A new gene expression atlas has now mapped the ‘noisy genes’ responsible for phenotypic variation ― differences in physical characteristics ― that often exists between genetically identical plants, even in the same environment. The work explored gene expression of Arabidopsis thaliana, or thale cress, and is described in a new paper published on 24 January in the journal Molecular Systems Biology (1). The authors suggest that plants may, in fact, be hedging their bets against environmental stressors such as drought, high salinity, and extreme temperatures.
The same way identical twins are never exactly “identical”, the same holds true in the plant world. Therefore, examining the genome of a single plant is not sufficient to determine the variable range of plant characteristics. Whereas this variability allows plant species to be less vulnerable to climate change and extreme weather events, in the controlled agricultural environment in which farmers rely on uniform crops that respond in the same way to fertilisers and irrigation, this can pose problems.
Thus, the evolution of gene expression may be increasing the robustness of plant populations without actually changing their genes.
Unlike animals, plants can’t move, so they must have constantly sense and respond to environmental threats by varying their gene expression. This so-called “noise” will be important in understanding how and whether wild plant populations can survive more frequent climate change-induced weather extremes. The plant’s genome or genetic code is used as a set of instruction to direct the synthesis a protein or some other functional molecule within a cell. The first step of this process, called transcription, involves converting a segment of the DNA sequence into RNA, which is where these differences can arise. According to the authors, “transcriptional variability is rarely considered although it could influence the relationship between genotype and phenotype.”
The team of researchers led by Dr James Locke from the University of Cambridge studied the seedings of Arabidopsis and performed RNA-sequencing on individual seedlings every two hours over a 24-hour period to analyse variations in the 15,646 individual genes of the plant’s genome. The small flowering plant, often considered a weed, is native to Eurasia and Africa. Its short life cycle, small size, and efficient reproduction through self-pollination have made Arabidopsis a popular model genetic organism for studying induced mutations in plants.
The findings showed that nine per cent of genes (1,358 genes) exhibited high variability at least once within the 24-hour period. The variable genes fell into two categories, those that are more variable during the day and those that exhibit higher gene expression variation at night. The researchers also identified certain factors that may increase this variation, including gene length, number of transcription factors, and chromatin environment, which determines whether gene expression can actually be altered without changing a cell’s DNA. In particular, variable genes were found to be shorter, often the target of several transcription factors, and had a “closed” chromatin environment.
The scientists have now established an online open-access atlas called AraNoisy. The resource will allow plant scientists and growers around the world to study the influence of gene expression variability on plant survival and diversity within clonal populations. This new data could lead to further important insights to potentially help tailor plant conservation efforts ― “precision conservation” is already showing both economic and environmental benefits ― as well as future crop development strategies.
The authors “revealed the extent of gene expression variability between plants and how it might be regulated,” which they suggest “sets the stage for future work examining the potential function and specific mechanism of variability for each noisy pathway.”
(1) Cortijo, S. et al. Widespread inter‐individual gene expression variability in Arabidopsis thaliana. Molecular Systems Biology (2019). DOI: 10.15252/msb.20188591