Allelic value in gene regulation-implications for gene editing

Gene editing has emerged as the most precise trait modification tool in plant breeding. However, an understanding of what to target and in which genetic background to obtain the intended phenotype is still emerging. This perspective presents an analytical overview of traits targeted, particularly in tomato and rice, where extensive data on gene editing are available in the public domain.

The available gene editing data on allelic values for a given molecular pathway in crops like tomato and rice are revisited. The phenotypes of edits generated across genetic backgrounds were assessed and compared with available resequencing and phenotypic data. The traits evaluated in the current perspective were de novo domestication, grain quality, fruit colour, yield-related traits and stress tolerance to check whether the data available give significant leads to address these traits via editing in other crops. The rationale for editing a particular gene lies in the understanding of the diverse alleles generated, and in this perspective we attempt to discern both the advancements made and the bottlenecks encountered.

The effectiveness of gene editing relies significantly on the roles of alleles generated in regulating specific genetic pathways. It is essential to conduct functional validation of the targeted allele across multiple distinct genetic backgrounds to ascertain its utility. The influence an allele exerts on a given trait is contingent upon factors like the nature of the trait, the position of the gene within a given pathway, and the genetic background in which it has been/will be tested. This perspective highlights how editing has led to a range of phenotypic variations influenced by the genetic background, with certain lines achieving the desired phenotype alongside pleiotropic effects, whereas others do not manifest the expected phenotype. This challenge may be addressed by prioritizing the identification of the right candidate and specific motifs in the regulatory regions as potential targets rather than directly intervening in coding sequences.