Genome size variation among accessions of Arabidopsis thaliana

BACKGROUND AND AIMS: Estimates of the amount of nuclear DNA of Arabidopsis thaliana, known to be among the lowest within angiosperms, vary considerably. This study aimed to determine genome size of a range of accessions from throughout the entire Eurasian range of the species. METHODS: Twenty accessions from all over Europe and one from Japan were examined using flow cytometry. KEY RESULTS: Significant differences in mean C-values were detected over a 1.1-fold range. Mean haploid (1C) genome size was 0.215 pg (211 Mbp) for all analysed accessions. Two accessions were tetraploid. CONCLUSIONS: A closer investigation of the DNA fractions involved in intraspecific genome size differences in this experimentally accessible species may provide information on the factors involved in stability and evolution of genome sizes.     

Natural variation of submergence tolerance among Arabidopsis thaliana accessions

? The exploitation of natural variation in Arabidopsis thaliana (Arabidopsis) provides a huge potential for the identification of the molecular mechanisms underlying this variation as a result of the availability of a vast array of genetic and genomic resources for this species. Eighty-six Arabidopsis accessions were screened for natural variation in flooding tolerance. This forms the first step towards the identification and characterization of the role of candidate genes contributing to flooding tolerance. ? Arabidopsis accessions at the 10-leaf stage were subjected to complete submergence in the dark. Survival curves were plotted to estimate median lethal times as a measure of tolerance. Flooding-associated survival parameters, such as root and shoot oxygen content, initial carbohydrate content and petiole elongation under water, were also measured. ? There was a significant variation in submergence tolerance among Arabidopsis accessions. However, the order of tolerance did not correlate with root and shoot oxygen content or initial amounts of shoot starch and total soluble sugars. A negative correlation was observed between submergence tolerance and underwater petiole elongation. ? Arabidopsis accessions show considerable variation in the ability to tolerate complete submergence, making it a good species in which to identify and characterize genes and to study mechanisms that contribute to survival under water.     

Multiple resistance traits control Plum pox virus infection in Arabidopsis thaliana

Twelve Arabidopsis accessions were challenged with Plum pox potyvirus (PPV) isolates representative of the four PPV strains. Each accession supported local and systemic infection by at least some of the PPV isolates, but high variability was observed in the behavior of the five PPV isolates or the 12 Arabidopsis accessions. Resistance to local infection or long-distance movement occurred in about 40% of all the accession-isolate combinations analyzed. Except for Nd-1, all accessions showed resistance to local infection by PPV-SoC; in the Landsberg erecta (Ler) accession, this resistance was compromised by sgt1 and rar1 mutations, suggesting that it could be controlled by an R gene-mediated resistance pathway. While most of the susceptible accessions were symptomless, PPV induced severe symptoms on inflorescences in C24, Ler, and Bay-0 as early as 15 days after inoculation. Genetic analyses indicated that these interaction phenotypes are controlled by different genetic systems. The restriction of long-distance movement of PPV-El Amar and of another member of genus Potyvirus, Lettuce mosaic virus, in Col-0 requires the RTM genes, indicating for the first time that the RTM system may provide a broad range, potyvirus-specific protection against systemic infection. The restriction to PPV-PS long-distance movement in Cvi-1 is controlled by a single recessive gene, designated rpv1, which was mapped to chromosome 1. The nuclear inclusion polymerase b-capsid protein region of the viral genome appears to be responsible for the ability of PPV-R to overcome rpv1-mediated resistance.     

Variation in chiasma frequency among eight accessions of Arabidopsis thaliana

Natural variation in meiotic recombination frequency in Arabidopsis thaliana has been assessed by analyzing chiasma frequency variation among a range of geographically and ecologically diverse accessions. Fifty pollen mother cells at metaphase I of meiosis were analyzed from each of eight accessions and fluorescence in situ hybridization was applied to enable identification of all 10 chromosome arms. There was no significant variation in mean chiasma frequency between plants within accessions, but there was significant variation between accessions. Further analysis confirmed this finding and identified two particular accessions, Cvi and Ler, as having chiasma frequencies significantly lower than those of the other accessions. The analysis also revealed that the pattern of chiasma distribution between arms and among chromosomes is not consistent over accessions. Further detailed analyses were conducted on each individual chromosome (1-5) in turn, revealing that chromosome 4, one of the acrocentric chromosomes, is the least variable while the other acrocentric chromosome (2) is the most variable. These findings indicate the existence of recombination regulatory elements in Arabidopsis and we conclude that it may be possible in the future to identify these elements and determine their mode of action. The practical implications of such developments are considerable.     

Priming for enhanced ARGONAUTE2 activation accompanies induced resistance to cucumber mosaic virus in Arabidopsis thaliana

Systemic acquired resistance (SAR) is a broad-spectrum disease resistance response that can be induced upon infection from pathogens or by chemical treatment, such as with benzo-(1,2,3)-thiadiazole-7-carbothioic acid S-methyl ester (BTH). SAR involves priming for more robust activation of defence genes upon pathogen attack. Whether priming for SAR would involve components of RNA silencing remained unknown. Here, we show that upon leaf infiltration of water, BTH-primed Arabidopsis thaliana plants accumulate higher amounts of mRNA of ARGONAUTE (AGO)2 and AGO3, key components of RNA silencing. The enhanced AGO2 expression is associated with prior-to-activation trimethylation of lysine 4 in histone H3 and acetylation of histone H3 in the AGO2 promoter and with induced resistance to the yellow strain of cucumber mosaic virus (CMV[Y]). The results suggest that priming A. thaliana for enhanced defence involves modification of histones in the AGO2 promoter that condition AGO2 for enhanced activation, associated with resistance to CMV(Y). Consistently, the fold-reduction in CMV(Y) coat protein accumulation by BTH pretreatment was lower in ago2 than in wild type, pointing to reduced capacity of ago2 to activate BTH-induced CMV(Y) resistance. A role of AGO2 in pathogen-induced SAR is suggested by the enhanced activation of AGO2 after infiltrating systemic leaves of plants expressing a localized hypersensitive response upon CMV(Y) infection. In addition, local inoculation of SAR-inducing Pseudomonas syringae pv. maculicola causes systemic priming for enhanced AGO2 expression. Together our results indicate that defence priming targets the AGO2 component of RNA silencing whose enhanced expression is likely to contribute to SAR.     

Clinal variation in freezing tolerance among natural accessions of Arabidopsis thaliana

Low temperature represents a form of abiotic stress that varies predictably with latitude and altitude and to which organisms have evolved multiple physiological responses. Plants provide an especially useful experimental system for investigating the ecological and evolutionary dynamics of tolerance to low temperature because of their sessile lifestyle and inability to escape ambient atmospheric conditions. Here, intraspecific variation in freezing tolerance was investigated in Arabidopsis thaliana by conducting freezing tolerance assays on 71 accessions collected from across the native range of the species. Assays were performed at multiple minimum temperatures and on both cold-acclimated and non-cold-acclimated individuals. Considerable variation in freezing tolerance was observed among accessions both with and without a prior cold-acclimation treatment, suggesting that differences among accessions in cold-acclimation capacity as well as differences in intrinsic physiology contribute to variation in this phenotype. A highly significant positive relationship was observed between freezing tolerance and latitude of origin of accessions, consistent with a major role for natural selection in shaping variation in this phenotype. Clinal variation in freezing tolerance in A. thaliana coupled with considerable knowledge of the underlying genetics and physiology of this phenotype should allow evolutionary genetic analysis at multiple levels.     

Variation in selenium tolerance and accumulation among 19 Arabidopsis thaliana accessions

Selenium (Se) is an essential element for many organisms but also toxic at higher levels. The objective of this study was to identify accessions from the model species Arabidopsis thaliana that differ in Se tolerance and accumulation. Nineteen Arabidopsis accessions were grown from seed on agar medium with or without selenate (50 microM) or selenite (20 microM), followed by analysis of Se tolerance and accumulation. Tissue sulfur levels were also compared. The Se Tolerance Index (root length+Se/root length control) varied among the accessions from 0.11 to 0.44 for selenite and from 0.05 to 0.24 for selenate. When treated with selenite, the accessions differed by two-fold in shoot Se concentration (up to 250 mgkg(-1)) and three-fold in root Se concentration (up to 1000 mgkg(-1)). Selenium accumulation from selenate varied 1.7-fold in shoot (up to 1000 mgkg(-1)) and two-fold in root (up to 650 mgkg(-1)). Across all accessions, a strong correlation was observed between Se and S concentration in both shoot and root under selenate treatment, and in roots of selenite-treated plants. Shoot Se accumulation from selenate and selenite were also correlated. There was no correlation between Se tolerance and accumulation, either for selenate or selenite. The F(1) offspring from a cross between the extreme selenate-sensitive Dijon G and the extreme selenate-tolerant Estland accessions showed intermediate selenate tolerance. In contrast, the F(1) offspring from a cross between selenite-sensitive and -tolerant accessions (Dijon GxCol-PRL) were selenite tolerant. The results from this study give new insight into the mechanisms of plant selenium (Se) tolerance and accumulation, which may help develop better plants for selenium phytoremediation or as fortified foods.     

Nitric oxide as a signaling molecule in brassinosteroid‐mediated virus resistance to Cucumber mosaic virus in Arabidopsis thaliana

Brassinosteroids (BRs) are growth‐promoting plant hormones that play a crucial role in biotic stress responses. Here, we found that BR treatment increased nitric oxide (NO) accumulation, and a significant reduction of virus accumulation in Arabidopsis thaliana. However, the plants pre‐treated with NO scavenger [2‐(4‐carboxyphenyl)‐4,4,5,5‐tetramethyl‐imidazoline‐1‐1‐oxyl‐3‐oxide (PTIO)] or nitrate reductase (NR) inhibitor (tungstate) hardly had any NO generation and appeared to have the highest viral replication and suffer more damages. Furthermore, the antioxidant system and photosystem parameters were up‐regulated in brassinolide (BL)‐treated plants but down regulated in PTIO‐ or tungstate‐treated plants, suggesting NO may be involved in BRs‐induced virus resistance in Arabidopsis. Further evidence showed that NIA1 pathway was responsible for BR‐induced NO accumulation in Arabidopsis. These results indicated that NO participated in the BRs‐induced systemic resistance in Arabidopsis. As BL treatment could not increase NO levels in nia1 plants in comparison to nia2 plants. And nia1 mutant exhibited decreased virus resistance relative to Col‐0 or nia2 plants after BL treatment. Taken together, our study addressed that NIA1‐mediated NO biosynthesis is involved in BRs‐mediated virus resistance in A. thaliana.     

Source verification of mis-identified Arabidopsis thaliana accessions

A major strength of Arabidopsis thaliana as a model lies in the availability of a large number of naturally occurring inbred lines. Recent studies of A. thaliana population structure, using thousands of accessions from stock center and natural collections, have revealed a robust pattern of isolation by distance at several spatial scales, such that genetically identical individuals are generally found close to each other. However, some individual accessions deviate from this pattern. While some of these may be the products of rare long‐distance dispersal events, many deviations may be the result of mis‐identification, in the sense that the data regarding location of origin data are incorrect. Here, we aim to identify such discrepancies. Of the 5965 accessions examined, we conclude that 286 deserve special attention as being potentially mis‐identified. We describe these suspicious accessions and their possible origins, and advise caution with regard to their use in experiments in which accurate information on geographic origin is important. Finally, we discuss possibilities for maintaining the integrity of stock lines.     

Natural variation in ozone sensitivity among Arabidopsis thaliana accessions and its relation to stomatal conductance

Genetic variation between naturally occurring populations provides a unique source to unravel the complex mechanisms of stress tolerance. Here, we have analysed O₃ sensitivity of 93 natural Arabidopsis thaliana accessions together with five O₃‐sensitive mutants to acute O₃ exposure. The variation in O₃ sensitivity among the natural accessions was much higher than among the O₃‐sensitive mutants and corresponding wild types. A subset of nine accessions with major variation in their O₃ responses was studied in more detail. Among the traits assayed, stomatal conductance (g_st) was an important factor determining O₃ sensitivity of the selected accessions. The most O₃‐sensitive accession, Cvi‐0, had constitutively high g_st, leading to high initial O₃ uptake rate and dose received during the first 30 min of exposure. Analyzing O₃‐induced changes in stress hormone concentrations indicated that jasmonate (JA) concentration was also positively correlated with leaf damage. Quantitative trait loci (QTL) mapping in a Col‐0 × Cvi‐0 recombinant inbred line (RIL) population identified three QTLs for O₃ sensitivity, and one for high water loss of Cvi‐0. The major O₃ QTL mapped to the same position as the water loss QTL further supporting the role of stomata in regulating O₃ entry and damage.     

Pathogenic interactions between variants of cauliflower mosaic virus and Arabidopsis thaliana

Pathogenic interactions between genetic variants of cauliflower mosaic virus (CaMV) and Arabidopsis thaliana were characterized to identify combinations potentially useful in molecular genetic analysis. Infections of a glabrous mutant (gl1) of Arabidopsis ecotype Columbia (Col-0 gl1) by 30 CaMV isolates were assessed by recording symptom character. Thirteen isolates failed to cause symptoms; the remainder induced symptoms that varied between mild and very severe. Some CaMV isolates produced symptoms in Arabidopsis that differed significantly in severity or character from those produced in a standard host Brassica rapa (turnip). A greater variety of symptom types was observed in a single Arabidopsis ecotype infected with a range of CaMV isolates than was found in a range of Arabidopsis ecotypes infected with a single, typical CaMV isolate (Cabb B-JI). One isolate, Bari-1, that was asymptomatic but accumulated virus in Arabidopsis ecotype Col-0 gl1, caused mild symptoms in ecotype Ler gl1. A hybrid virus constructed from CaMV isolates Cabb B-JI and Bari-1 produced symptoms in Arabidopsis variants that were more severe than in either parental isolate. From a screen of EMS-mutagenized Arabidopsis, one mutant (Col-0 dv1) with a pale-green, dark-vein phenotype which had an altered symptom response to CaMV, was isolated. From this, a phenotypically near-normal revertant (Col-0 dv1R) spontaneously arose, but which showed altered responses to CaMV. Infection of Col-0 dv1R by CaMV isolate Bari-1 elicited symptoms unlike the parent Arabidopsis ecotype (Col-0 gl1). Also, Col-0 dv1 and Col-0 dv1R expressed an uncharacteristic necrotic reaction to CaMV.     

Mapping the virus and host genes involved in the resistance response in cucumber mosaic virus-Infected Arabidopsis thaliana

A yellow strain of cucumber mosaic virus (CMV) [CMV(Y)] induces a resistance response characterized by inhibition of virus systemic movement with development of necrotic local lesions in the virus-inoculated leaves of Arabidopsis thaliana ecotype C24. In this report, the avirulence determinant in the virus genome was defined and the resistance gene (RCY1) of C24 was genetically mapped. The response of C24 to CMV containing the chimeric RNA3 between CMV(Y) and a virulent strain of CMV indicated that the coat protein gene of CMV(Y) determined the localization of the virus in the inoculated leaves of C24. The RCY1 locus was mapped between two CAPS markers, DFR and T43968, which were located in the region containing genetically defined disease resistance genes and their homologues. These results indicate that the resistance response to CMV(Y) in C24 is determined by the combination of the coat protein gene and RCY1 on chromosome 5.     

Salicylic acid-induced resistance to Cucumber mosaic virus in squash and Arabidopsis thaliana: contrasting mechanisms of induction and antiviral action

Salicylic acid (SA)-induced resistance to Cucumber mosaic virus (CMV) in tobacco (Nicotiana tabacum) results from inhibition of systemic virus movement and is induced via a signal transduction pathway that also can be triggered by antimycin A, an inducer of the mitochondrial enzyme alternative oxidase (AOX). In Arabidopsis thaliana, inhibition of CMV systemic movement also is induced by SA and antimycin A. These results indicate that the mechanisms underlying induced resistance to CMV in tobacco and A. thaliana are very similar. In contrast to the situation in tobacco and A. thaliana, in squash (Cucurbita pepo), SA-induced resistance to CMV results from inhibited virus accumulation in directly inoculated tissue, most likely through inhibition of cell-to-cell movement. Furthermore, neither of the AOX inducers antimycin A or KCN induced resistance to CMV in squash. Additionally, AOX inhibitors that compromise SA-induced resistance to CMV in tobacco did not inhibit SA-induced resistance to the virus in squash. The results show that different host species may use significantly different approaches to resist infection by the same virus. These findings also imply that caution is required when attempting to apply findings on plant-virus interactions from model systems to a wider range of host species.     

Resistances to turnip mosaic potyvirus in Arabidopsis thaliana.

The responses of a collection of Arabidopsis thaliana ecotypes to mechanical inoculation with turnip mosaic potyvirus were assessed. The virus induced characteristic severe symptoms of infection in systemically infected plants. Resistance was found in four ecotypes: Bay-0, Di-0, Er-0, and Or-0. Enzyme-linked immunosorbent assay results of the resistant ecotypes suggested that ecotypes Di-0, Er-0, and Or-0 actually consist of mixed genotypes with resistances acting at different levels in the virus life cycle. Another form of resistance was found in ecotype Bay-0, for which several lines of evidence indicated an interference with viral cell-to-cell movement in the inoculated leaves.     

Susceptibility and symptom development in Arabidopsis thaliana to Tobacco mosaic virus is influenced by virus cell-to-cell movement

To identify host factors that regulate susceptibility to Tobacco mosaic virus (TMV), 14 Arabidopsis thaliana ecotypes were screened for their ability to support TMV systemic movement. The susceptibility phenotypes observed included one ecotype that permitted rapid TMV movement accompanied by symptoms, nine ecotypes that allowed a slower intermediate rate of systemic movement without symptoms, and four ecotypes that allowed little or no systemic TMV movement. Molecular comparisons between ecotypes representing the rapid (Shahdara), intermediate (Col-1), and slow (Tsu-1) movement phenotypes revealed a positive correlation between the ability of TMV to move cell to cell and its speed of systemic movement. Additionally, protoplasts prepared from all three ecotypes supported similar levels of TMV replication, indicating that viral replication did not account for differences in systemic movement. Furthermore, induction of the pathogenesis-related genes PR-1 and PR-5 occurred only in the highly susceptible ecotype Shahdara, demonstrating that reduced local and systemic movement in Col-1 and Tsu-1 was not due to the activation of known host defense responses. Genetic analysis of F2 progeny derived from crosses made between Shahdara and Tsu-1 or Col-1 and Tsu-1 showed the faster cell-to-cell movement phenotypes of Shahdara and Col-1 segregated as single dominant genes. In addition, the Shahdara symptom phenotype segregated independently as a single recessive gene. Taken together, these findings suggest that, within Arabidopsis ecotypes, at least two genes modulate susceptibility to TMV.