The movement of transposons gives rice a greater capacity for adaptation

A new study lead by the CRAG researchers Josep Maria Casacuberta and Raúl Castanera and published in eLife journal reveals that transposons, DNA fragments that can change position within the genome, are a major source of variation in the expression of genes and can influence the response of crops to different environmental and agricultural conditions.

Rice is one of the most important crops in the world, as it feeds more than half of the human population. Therefore, it is essential to know the genetic factors that determine its diversity and adaptation to different environments.

Transposons account for an important fraction of plant and animal genomes. Almost 50% of the human genome and as much as 85% of the maize genome. These elements, that were considered as selfish for a long time, are now recognized as an important source of genome variability, endowing genomes with a high plasticity, in particular in plants.

In this work, CRAG researchers, in collaboration with researchers of the New York University analysed how transposon insertions affect the variability of gene expression on rice populations subjected to domestication and selection by humans. To this end, they used RNA and DNA sequencing data from more than 200 rice varieties from different geographic origins. They tracked the presence of 45,000 transposon insertions across these varieties and found that they often modified the expression of surrounding genes, highlighting their role as drivers of genetic variability.

Interestingly, most of these insertions were already present in the wild ancestor of cultivated rice and were specifically selected in rice populations cultivated under particular environmental conditions. This highlights the importance of the standing variation for plant adaptation. The transcriptional variation induced by transposons was maintained at low frequency in the wild ancestor of rice, as it was kept ready to be used when needed, and was positively selected during rice domestication and breeding, when the growth conditions drastically changed. This shows that transposons, once known as selfish elements, are an excellent tool that gives plants a great capacity for adaptation.

The results of this study point transposons as key elements to take into account when studying genetic variability and reveal a molecular mechanism by which transposons can contribute to adaptation of crops to different ecological and agronomic conditions. The knowledge on the genes whose transcription was altered by transposons selected in different rice populations will help understanding the mechanisms of rice adaptation and could be useful to develop new rice varieties better adapted to changing agroecological conditions.

Reference article

Castanera Raúl, Morales-Díaz Noemia, Gupta Sonal, Purugganan Michael, Casacuberta Josep M. (2023) Transposons are a major contributor to gene expression variability under selection in rice populations eLife 12:RP86324 https://doi.org/10.7554/eLife.86324.1

About the authors and funding of the study

This work was funded by the Spanish Ministerio de Ciencia e Innovación (PID2019-106374RB-I00/AEI/10.13039/501100011033). With the financial support from the Spanish Ministerio de Economía y Competitividad through the ″Severo Ochoa Program for Centers of Excellence in R&D″ 2016–2019 (SEV-2015-0533) and CEX2019–000902-S funded by MCIN/AEI/10.13039/501100011033. This work was also supported by grants SEV - 2015 - 0533 and CEX2019-000902-S funded by MCIN/AEI/10.13039/501100011033, and by the CERCA Program / Generalitat de Catalunya.