Genomic Survey of Gene Expression Diversity in<i>Arabidopsis thaliana</i>

Kliebenstein, Daniel J.; West, Michael A.; Leeuwen, Johannes P.T.M. van; Kim, Kyunga; Doerge, R. W.; Michelmore, Richard W.; Clair, Dina A. St.

doi:10.1534/genetics.105.049353

Cited by 107 publications

(123 citation statements)

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“…This small degree of overlap was not surprising as calculations of gene expression levels average the hybridization intensities for all probes of a probe set and specifically eliminate the outlier probe values (http://www.affymetrix.com). Individual SFPs have only a small effect on quantifying gene expression levels (Kliebenstein et al 2006), and >95% of Arabidopsis genes with a SFP contain fewer than three SFPs per probe set (Borevitz et al 2003). Both the GEMs and SFP markers were randomly distributed throughout the genome with no evidence of clustering.…”

Section: Sfp Detection With Ril Datamentioning

confidence: 99%

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

West¹,

Leeuwen²,

Kozik³

et al. 2006

Genome Res.

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164

204

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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.

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Section: Sfp Detection With Ril Datamentioning

confidence: 99%

“…RNA was extracted, labeled, and hybridized to Affymetrix ATH1 GeneChips representing 22,810 genes, as previously described (Kliebenstein et al 2006). GeneChips were scanned on an Affymetrix GeneArray Scanner using GCOS software (Affymetrix).…”

Section: Rna Isolation and Microarray Hybridizationmentioning

confidence: 99%

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

West¹,

Leeuwen²,

Kozik³

et al. 2006

Genome Res.

Self Cite

164

204

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“…Recent studies of Arabidopsis populations have revealed considerable variation in both the genomic and the transcriptomic level (Kliebenstein et al, 2006;Clark et al, 2007;Kim et al, 2007). It is very unlikely that only one or a few genetic changes differentiate AZ and UT.…”

Section: Ecological and Evolutionary Significancementioning

confidence: 99%

“…ELPs in response to exogenously applied salicylic acid and jasmonic acid (JA) have been shown for many genes among different Arabidopsis accessions (Traw et al, 2003;Kliebenstein et al, 2006;van Leeuwen et al, 2007). In different populations, ELPs in particular genes have been shown to produce variation in pathogen resistance (Grant et al, 1995;Gassmann et al, 1999), flowering time (Johanson et al, 2000;Lempe et al, 2005;Werner et al, 2005), herbivore resistance, and secondary metabolite production (Kliebenstein et al, , 2002Lambrix et al, 2001).…”

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confidence: 99%

A Comparison of Two Nicotiana attenuata Accessions Reveals Large Differences in Signaling Induced by Oral Secretions of the Specialist Herbivore Manduca sexta

Hettenhausen

Schuman

et al. 2008

Plant Physiology

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Genetic variation within and among populations provides the raw material for evolution. Although many studies describe inter-and intraspecific variation of defensive metabolites, little is known about variation among plant populations within early signaling responses elicited by herbivory or by herbivore oral secretions (OS) introduced into wounds during feeding. In this study, we compare the OS-elicited early responses as well as the antiherbivore defensive metabolites in two accessions of the wild tobacco Nicotiana attenuata and show that, compared with an accession collected from Utah, an Arizona accession has lower herbivore-elicited activity of the salicylic acid-induced protein kinase, an important mitogen-activated protein kinase involved in herbivore resistance. These differences in salicylic acid-induced protein kinase activity were associated with substantially different levels of OS-elicited jasmonic acid, jasmonic acid-isoleucine conjugate, and ethylene bursts. Gene expression level polymorphism (ELP) determines phenotypic variation among populations, and we found the two accessions to have significantly different ELPs in the genes involved in early signaling responses to herbivory. In addition, we found differences between the Utah and the Arizona accessions in the concentrations of several secondary metabolites that contribute to N. attenuata's direct and indirect defenses. This study demonstrates significant natural variation in regulatory elements that mediate plant responses to herbivore attack, highlighting the role of ELP in producing a diversity of plant defense phenotypes.

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“…The generation of new pathways within species by evolution and selection requires the manipulation of genes to create new enzymes as well as new developmental structures to house these pathways via a variety of mechanisms [24][25][26]. An analysis of genetic variation within Arabidopsis showed that there was a high level of genetic diversity within the glucosinolate secondary metabolite pathway which arose within the Brassicales [27,28]. This secondary metabolite pathway diversity was also linked to elevated diversity in the genes of the sulfur associated pathways [27].…”

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confidence: 99%

Synthetic biology of metabolism: using natural variation to reverse engineer systems

Kliebenstein

2014

Current Opinion in Plant Biology

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A goal of metabolic engineering is to take a plant and introduce new or modify existing pathways in a directed and predictable fashion. However, existing data does not provide the necessary level of information to allow for predictive models to be generated. One avenue to reverse engineer the necessary information is to study the genetic control of natural variation in plant primary and secondary metabolism. These studies are showing that any engineering model will have to incorporate information about 1000s of genes in both the nuclear and organellar genome to optimize the function of the introduced pathway. Further, these genes may interact in an unpredictable fashion complicating any engineering approach as it moves from the one or two gene manipulation to higher order stacking efforts. Finally, metabolic engineering may be influenced by a previously unrecognized potential for a plant to measure the metabolites within it. In combination, these observations from natural variation provide a beginning to help improve current efforts at metabolic engineering. Introduction A significant goal of synthetic biology or biological engineering is to take an existant organism and alter it in a directed and predictive fashion to introduce a new phenotype that had not previously existed in that organism. Some of these efforts start with introducing a new metabolic pathway into an organism to provide a better source of a commercially important chemical or to make new chemicals entirely [1][2][3]. Other efforts are focused at taking agronomically important traits such as defensive chemicals, nitrogen fixation or perennial growth from one species and transferring these traits into other species that do not contain them [4 ,5,6]. However these efforts while exciting frequently run into great difficulty and for this review article, I will focus on one the potential of using information from natural variation studies to facilitate these efforts for metabolic engineering.To predictively engineer a new metabolic pathway into a plant with optimal efficiency requires a base level of knowledge that likely does not exist to any full level. To generate full predictive ability we would need much deeper understanding of the following questions. First, how many genes within the plant need to be manipulated to facilitate the integration of the new pathway into the organisms metabolic and regulatory network. How do these genes interact, are they solely additive or is there evidence of more complex epistasis that complicates predictive capacity? Finally, are these genes solely in the nuclear genome or is there causal variation also in the organellar genomes? Most efforts to answer these questions focus largely on forward or single-gene reverse genetics approaches which are highly time consuming and difficult to scale up to the necessary level.An alternative approach to understanding a system is to use the concept of reverse engineering [7,8]. The goal of reverse engineering is to take a functioning system, say an existing metabolic pathway, ...

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Genomic Survey of Gene Expression Diversity inArabidopsis thaliana

Cited by 107 publications

References 43 publications

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

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

A Comparison of Two Nicotiana attenuata Accessions Reveals Large Differences in Signaling Induced by Oral Secretions of the Specialist Herbivore Manduca sexta

Synthetic biology of metabolism: using natural variation to reverse engineer systems

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