A nuclear reaction: The genetic consequences for plants exposed to radiation
3 Jan 2013 by Evoluted New Media
In light of the Fukushima 2011 nuclear disaster, Dr Eric Belfield from Oxford University describes the genome sequence research conducted by his team to understand the genetic consequences of ionizing radiation exposure on plants
Ionising radiation is a naturally occurring phenomenon. Plants are constantly being bombarded by ultraviolet, gamma and x-ray radiation in the terrestrial environment. Significant sources of local variation in radiation include altitude, relative abundance in soils of radioactive isotopes, and nuclear accidents. Today, with the advent of whole-genome sequencing, it is possible to uncover the genetic consequences of radiation exposure on plants.
Scientists have known for some time that organisms exposed to radiation can induce a range of abnormalities, and that if the doses are high enough they may be sufficient to kill. For example, following the Chernobyl incident in 1986, plants and animals living in the higher exposure areas (in localized sites at distances up to 30 km from the reactor site) suffered acute adverse effects including increased mortality and reproductive losses, while those outside this exclusion zone showed no acute radiation-induced effects 1.
Recently, similar effects have been reported following the Fukushima 2011 nuclear disaster where scientists have found an increase in leg, antennae and wing shape mutations among butterflies2. However, the amount of radiation estimated to have been released at Fukushima is about 15 % of that released at Chernobyl according to Japan's Nuclear and Industrial Safety Agency.
Despite the necessity to monitor the effects of environmental ionising radiation on biological systems, the complexity of such systems makes current measures difficult to interpret. However, quantitative genome-wide studies of the DNA mutations induced by artificial radiation should model the effects of natural radiation and provide an insight to the genetic effects of radiation in both somatic and germ cells.
Now, a team from Oxford University have published a paper describing the incidence and molecular spectrum of mutations induced by fast-neutron (FN) ionising radiation of plant genomes. FNs exist naturally from high energy cosmic ray showers that make up between 10 to 15% of the background radiation on Earth. Artificially, FNs can be generated by reactors from recycled nuclear fuel such as those in the commercial electricity industry.
For decades researchers have used the power of FN radiation in forward genetic screens where the causal mutation responsible for a particular phenotype of an organism is identified. The Oxford University scientists describe the genomic consequences of exposing plants to FN ionizing radiation and report their findings in the journal Genome Research3.
The team used the mutagenic property of FN ionising radiation to irradiate the seeds of the flowering plant A. thaliana (a model organism with 5 chromosomes, and the first plant genome sequenced). Seeds were treated at the KFKI Atomic Energy Research Institute in Budapest with a FN dose of 60 Gy (Gray; the SI units typically associated with the absorbed dose of ionising radiation), a dose similar to that received by plants close to the Chernobyl nuclear power station accident site received4. After sowing the seeds, a screen was performed to isolate mutant seedlings with elongated hypocotyls (the stem structure of a germinating seedling). From a collection of several hundred thousand plants, six mutant seedlings were selected that ranged in stem height from 11 to 19 mm (in comparison to the 6 mm height of the non-irradiated control lines). The selected mutant lines served two scientific functions: Firstly, they showed researchers the nature of mutations they should expect to find in forward genetic screens of plant following ionizing radiation, and secondly, the study described for the first time the genome-wide effects of ionising radiation on an entire eukaryotic genome.
Genome sequencing was undertaken on the six independent mutant plant lines at the Wellcome Trust Centre for Human Genetics, GeneServices and the Beijing Genomics Institute using Illumina sequencing technology. Up to 43-fold coverage of the 120 megabase-sized genome was obtained and bioinformatic analyses revealed the frequency and molecular spectrum of mutations harbored in plants following radiation exposure.
A total of 108 homozygous genomic mutations were identified in the plants (the M3 generation) and included single base substitutions (SBSs), insertions and deletions. It was previously thought that the majority of mutations that result from FN irradiation were deletions between three-four kilobase in size. However, the most prominent class of mutations observed in this study were SBSs making up 59% of the total mutations, while deletions were the second most frequent (36%) and insertions had the lowest incidence, at just five percent. Interestingly, the most common deletions identified (36%) were just one bp in size possibly caused by replication slippage at homopolymeric stretches of bases. This latter result was a surprise; in fact, only one deletion was over the expected three-four kilobase in size, showing that previous widely held views regarding the classes of mutation most commonly induced in plant genomes by irradiation are unfounded.
The Oxford researchers found that most of the SBSs (80%) were located at pyrimidine dinucleotide sites (consecutive cytosine and or thymine bases) and of the nine different sub-classes of single nucleotide mutations, G:C to A:T transitions (31%) conversions were predominant. This latter observation is consistent with those mutations caused by UV radiation exposure and those of ‘‘background’’ mutations arising in A. thaliana plant lines spontaneously in a laboratory environment 5. However, the spectrum of transition (Ti) and transversion (Tv) mutations, and the calculated Ti/Tv ratio of SBSs identified in laboratory grown A. thaliana lines and those induced by FN mutagenesis, were significantly different and therefore could be used in diagnostics of environmental samples.
Overall, the effects of a FN-irradiation dose of 60 Gy increased the mutational rate by 50 fold (359.7 mutations per site per generation) compared with that observed naturally in plants. The observations of differential mutational rates and the distinct genome-wide mutation spectrum induced by ionizing radiation will be useful to those using ionizing radiation for gene function studies and to those interested in the biological consequences of environmental radiation on the genomes of plants growing in the wild.
The Author: Eric Belfield, researcher at The Department of Plant Sciences, University of Oxford. Contact: E-mail: eric.belfield@plants.ox.ac.uk Tel +44 (0)1865 275000
References
1: Chernobyl’s Legacy: Health, Environmental and Socio-Economic Impacts and Recommendations to the Governments of Belarus, the Russian Federation and Ukraine. The Chernobyl Forum: 2003–2005. International Atomic Energy Agency, Vienna International Centre, PO Box 100, A-1400 Vienna, Austria.
2: Hiyama A, Nohara C, Kinjo S, Taira W, Gima, S, Tanahara A and Otaki JM. The biological impacts of the Fukushima nuclear accident on the pale grass blue butterfly. Scientific Reports 2 570
3:Belfield E, Gan, X, Mithani A, Brown C, Jiang C, Franklin K, Alvey E, Wibowo A, Jung M, Bailey K, Kalwani S, Raggoussis J, Mott R, Harberd N. (2012) Genome-wide analysis of mutations in mutant lineages selected following fast-neutron irradiation mutagenesis of Arabidopsis thaliana. Genome Research 22: 1306-1315.
4: Kovalchuk I, Abramov V, Pogribny I, & Kovalchuk O (2004) Molecular aspects of plant adaptation to life in the Chernobyl zone. Plant Physiology 135 (1): 357-363.
5: Ossowski S, Schneeberger K, Lucas-Lledo JI, Warthmann N, Clark RM, Shaw RG, Weigel D, Lynch M. (2010). The rate and molecular spectrum of spontaneous mutations in Arabidopsis thaliana. Science 327: 92–94.
