Dataset Information

Structure and extent of DNA methylation-based epigenetic variation in wild emmer wheat (T. turgidum ssp. dicoccoides) populations.

ABSTRACT: The genetic structure and differentiation of wild emmer wheat suggests that genetic diversity is eco-geographically structured. However, very little is known about the structure and extent of the heritable epigenetic variation and its influence on local adaptation in natural populations.The structure and extent of the heritable methylation-based epigenetic variation were assessed within and among natural populations of Triticum turgidum ssp. dicoccoides. We used methylation sensitive amplified polymorphism (MSAP) and transposon methylation display (TMD) techniques, to assess the methylation status of random genomic CCGG sites and CCGG sites flanking transposable elements (TEs), respectively. Both techniques were applied to the DNA of 50 emmer accessions which were collected from five different geographically isolated regions. In order to ensure the assessment of heritable epigenetic variation, all accessions were grown under common garden conditions for two generations. In all accessions, the difference in methylation levels of CCGG sites, including CCGG sites that flanked TEs, were not statistically significant and relatively high, ranging between 46 and 76 %. The pattern of methylation was significantly different among accessions, such that clear and statistically significant population-specific methylation patterns were observed.In this study, we have observed population-unique heritable methylation patterns in emmer wheat accessions originating from five geographically isolated regions. Our data indicate that methylation-based epigenetic diversity might be eco-geographically structured and might be partly determined by climatic and edaphic factors.

SUBMITTER: Venetsky A

PROVIDER: S-EPMC4536863 | biostudies-literature | 2015 Aug

REPOSITORIES: biostudies-literature

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Structure and extent of DNA methylation-based epigenetic variation in wild emmer wheat (T. turgidum ssp. dicoccoides) populations.

Venetsky Anna A Levy-Zamir Adva A Khasdan Vadim V Domb Katherine K Kashkush Khalil K

BMC plant biology 20150814

<h4>Background</h4>The genetic structure and differentiation of wild emmer wheat suggests that genetic diversity is eco-geographically structured. However, very little is known about the structure and extent of the heritable epigenetic variation and its influence on local adaptation in natural populations.<h4>Results</h4>The structure and extent of the heritable methylation-based epigenetic variation were assessed within and among natural populations of Triticum turgidum ssp. dicoccoides. We use ...[more]

PMID: 26272589

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Project description:BackgroundNatural populations of the tetraploid wild emmer wheat (genome AABB) were previously shown to demonstrate eco-geographically structured genetic and epigenetic diversity. Transposable elements (TEs) might make up a significant part of the genetic and epigenetic variation between individuals and populations because they comprise over 80% of the wild emmer wheat genome. In this study, we performed detailed analyses to assess the dynamics of transposable elements in 50 accessions of wild emmer wheat collected from 5 geographically isolated sites. The analyses included: the copy number variation of TEs among accessions in the five populations, population-unique insertional patterns, and the impact of population-unique/specific TE insertions on structure and expression of genes.ResultsWe assessed the copy numbers of 12 TE families using real-time quantitative PCR, and found significant copy number variation (CNV) in the 50 wild emmer wheat accessions, in a population-specific manner. In some cases, the CNV difference reached up to 6-fold. However, the CNV was TE-specific, namely some TE families showed higher copy numbers in one or more populations, and other TE families showed lower copy numbers in the same population(s). Furthermore, we assessed the insertional patterns of 6 TE families using transposon display (TD), and observed significant population-specific insertional patterns. The polymorphism levels of TE-insertional patterns reached 92% among all wild emmer wheat accessions, in some cases. In addition, we observed population-specific/unique TE insertions, some of which were located within or close to protein-coding genes, creating allelic variations in a population-specific manner. We also showed that those genes are differentially expressed in wild emmer wheat.ConclusionsFor the first time, this study shows that TEs proliferate in wild emmer wheat in a population-specific manner, creating new alleles of genes, which contribute to the divergent evolution of homeologous genes from the A and B subgenomes.

Project description:Drought events or the combination of drought and heat conditions are expected to become more frequent due to global warming, and wheat yields may fall below their long-term average. One way to increase climate-resilience of modern high-yielding varieties is by their genetic improvement with beneficial alleles from crop wild relatives. In the present study, the effect of two beneficial QTLs introgressed from wild emmer wheat and incorporated in the three wheat varieties BarNir, Zahir and Uzan was studied under well-watered conditions and under drought stress using non-destructive High-throughput Phenotyping (HTP) throughout the life cycle in a single pot-experiment. Plants were daily imaged with RGB top and side view cameras and watered automatically. Further, at two time points, the quantum yield of photosystem II was measured with a top view FluorCam. The QTL carrying near isogenic lines (NILs) were compared with their corresponding parents by t-test for all non-invasively obtained traits and for the manually determined agronomic and yield parameters. Data quality of phenotypic traits (repeatability) in the controlled HTP experiment was above 85% throughout the life cycle and at maturity. Drought stress had a strong effect on growth in all wheat genotypes causing biomass reduction from 2% up to 70% at early and late points in the drought period, respectively. At maturity, the drought caused 47–55% decreases in yield-related traits grain weight, straw weight and total biomass and reduced TKW by 10%, while water use efficiency (WUE) increased under drought by 29%. The yield-enhancing effect of the introgressed QTLs under drought conditions that were previously demonstrated under field/screenhouse conditions in Israel, could be mostly confirmed in a greenhouse pot experiment using HTP. Daily precision phenotyping enabled to decipher the mode of action of the QTLs in the different genetic backgrounds throughout the entire wheat life cycle. Daily phenotyping allowed a precise determination of the timing and size of the QTLs effect (s) and further yielded information about which image-derived traits are informative at which developmental stage of wheat during the entire life cycle. Maximum height and estimated biovolume were reached about a week after heading, so experiments that only aim at exploring these traits would not need a longer observation period. To obtain information on different onset and progress of senescence, the CVa curves represented best the ongoing senescence of plants. The QTL on 7A in the BarNir background was found to improve yield under drought by increased biomass growth, a higher photosynthetic performance, a higher WUE and a “stay green effect.”

Dataset Information

Structure and extent of DNA methylation-based epigenetic variation in wild emmer wheat (T. turgidum ssp. dicoccoides) populations.

Publications

Structure and extent of DNA methylation-based epigenetic variation in wild emmer wheat (T. turgidum ssp. dicoccoides) populations.

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