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Istvan Nagy

The cytosine methylation landscape of spring barley revealed by a new reduced representation bisulfite sequencing pipeline, WellMeth

Publikation: Bidrag til tidsskrift/Konferencebidrag i tidsskrift /Bidrag til avisTidsskriftartikelForskningpeer review

  • Marta Malinowska
  • Istvan Nagy
  • Cornelis A M Wagemaker, Department of Experimental Plant Ecology, Institute for Water and Wetland Research, Radboud University, Heyendaalseweg 135, 6525 AJ, Nijmegen, the Netherlands.
  • ,
  • Anja K Ruud
  • Simon F Svane, Department of Plant and Environmental Sciences, University of Copenhagen, Denmark.
  • ,
  • Kristian Thorup-Kristensen, Københavns Universitet
  • ,
  • Christian S Jensen, DLF Seeds A/S
  • ,
  • Birger Eriksen, Sejet Plantbreeding
  • ,
  • Lene Krusell, Sejet Plant Breeding
  • ,
  • Ahmed Jahoor, Nordic Seed, Galten, Denmark.
  • ,
  • Jens Jensen, Nordic Seed, Galten, Denmark.
  • ,
  • Lars Bonde Eriksen, SEGES, Limagrain A/S, Horsens
  • ,
  • Torben Asp
Patterns and level of cytosine methylation vary widely among plant species and are associated with genome size as well as the proportion of transposons and other repetitive elements in the genome. We explored epigenetic patterns and diversity in a representative proportion of the spring barley (Hordeum vulgare L.) genome across several commercial and historical cultivars. This study adapted a genotyping‐by‐sequencing (GBS) approach for the detection of methylated cytosines in genomic DNA. To analyze the data, we developed WellMeth, a complete pipeline for analysis of reduced representation bisulfite sequencing. WellMeth enabled quantification of context‐specific DNA methylation at the single‐base resolution as well as identification of differentially methylated sites (DMCs) and regions (DMRs). On average, DNA methylation levels were significantly higher than what is commonly observed in many plants species, reaching over 10‐fold higher levels than those in Arabidopsis thaliana (L.) Heynh. in the CHH methylation. Preferential methylation was observed within and at the edges of long‐terminal repeats (LTR) retrotransposons Gypsy and Copia. From a pairwise comparison of cultivars, numerous DMRs could be identified of which more than 5,000 were conserved within the analyzed set of barley cultivars. The subset of regions overlapping with genes showed enrichment in gene ontology (GO) categories associated with chromatin and cellular structure and organization. A significant correlation between genetic and epigenetic distances suggests that a considerable portion of methylated regions is under strict genetic control in barley. The data presented herein represents the first step in efforts toward a better understanding of genome‐level structural and functional aspects of methylation in barley.
TidsskriftThe Plant Genome
Sider (fra-til)e20049
StatusUdgivet - nov. 2020

Bibliografisk note

© 2020 The Authors. The Plant Genome published by Wiley Periodicals, Inc. on behalf of Crop Science Society of America.

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