Biomedical subjects

Daniel J Kliebenstein

Publications and source records attributed to Daniel J Kliebenstein.

14 recordsLinked to original sources

PubMed2006

Global eQTL mapping reveals the complex genetic architecture of transcript-level variation in Arabidopsis.

The genetic architecture of transcript-level variation is largely unknown. The genetic determinants of transcript-level variation were characterized in a recombinant inbred line (RIL) population (n = 211) of Arabidopsis thaliana using whole-genome microarray analysis and expression quantitative trait loci (eQTL) mapping of transcript levels as expression traits (e-traits). Genetic control of transcription was highly complex: one-third of the quantitatively controlled transcripts/e-traits were regulated by cis-eQTL, and many trans-eQTL mapped to hotspots that regulated hundreds to thousands of e-traits. Several thousand eQTL of large phenotypic effect were detected, but almost all (93%) of the 36,871 eQTL were associated with small phenotypic effects (R(2) < 0.3). Many transcripts/e-traits were controlled by multiple eQTL with opposite allelic effects and exhibited higher heritability in the RILs than their parents, suggesting nonadditive genetic variation. To our knowledge, this is the first large-scale global eQTL study in a relatively large plant mapping population. It reveals that the genetic control of transcript level is highly variable and multifaceted and that this complexity may be a general characteristic of eukaryotes.

Arabidopsis↗

PubMed2006

Identification of QTLs controlling gene expression networks defined a priori.

BACKGROUND: Gene expression microarrays allow the quantification of transcript accumulation for many or all genes in a genome. This technology has been utilized for a range of investigations, from assessments of gene regulation in response to genetic or environmental fluctuation to global expression QTL (eQTL) analyses of natural variation. Current analysis techniques facilitate the statistical querying of individual genes to evaluate the significance of a change in response, also known as differential expression. Since genes are also known to respond as groups due to their membership in networks, effective approaches are needed to investigate transcriptome variation as related to gene network responses. RESULTS: We describe a statistical approach that is capable of assessing higher-order a priori defined gene network response, as measured by microarrays. This analysis detected significant network variation between two Arabidopsis thaliana accessions, Bay-0 and Shahdara. By extending this approach, we were able to identify eQTLs controlling network responses for 18 out of 20 a priori-defined gene networks in a recombinant inbred line population derived from accessions Bay-0 and Shahdara. CONCLUSION: This approach has the potential to be expanded to facilitate direct tests of the relationship between phenotypic trait and transcript genetic architecture. The use of a priori definitions for network eQTL identification has enormous potential for providing direction toward future eQTL analyses.

Arabidopsis↗

PubMed2006

High-density haplotyping with microarray-based expression and single feature polymorphism markers in Arabidopsis.

Expression microarrays hybridized with RNA can simultaneously provide both phenotypic (gene expression) and genotypic (marker) data. We developed two types of genetic markers from Affymetrix GeneChip expression data to generate detailed haplotypes for 148 recombinant inbred lines (RILs) derived from Arabidopsis thaliana accessions Bayreuth and Shahdara. Gene expression markers (GEMs) are based on differences in transcript levels that exhibit bimodal distributions in segregating progeny, while single feature polymorphism (SFP) markers rely on differences in hybridization to individual oligonucleotide probes. Unlike SFPs, GEMs can be derived from any type of DNA-based expression microarray. Our method identifies SFPs independent of a gene's expression level. Alleles for each GEM and SFP marker were ascertained with GeneChip data from parental accessions as well as RILs; a novel algorithm for allele determination using RIL distributions capitalized on the high level of genetic replication per locus. GEMs and SFP markers provided robust markers in 187 and 968 genes, respectively, which allowed estimation of gene order consistent with that predicted from the Col-0 genomic sequence. Using microarrays on a population to simultaneously measure gene expression variation and obtain genotypic data for a linkage map will facilitate expression QTL analyses without the need for separate genotyping. We have demonstrated that gene expression measurements from microarrays can be leveraged to identify polymorphisms across the genome and can be efficiently developed into genetic markers that are verifiable in a large segregating RIL population. Both marker types also offer opportunities for massively parallel mapping in unsequenced and less studied species.

Arabidopsis↗

PubMed2006

The gene controlling the quantitative trait locus EPITHIOSPECIFIER MODIFIER1 alters glucosinolate hydrolysis and insect resistance in Arabidopsis.

Glucosinolates are sulfur-rich plant secondary metabolites whose breakdown products have a wide range of biological activities in plant-herbivore and plant-pathogen interactions and anticarcinogenic properties. In Arabidopsis thaliana, hydrolysis by the enzyme, myrosinase, produces bioactive nitriles, epithionitriles, or isothiocyanates depending upon the plant's genotype and the glucosinolate's structure. A major determinant of this structural specificity is the epithiospecifier locus (ESP), whose protein causes the formation of epithionitriles and nitriles. A quantitative trait locus (QTL) on chromosome 3 epistatically affects nitrile formation in combination with ESP; this QTL has been termed EPITHIOSPECIFIER MODIFIER1 (ESM1). We identified a myrosinase-associated protein as the ESM1 QTL in Arabidopsis using map-based cloning with recombinant inbred lines, natural variation transcriptomic analysis, and metabolic profiling. In planta and in vitro analyses with natural ESM1 alleles, ESM1 knockouts, and overexpression lines show that ESM1 represses nitrile formation and favors isothiocyanate production. The glucosinolate hydrolysis profile change influenced by ESM1 is associated with the ability to deter herbivory by Trichoplusia ni. This gene could provide unique approaches toward improving human nutrition.

Animals↗

PubMed2006

Convergence, constraint and the role of gene expression during adaptive radiation: floral anthocyanins in Aquilegia.

Convergent phenotypes are testament to the role of natural selection in evolution. However, little is known about whether convergence in phenotype extends to convergence at the molecular level. We use the independent losses of floral anthocyanins in columbines (Aquilegia) to determine the degree of molecular convergence in gene expression across the anthocyanin biosynthetic pathway (ABP). Using a phylogeny of the North American Aquilegia clade, we inferred six independent losses of floral anthocyanins. Via semiquantitative reverse transcriptase-polymerase chain reaction (RT-PCR), we monitored developmental and tissue-specific variation in expression of the six major structural ABP loci in three Aquilegia species, two that produce anthocyanins (A+) and one that does not (A-). We then compared ABP expression in petals of old-bud and pre-anthesis flowers of 13 Aquilegia species, eight wild species and two horticultural lines representing seven independent A- lineages as well as three wild A+ species. We only found evidence of down-regulation of ABP loci in A- lineages and losses of expression were significantly more prevalent for genes late in the pathway. Independent contrast analysis indicates that changes in expression of dihydroflavonol reductase (DFR) and anthocyanidin synthase (ANS) are strongly phylogenetically correlated consistent with the multilocus targets of trans-regulatory elements in the ABP of other systems. Our findings strongly suggest that pleiotropy constrains the evolution of loss of floral anthocyanins to mutations affecting genes late in the ABP mostly through convergent changes in regulatory genes. These patterns support the hypothesis that rapid evolutionary change occurs largely through regulatory rather than structural mutations.

Adaptation, Biological↗

PubMed2005

A UV-B-specific signaling component orchestrates plant UV protection.

UV-B radiation in sunlight has diverse effects on humans, animals, plants, and microorganisms. UV-B can cause damage to molecules and cells, and consequently organisms need to protect against and repair UV damage to survive in sunlight. In plants, low nondamaging levels of UV-B stimulate transcription of genes involved in UV-protective responses. However, remarkably little is known about the underlying mechanisms of UV-B perception and signal transduction. Here we report that Arabidopsis UV RESISTANCE LOCUS 8 (UVR8) is a UV-B-specific signaling component that orchestrates expression of a range of genes with vital UV-protective functions. Moreover, we show that UVR8 regulates expression of the transcription factor HY5 specifically when the plant is exposed to UV-B. We demonstrate that HY5 is a key effector of the UVR8 pathway, and that it is required for survival under UV-B radiation. UVR8 has sequence similarity to the eukaryotic guanine nucleotide exchange factor RCC1, but we found that it has little exchange activity. However, UVR8, like RCC1, is located principally in the nucleus and associates with chromatin via histones. Chromatin immunoprecipitation showed that UVR8 associates with chromatin in the HY5 promoter region, providing a mechanistic basis for its involvement in regulating transcription. We conclude that UVR8 defines a UV-B-specific signaling pathway in plants that orchestrates the protective gene expression responses to UV-B required for plant survival in sunlight.

Arabidopsis↗

PubMed2005

Genomic survey of gene expression diversity in Arabidopsis thaliana.

Differential gene expression controls variation in numerous plant traits, such as flowering time and plant/pest interactions, but little is known about the genomic distribution of the determinants of transcript levels and their associated variation. Affymetrix ATH1 GeneChip microarrays representing 22,810 genes were used to survey the transcriptome of seven Arabidopsis thaliana accessions in the presence and absence of exogenously applied salicylic acid (SA). These accessions encompassed approximately 80% of the moderate- to high-frequency nucleotide polymorphisms in Arabidopsis. A factorial design, consisting of three biological replicates per accession for the two treatments at three time points (4, 28, and 52 hr post-treatment), and a total of 126 microarrays were used. Between any pair of Arabidopsis accessions, we detected on average 2234 genes (ranging from 1428 to 3334) that were significantly differentially expressed under the conditions of this experiment, using a split-plot analysis of variance. Upward of 6433 genes were differentially expressed between at least one pair of accessions. These results suggest that analysis of additional genetic, developmental, and environmental conditions may show that a significant fraction of the Arabidopsis genome is differentially expressed. Examination of sequence diversity demonstrated a significant positive association with diversity in gene expression.

Analysis of Variance↗

PubMed2005

Geographic and evolutionary diversification of glucosinolates among near relatives of Arabidopsis thaliana (Brassicaceae).

Glucosinolates are biologically active secondary metabolites that display both intra- and interspecific variation in the order Brassicales. Glucosinolate profiles have not been interpreted within a phylogenic framework and little is known regarding the processes that influence the evolution of glucosinolate diversity at a macroevolutionary scale. We have analyzed leaf glucosinolate profiles from members of the Brassicaceae that have diverged from Arabidopsis thaliana within the last 15 million years and interpreted our findings relative to the phylogeny of this group. We identified several interspecific polymorphisms in glucosinolate composition. A majority of these polymorphisms are lineage-specific secondary losses of glucosinolate characters, but a gain-of-character polymorphism was also detected. The genetic basis of most observed polymorphisms appears to be regulatory. In the case of A. lyrata, geographic distribution is also shown to contribute to glucosinolate metabolic diversity. Further, we observed evidence of gene-flow between sympatric species, parallel evolution, and the existence of genetic constraints on the evolution of glucosinolates within the Brassicaceae.

Brassicaceae↗

PubMed2005

Secondary metabolites influence Arabidopsis/Botrytis interactions: variation in host production and pathogen sensitivity.

Numerous studies have suggested that plant/pathogen interactions are partially mediated via plant secondary metabolite production and corresponding pathogen tolerance. However, there are inconsistent reports on the ability of particular compounds to provide resistance to a pathogen. Most of these studies have focused on individual isolates of a given pathogen, suggesting that pathogens vary in their sensitivity to plant-produced toxins. We tested variability in virulence among pathogen isolates, and the impact on this by plant production of, and pathogen tolerance to, secondary metabolites. Botrytis cinerea isolates showed differing sensitivity to purified camalexin, and camalexin-sensitive isolates produced larger lesions on camalexin-deficient Arabidopsis genotypes than on the wild type. In contrast, the camalexin-insensitive isolate produced lesions of similar size on wild-type and camalexin-deficient Arabidopsis. Additional analysis with Arabidopsis secondary metabolite biosynthetic mutants suggests that Botrytis also has variable sensitivity to phenylpropanoids and glucosinolates. Furthermore, Botrytis infection generates a gradient of secondary metabolite responses emanating from the developing lesion, with the Botrytis isolate used determining the accumulation pattern. Collectively, our results indicate that Arabidopsis/Botrytis interactions are influenced at the metabolic level by variations in toxin production in the host and sensitivity in the pathogen.

Arabidopsis↗

PubMed2004

Identification of Botrytis cinerea susceptibility loci in Arabidopsis thaliana.

Botrytis cinerea is a major pathogen of fruit and vegetable crops causing both pre- and post-harvest grey mould. We have analysed 16 Arabidopsis thaliana ecotypes for natural variation in B. cinerea susceptibility. Susceptibility was associated with lower camalexin accumulation, and three ecotypes (Cape Verdi Islands (Cvi-0), Slavice (Sav-0) and Kindalville (Kin-0)) showed differential susceptibility to the two B. cinerea isolates used. Subsequently, to better understand the genetic control of grey mould disease, we assayed the Arabidopsis Landsberg erecta (Ler) x Columbia (Col-0) recombinant inbred population with the two isolates, and identified multiple small-to-medium-effect quantitative trait loci (QTL) governing susceptibility. Interestingly, the QTL for each isolate are distinct, suggesting that different mechanisms govern defence against these two isolates. Two QTL for each isolate exhibited epistatic interactions with specific allele combinations generating heightened B. cinerea susceptibility.

Arabidopsis↗

PubMed2002

Disarming the mustard oil bomb.

Plants are attacked by a broad array of herbivores and pathogens. In response, plants deploy an arsenal of defensive traits. In Brassicaceae, the glucosinolate-myrosinase complex is a sophisticated two-component system to ward off opponents. However, this so-called "mustard oil bomb" is disarmed by a glucosinolate sulfatase of a crucifer specialist insect, diamondback moth, Plutella xylostella (Lepidoptera: Plutellidae). Sulfatase activity of this enzyme largely prevents the formation of toxic hydrolysis products arising from this plant defense system. Importantly, the enzyme acts on all major classes of glucosinolates, thus enabling diamondback moths to use a broad range of cruciferous host plants.

Amino Acid Sequence↗

PubMed2002

Benzoic acid glucosinolate esters and other glucosinolates from Arabidopsis thaliana.

The spectacular recent progress in Arabidopsis thaliana molecular genetics furnishes outstanding tools for studying the formation and function of all metabolites in this cruciferous species. One of the major groups of secondary metabolites in A. thaliana is the glucosinolates. These hydrophilic, sulfur-rich glycosides appear to serve as defenses against some generalist herbivores and pathogens, and as feeding and oviposition stimulants to specialist herbivores. To help study their biosynthesis and role in plant-insect interactions, we wanted to determine the complete glucosinolate content of A. thaliana. In previous studies, 24 glucosinolates had been identified from ecotype Columbia. We reinvestigated Columbia as well as additional ecotypes and mutant lines, and identified 12 further glucosinolates, including five novel compounds. Structures were elucidated by MS and NMR spectroscopy of their desulfated derivatives, and by enzymatic cleavage of the attached ester moieties. Four of the novel glucosinolates are benzoate esters isolated from the seeds. In all but one of these compounds, esterification is on the glucose moiety rather than the side chain, a very unusual feature for glucosinolates. Among additional glucosinolates identified were the first non-chain elongated, methionine-derived glucosinolate from A. thaliana and the first compounds that appear to be derived from leucine.

Arabidopsis↗

PubMed2002

Genetic architecture of plastic methyl jasmonate responses in Arabidopsis thaliana.

The ability of a single genotype to generate different phenotypes in disparate environments is termed phenotypic plasticity, which reflects the interaction of genotype and environment on developmental processes. However, there is controversy over the definition of plasticity genes. The gene regulation model states that plasticity loci influence trait changes between environments without altering the means within a given environment. Alternatively, the allelic sensitivity model argues that plasticity evolves due to selection of phenotypic values expressed within particular environments; hence plasticity must be controlled by loci expressed within these environments. To identify genetic loci controlling phenotypic plasticity and address this controversy, we analyzed the plasticity of glucosinolate accumulation under methyl jasmonate (MeJa) treatment in Arabidopsis thaliana. We found genetic variation influencing multiple MeJa signal transduction pathways. Analysis of MeJa responses in the Landsberg erecta x Columbia recombinant inbred lines identified a number of quantitative trait loci (QTL) that regulate plastic MeJa responses. All significant plasticity QTL also impacted the mean trait value in at least one of the two "control" or "MeJa" environments, supporting the allelic sensitivity model. Additionally, we present an analysis of MeJa and salicylic acid cross-talk in glucosinolate regulation and describe the implications for glucosinolate physiology and functional understanding of Arabidopsis MeJa signal transduction.

Acetates↗

PubMed2002

Arabidopsis UVR8 regulates ultraviolet-B signal transduction and tolerance and contains sequence similarity to human regulator of chromatin condensation 1.

To further our understanding of how plants defend against the harmful effects of ultraviolet (UV) light, we characterized an Arabidopsis mutant hypersensitive to UV-B. This mutant, UV resistance locus 8-1 (uvr8-1), contains a single recessive mutation at the bottom of chromosome 5. Fine-scale mapping localized uvr8-1 to a 21-kb locus containing five predicted open reading frames. Sequencing of this entire region revealed that the uvr8-1 allele contains a 15-nucleotide deletion in a gene similar to the human guanine nucleotide exchange factor regulator of chromatin condensation 1. This mutation reduces the UV-B-mediated induction of flavonoids and blocks chalcone synthase mRNA and protein induction. In contrast, uvr8-1 has enhanced induction of PR1 and PR5 proteins in response to UV-B, an indication of increased UV-B injury. These results suggest that UVR8 acts in a UV-B signal transduction pathway leading to induction of flavonoid biosynthesis.

Acyltransferases↗