Epigenetic Regulation of Transposable Elements in Plants

Lisch, Damon

doi:10.1146/annurev.arplant.59.032607.092744

Cited by 398 publications

(308 citation statements)

References 157 publications

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“…The high number of copies and their location throughout the genome suggest that the amplification could have originated via a transposon-or RNA-mediated mechanism, followed by selection of a highly amplified individual from the population. Most transposons in plant genomes are inactive but may be activated by various conditions, including abiotic stress (30). Therefore, a testable hypothesis is that the original EPSPS locus was associated with a mobile genetic element that activated and amplified the EPSPS gene.…”

Section: Discussionmentioning

confidence: 99%

Gene amplification confers glyphosate resistance in Amaranthus palmeri

Gaines

Zhang

Wang

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

581

857

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The herbicide glyphosate became widely used in the United States and other parts of the world after the commercialization of glyphosate-resistant crops. These crops have constitutive overexpression of a glyphosate-insensitive form of the herbicide target site gene, 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS). Increased use of glyphosate over multiple years imposes selective genetic pressure on weed populations. We investigated recently discovered glyphosate-resistant Amaranthus palmeri populations from Georgia, in comparison with normally sensitive populations. EPSPS enzyme activity from resistant and susceptible plants was equally inhibited by glyphosate, which led us to use quantitative PCR to measure relative copy numbers of the EPSPS gene. Genomes of resistant plants contained from 5-fold to more than 160-fold more copies of the EPSPS gene than did genomes of susceptible plants. Quantitative RT-PCR on cDNA revealed that EPSPS expression was positively correlated with genomic EPSPS relative copy number. Immunoblot analyses showed that increased EPSPS protein level also correlated with EPSPS genomic copy number. EPSPS gene amplification was heritable, correlated with resistance in pseudo-F 2 populations, and is proposed to be the molecular basis of glyphosate resistance. FISH revealed that EPSPS genes were present on every chromosome and, therefore, gene amplification was likely not caused by unequal chromosome crossing over. This occurrence of gene amplification as an herbicide resistance mechanism in a naturally occurring weed population is particularly significant because it could threaten the sustainable use of glyphosate-resistant crop technology.5-enolpyruvylshikimate-3-phosphate synthase | herbicide resistance | mobile genetic element | evolution | Palmer amaranth

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Section: Discussionmentioning

confidence: 99%

Gene amplification confers glyphosate resistance in Amaranthus palmeri

Gaines

Zhang

Wang

et al. 2009

Proc. Natl. Acad. Sci. U.S.A.

581

857

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“…Four distinct functional contributions of TEs are now recognized, including their roles in determining genome size and rearrangements, in generating mutations, in altering chromosome architecture and in the regulation of gene expression. TEs are now recognized as an abundant and unexplored natural source of regulatory sequences for host genes, and TE biology has become an active research area in recent years [5][6][7][8][9][10] . Sequencing technologies such as Illumina HiSeq X Ten and PacBio RS II sequencing, and new library construction methods such as 10x Genomics, as well as new assembly techniques such as DeNovoMAGIC2 11,12 , are now significantly accelerating the progress of wheat genome sequencing efforts.…”

mentioning

confidence: 99%

The Aegilops tauschii genome reveals multiple impacts of transposons

Zhao¹,

Zou²,

et al. 2017

Nature Plants

163

100

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Wheat is an important global crop with an extremely large and complex genome that contains more transposable elements (TEs) than any other known crop species. Here, we generated a chromosome-scale, high-quality reference genome of Aegilops tauschii, the donor of the wheat D genome, in which 92.5% sequences have been anchored to chromosomes. Using this assembly, we accurately characterized genic loci, gene expression, pseudogenes, methylation, recombination ratios, microRNAs and especially TEs on chromosomes. In addition to the discovery of a wave of very recent gene duplications, we detected that TEs occurred in about half of the genes, and found that such genes are expressed at lower levels than those without TEs, presumably because of their elevated methylation levels. We mapped all wheat molecular markers and constructed a high-resolution integrated genetic map corresponding to genome sequences, thereby placing previously detected agronomically important genes/ quantitative trait loci (QTLs) on the Ae. tauschii genome for the first time. NaTuRe PLaNTs

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“…tauschii (5.08 and 5.1 pg DnA) (Özkan et al 2003Furuta et al 1986;rees and Walters 1965) and indicate that their genomes underwent different evolutionary changes. As the number of genes per monoploid genome is similar in plant species, differences in genome size are mainly due to repetitive DnA sequences, of which retroelements are considered to play a dominant role in genome expansion (Bennetzen 2007;Feuillet and Keller 2002;lisch 2009). Charles et al (2008) showed that specific types of transposable elements underwent differential proliferation in various wheat genomes during their evolution.…”

Section: Discussionmentioning

confidence: 99%