New collaborative paper involving the Johannes lab is out.
Identification and characterisation of hypomethylated DNA loci controlling quantitative resistance in Arabidopsis.
Leonardo Furci, Ritushree Jain, Joost Stassen, Oliver Berkowitz, James Whelan, David Roquis, Victoire Baillet, Vincent Colot, Frank Johannes and Jurriaan Ton (2019).
Variation in DNA methylation enables plants to inherit traits independently of changes to DNA sequence. Here, we have screened an Arabidopsis population of epigenetic recombinant inbred lines (epiRILs) for resistance againstHyaloperonospora arabidopsidis (Hpa). These lines share the same genetic background, but show variation in heritable patterns of DNA methylation. We identified 4 epigenetic quantitative trait loci (epiQTLs) that provide quantitative resistance without reducing plant growth or resistance to other (a)biotic stresses. Phenotypic characterisation and RNA-sequencing analysis revealed that Hpa-resistant epiRILs are primed to activate defence responses at the relatively early stages of infection. Collectively, our results show that hypomethylation at selected pericentromeric regions is sufficient to provide quantitative disease resistance, which is associated with genome-wide priming of defence-related genes. Based on comparisons of global gene expression and DNA methylation between the wild-type and resistant epiRILs, we discuss mechanisms by which the pericentromeric epiQTLs could regulate the defence-related transcriptome.
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Epigenetic mapping of the Arabidopsis metabolome reveals mediators of the epigenotype-phenotype map. https://genome.cshlp.org/content/early/2018/11/30/gr.232371.117
Genome Res. (in press)
Rik Kooke, Lionel Morgado, Frank F.M. Becker, Henriette van Eekelen, Rashmi Hazarika, Qunfeng F. Zhan, Ric C.H. de Vos, Frank Johannes and Joost J.B. Keurentjes (2018).
Identifying the sources of natural variation underlying metabolic differences between plants will enable a better understanding of plant metabolism and provide insights into the regulatory networks that govern plant growth and morphology. So far, however, the contribution of epigenetic variation to metabolic diversity has been largely ignored. In the present study, we utilized a panel of Arabidopsis thaliana epigenetic recombinant inbred lines (epiRILs) to assess the impact of epigenetic variation on the metabolic composition. Thirty epigenetic QTL (QTLepi) were detected, which partly overlap with QTLepi linked to growth and morphology. In an effort to identify causal candidate genes in the QTLepi regions or their putative trans-targets we performed in silico small RNA and qPCR analyses. Differentially expressed genes were further studied by phenotypic and metabolic analyses of knockout mutants. Three genes were detected that recapitulated the detected QTLepi effects, providing evidence for epigenetic regulation in cis and in trans. These results indicate that epigenetic mechanisms impact metabolic diversity, possibly via small RNAs, and thus aid in further disentangling the complex epigenotype-phenotype map.
