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Open Access Highly Accessed Research article

A Hypomethylated population of Brassica rapa for forward and reverse Epi-genetics

Stephen Amoah1, Smita Kurup1, Carlos Marcelino Rodriguez Lopez3, Sue J Welham1, Stephen J Powers1, Clare J Hopkins14, Michael J Wilkinson3 and Graham J King12*

Author Affiliations

1 Rothamsted Research, Harpenden, Herts AL5 2JQ, UK

2 Current address: Southern Cross Plant Science, Southern Cross University, Lismore, NSW 2480, Australia

3 Plant Research Centre, School of Agriculture, Food and Wine, Faculty of Sciences, University of Adelaide, Waite Campus, PMB1, Glen Osmond, SA, 5064, Australia

4 Department of Pathology, The University of Melbourne, Melbourne, VIC, 3010, Australia

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BMC Plant Biology 2012, 12:193  doi:10.1186/1471-2229-12-193

Published: 20 October 2012

Abstract

Background

Epigenetic marks superimposed on the DNA sequence of eukaryote chromosomes provide agility and plasticity in terms of modulating gene expression, ontology, and response to the environment. Modulating the methylation status of cytosine can generate epialleles, which have been detected and characterised at specific loci in several plant systems, and have the potential to generate novel and relatively stable phenotypes. There have been no systematic attempts to explore and utilise epiallelic variation, and so extend the range of phenotypes available for selection in crop improvement. We developed an approach for generating novel epialleles by perturbation of the DNA methylation status. 5- Azacytidine (5-AzaC) provides selective targeting of 5mCG, which in plants is associated with exonic DNA. Targeted chemical intervention using 5-AzaC has advantages over transgenic or mutant modulation of methyltransferases, allowing stochastic generation of epialleles across the genome.

Results

We demonstrate the potential of stochastic chemically-induced hypomethylation to generate novel and valuable variation for crop improvement. Systematic analysis of dose–response to 5-AzaC in B. rapa guided generation of a selfed stochastically hypomethylated population, used for forward screening of several agronomic traits. Dose–response was sigmoidal for several traits, similar to that observed for chemical mutagens such as EMS. We demonstrated transgenerational inheritance of some phenotypes. BraRoAZ is a unique hypomethylated population of 1000 E2 sib lines. When compared to untreated controls, 5-Aza C-treated lines exhibited reduced immuno-staining of 5mC on pachytene chromosomes, and Methylation Sensitive Amplified Polymorphism (MSAP) profiles that were both divergent and more variable. There was coincident phenotypic variation among these lines for a range of seed yield and composition traits, including increased seed protein content and decreased oil content, as well as decreased erucic acid and corresponding increases in linoleic and/or palmitic acid. Each 5-AzaC-treated line represents a unique combination of hypomethylated epialleles.

Conclusions

The approach and populations developed are available for forward and reverse screening of epiallelic variation and subsequent functional and inheritance studies. The generation of stochastically hypomethylated populations has utility in epiallele discovery for a wide range of crop plants, and has considerable potential as an intervention strategy for crop improvement.

Keywords:
DNA methylation; Hypomethylation; Epigenetics; Crop plants; Brassica; 5-Azacytidine