Epigenetic variation contributes to environmental adaptation of <i>Arabidopsis thaliana</i>

Kooke, Rik; Keurentjes, Joost J. B.

doi:10.1080/15592324.2015.1057368

Cited by 15 publications

(11 citation statements)

References 9 publications

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“…It has been shown in particular isogenic epigenetic recombinant inbred lines (epiRILs) that heritable morphological variation in Arabidopsis plants can be caused exclusively by epigenetic factors (Johannes et al, 2009;Roux et al, 2011;Cortijo et al, 2014;Kooke and Keurentjes, 2015). To specifically address the contribution of parental epigenetic variation to F1 heterosis, we made use of the same epiRILs (Johannes et al, 2009;Reinders et al, 2009) to generate F1 epigenetic hybrids, hereafter called epiHybrids (Dapp et al, 2015).…”

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Parental DNA Methylation States Are Associated with Heterosis in Epigenetic Hybrids

et al. 2017

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Despite the importance and wide exploitation of heterosis in commercial crop breeding, the molecular mechanisms behind this phenomenon are not completely understood. Recent studies have implicated changes in DNA methylation and small RNAs in hybrid performance; however, it remains unclear whether epigenetic changes are a cause or a consequence of heterosis. Here, we analyze a large panel of over 500 Arabidopsis (Arabidopsis thaliana) epigenetic hybrid plants (epiHybrids), which we derived from near-isogenic but epigenetically divergent parents. This proof-of-principle experimental system allowed us to quantify the contribution of parental methylation differences to heterosis. We measured traits such as leaf area, growth rate, flowering time, main stem branching, rosette branching, and final plant height and observed several strong positive and negative heterotic phenotypes among the epiHybrids. Using an epigenetic quantitative trait locus mapping approach, we were able to identify specific differentially methylated regions in the parental genomes that are associated with hybrid performance. Sequencing of methylomes, transcriptomes, and genomes of selected parent-epiHybrid combinations further showed that these parental differentially methylated regions most likely mediate the remodeling of methylation and transcriptional states at specific loci in the hybrids. Taken together, our data suggest that locus-specific epigenetic divergence between the parental lines can directly or indirectly trigger heterosis in Arabidopsis hybrids independent of genetic changes. These results add to a growing body of evidence that points to epigenetic factors as one of the key determinants of hybrid performance.

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Parental DNA Methylation States Are Associated with Heterosis in Epigenetic Hybrids

et al. 2017

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“…Extensive natural disparity in phytochemical profiles occurs between and within species of plants as an adaptation measure to different abiotic and biotic environments [ 32 ]. The most important players in the biosynthesis and accumulation of secondary metabolites include genetics, epigenetics, morphogenetic, ontogenic, and environmental factors [ 33 ]. The PCA, as shown in Figure 3 A, indicates that Nanyuki and Machakos populations of D. viscosa are closely related while the plants from the Nairobi and Narok areas are from a similar chemical lineage.…”

Section: Resultsmentioning

confidence: 99%

LC-MS-Based Metabolomics for the Chemosystematics of Kenyan Dodonaea viscosa Jacq (Sapindaceae) Populations

et al. 2020

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Dodonaea viscosa Jacq (Sapindaceae) is a medicinal plant with a worldwide distribution. The species has undergone enormous taxonomic changes which caused confusion amongst plant users. In Kenya, for example, two varieties are known to exist based on morphology, i.e., D. viscosa var. viscosa along the coast, and D. viscosa var. angustifolia in the Kenyan inland. These two taxa are recognized as distinct species in some reports. This prompted us to apply metabolomics to understand the relationship among naturally occurring populations of D. viscosa in Kenya, and to identify compounds that can assist in taxonomic delineation of the different varieties of D. viscosa from different parts of Kenya. The phytochemical variability of Kenyan D. viscosa var. angustifolia populations collected from four different geographical regions (Nanyuki, Machakos, Nairobi, and Narok) and one coastal D. viscosa var. viscosa (the Gazi) were analyzed by LC-MS using a metabolomics-driven approach. Four known compounds, two diterpenoids (dodonic acid (1), hautriwaic acid lactone (3), and two flavonoids (5,7,4′,5′-tetrahydroxy-3,6,2′-trimethoxyflavone (2) and catechin (4)) were isolated and purified from the Gazi coastal collection. The presence of these compounds and their relative abundance in other populations was determined by LC-MS analyses. Multivariate statistical analyses of LC-MS data was used for the visualization of the patterns of variation and identification of additional compounds. Eleven discriminant compounds responsible for separating chemometric clusters were tentatively identified. In an antimicrobial assay, hautriwaic acid lactone (3) and catechin (4) were the most active compounds followed by the extract from the coastal (Gazi) population. The clustering pattern of the five populations of D. viscosa suggested that the metabolite profiles were influenced by geo-environmental conditions and did not support the current classification of D. viscosa based on morphology. This study disputes the current classification of D. viscosa in Kenya and recommends revision using tools such as molecular phylogenetics.

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“…But if the estimates of V C , γ 2 , and the transmissibility coefficient are greater than zero, then the heritability may be partially generated by epigenetic mechanisms. The specific epigenetic mechanisms that contribute to heritability in the inbred lines could be examined in follow-up studies that use epigenomic mapping techniques (e.g., Zhang et al 2013;Cortijo et al 2014;Kooke and Keurentjes 2015). Overall, the Tal et al (2010) study provides a pragmatic approach for teasing out epigenetic influences on phenotypic variance and heritability, but the methods developed so far are imperfect and require further development to accurately quantify epigenetic influences.…”

Section: Methods For Incorporating Epigenetic Effects Into Quantitatimentioning

confidence: 99%

“…In another example linking epigenetic variation and phenotypic variation, Johannes et al (2009) developed a recombinant inbred line (RIL) population of the model plant Arabidopsis thaliana that segregates for differentially methylated positions (DMPs)-differences in whether individual cytosines are methylated or not. The epigenetic recombinant inbred lines (epiRILs) are nearly isogenic in terms of the DNA sequences, but show variation and high heritability for many traits relating to growth and morphology, including plant height, flowering time, and primary root length (Zhang et al 2013;Cortijo et al 2014;Kooke and Keurentjes 2015). The epiRILs were derived from crosses between the Columbia wild-type genotype and a mutant line derived from the Columbia wild-type with a mutation in the DECREASED DNA METHYLATION 1 (DDM1) locus.…”

Section: Epigenetics and The Missing Heritability Problemmentioning

confidence: 99%

Quantitative epigenetics and evolution

Banta

Richards

2018

Heredity

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Epigenetics refers to chemical modifications of chromatin or transcribed DNA that can influence gene activity and expression without changes in DNA sequence. The last 20 years have yielded breakthroughs in our understanding of epigenetic processes that impact many fields of biology. In this review, we discuss how epigenetics relates to quantitative genetics and evolution. We argue that epigenetics is important for quantitative genetics because: (1) quantitative genetics is increasingly being combined with genomics, and therefore we should expand our thinking to include cellular-level mechanisms that can account for phenotypic variance and heritability besides just those that are hard-coded in the DNA sequence; and (2) epigenetic mechanisms change how phenotypic variance is partitioned, and can thereby change the heritability of traits and how those traits are inherited. To explicate these points, we show that epigenetics can influence all aspects of the phenotypic variance formula: V (total phenotypic variance) = V (genetic variance) + V (environmental variance) + V (genotype-by-environment interaction) + 2COV (the genotype-environment covariance) + V (residual variance), requiring new strategies to account for different potential sources of epigenetic effects on phenotypic variance. We also demonstrate how each of the components of phenotypic variance not only can be influenced by epigenetics, but can also have evolutionary consequences. We argue that no sources of epigenetic effects on phenotypic variance can be easily cast aside in a quantitative genetic research program that seeks to understand evolutionary processes.

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Epigenetic variation contributes to environmental adaptation of Arabidopsis thaliana

Cited by 15 publications

References 9 publications

Parental DNA Methylation States Are Associated with Heterosis in Epigenetic Hybrids

Parental DNA Methylation States Are Associated with Heterosis in Epigenetic Hybrids

LC-MS-Based Metabolomics for the Chemosystematics of Kenyan Dodonaea viscosa Jacq (Sapindaceae) Populations

Quantitative epigenetics and evolution

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