. BTP-Cl− stimulation of ΔpH was greater in vesicles isolated from control roots obtained from the wild Lc-1401 as compared with the cultivated Heinz-1350. However, the reverse was true in vesicles isolated from salt-stressed roots. Cl− stimulated proton pumping to a greater degree in vesicles from Heinz-1350 than Lc-1401. Both K+ or Na+ (added as K+- or Na+-Mes along with 100 mM BTP-Cl−) stimulated H+-pumping activity in plasma membrane vesicles from both Heinz-1350 and Lc-1401. In most cases, K+ stimulation of H+-pumping activity was higher in vesicles isolated from salt-stressed than from non-stressed plants.
[Show abstract][Hide abstract] ABSTRACT: Rice (Oryza sativa), a salt-sensitive species, has considerable genetic variation for salt tolerance within the cultivated gene pool. Two indica rice genotypes, FL478, a recombinant inbred line derived from a population developed for salinity tolerance studies, and IR29, the sensitive parent of the population, were selected for this study. We used the Affymetrix rice genome array containing 55,515 probe sets to explore the transcriptome of the salt-tolerant and salt-sensitive genotypes under control and salinity-stressed conditions during vegetative growth. Response of the sensitive genotype IR29 is characterized by induction of a relatively large number of probe sets compared to tolerant FL478. Salinity stress induced a number of genes involved in the flavonoid biosynthesis pathway in IR29 but not in FL478. Cell wall-related genes were responsive in both genotypes, suggesting cell wall restructuring is a general adaptive mechanism during salinity stress, although the two genotypes also had some differences. Additionally, the expression of genes mapping to the Saltol region of chromosome 1 were examined in both genotypes. Single-feature polymorphism analysis of expression data revealed that IR29 was the source of the Saltol region in FL478, contrary to expectation. This study provides a genome-wide transcriptional analysis of two well-characterized, genetically related rice genotypes differing in salinity tolerance during a gradually imposed salinity stress under greenhouse conditions.
[Show abstract][Hide abstract] ABSTRACT: The success of salt tolerance breeding programs employing traditional screening and selection has been limited in the past decades. This study was designed to characterize the genetic diversity within a subset of rice germplasm with different adaptations to saline soils using microsatellite markers. Salt tolerance was then analyzed among molecularly characterized genotypes. Plants of 33 genotypes were grown in sand tanks under greenhouse condition and irrigated with Yoshida nutrient solution. Two salt treatments were imposed with electrical conductivities of 0.9 dS m−1 (control) and 6.5 dS m−1 (6:1 molar ratio of NaCl and CaCl2). A total of 123 alleles were generated at 25 microsatellite loci among the 33 genotypes. Genotypes of japonica rice grouped into three clusters and those of indica rice grouped into two clusters based on microsatellite markers. Thirty percent of the alleles detected in 20 breeding lines were not identified in the cultivars analyzed. These alleles may provide favorable allelic combinations if the breeding lines are used for intercrosses. Physiological and morphological characters under salt stress were significantly (P=0.05) different among microsatellite clusters. There was a highly significant correlation (r=−0.25; P=0.005) between the matrices of Jaccard genetic similarity based on microsatellite markers and taxonomic distance based on ion data. These results indicate that the adaptation of rice to saline soils is different among genotypes with diverse genetic backgrounds. Implications for engineering salt tolerance are: (1) Improving salt tolerance can be achieved by selecting parental genotypes prior to intercrossing based on microsatellite markers. (2) Phenotypic variation of ion contents in segregating populations can be increased by selecting parental genotypes prior to intercrossing based on microsatellite markers. (3) Different salt tolerance components can be combined into a cultivar by intercrossing genotypes from different microsatellite clusters with diverse salt tolerance mechanisms.
[Show abstract][Hide abstract] ABSTRACT: The use of physiological characters as selection criteria in salt tolerance breeding requires the identification of the contribution each individual character makes to salt tolerance. Rice genotypes were evaluated for salt tolerance in terms of grain yield and physiological characters. Plants of twelve genotypes were grown in sand tanks in a greenhouse and irrigated with Yoshida nutrient solution. Sodium chloride and calcium chloride (5:1 molar ratio) were added at two concentrations to give moderate (4.5 dS m-1) and high (8.3 dS m-1) salinity treatments. One set of plants was harvested at 635 °Cċd (accumulative thermal time) after planting to determine LAI and mineral ion concentrations. Another set of plants was allowed to grow to maturity. High genotypic diversity for LAI and shoot ion contents was observed. LAI contributed the most to the variation of the grain yield under salt stress. Significant
correlations between LAI and yield components in both salt-tolerant and-sensitive genotypes further confirmed the significant contribution of LAI to grain yield. K-Na selectivity increased with increasing salinity. Conversely, Na-Ca selectivity decreased with increasing salinity. Significant correlations were identified between grain yield and both Na-Ca and K-Na selectivity. Highly significant (p<0.001) correlations were identified between Na-Ca selectivity and the rankings among genotypes for grain yield. Thus, Na-Ca selectivity could be one salt tolerance component and an useful selection criterion in screening for salt tolerance.