The Role of mobile RNAs in grafting-induced traits in solanaceous crops.

Jeynes-Cupper, Katherine E ORCID: 0009-0000-1350-1371 (2025). The Role of mobile RNAs in grafting-induced traits in solanaceous crops. University of Birmingham. Ph.D.

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Abstract

Across Europe and America, tomato cultivation exploits plant grafting to combines plant traits from two different genotypes into a single plant. For
example, drought resistance to a productive cultivar. This example can be explained by the intrinsic properties of the rootstock. Yet, other traits that alter the architecture and physiology of the scion may not be as easily or simply explained. In research, plant grafting has been extensively used as an experimental tool to discover and demonstrate the short- and long-distance signalling of proteins, hormones and RNAs in plants. This includes the movement of small RNAs and their ability to introduce epigenetic alterations in the destination tissue. Interestingly, epigenetic alterations have been linked to responses to environmental and developmental stimuli to regulate proper growth and development. However, researchers have yet to fully describe whether mobile small RNAs are a primary driver of grafting-induced traits.

To further understand the role of mobile RNAs in grafting-induced traits, these works aim to improve upon existing detection methods and investigated the mobility of RNAs in solanaceous plants using grafting. Throughout the previous studies there lacked a standardised computational approach to characterise mobile RNAs using Next Generation Sequencing (NGS) technology. Using real and simulated data, we demonstrate that previous methods generate high levels of false positives and background data noise. Inspired by pan-genomes, we devised an alternative method which showed a remarkedly improved ability to discriminate and place reads to their genome of origin. This method was wrapped into a Bioconductor/R package, mobileRNA, to support further research efforts. As of December 2024, mobileRNA has 1,805 downloads from Bioconductor.

Unlike other plant families, species within the Solanaceous family can be joined via grafting, known as interspecific grafting. In industry, it’s popular to graft productive tomato scions onto hybrids rootstocks to further boost crop vigour in non-stress conditions, yet the underlying mechanisms introducing these alterations is poorly understood. To further understand how rootstocks drive architectural changes to the scion, we investigated tomato and eggplant heterografting using a comprehensive approach that integrated three different angles: phenotypic analysis, physiological analysis, and genomic analysis. The results indicate that a relatively small population of mobile RNAs could have profound effect on the scion architecture. More specifically, the rootstock altered the fruit weight, and we observed an increase in triose phosphate utilisation in the leaves. The results highlight the possible role of mobile sRNA in re-programming the re-allocation of carbon to stress responses, such as cell wall modifications, instead of fruit production. We further suggest that based on a statistical enrichment, mobile messenger RNAs could be the source of the rootstock-derived sRNAs in the scion. This delivery method could possibly ensure greater RNA stability before reaching the destination. Overall, we demonstrate how grafting could be a valuable tool as an alternative perspective to investigating the molecular basis of phenotypic traits, thereby laying the groundwork for further investigations aimed at optimizing crop yields.

Type of Work:

Thesis (Doctorates > Ph.D.)

Award Type:

Doctorates > Ph.D.

Supervisor(s):