Allelic value in gene regulation-implications for gene editing

Area of Science:

• Plant genetics and breeding
• Molecular biology
• Agricultural science

Background:

• Gene editing is a precise tool for plant trait modification, yet understanding optimal targets and genetic backgrounds for desired phenotypes remains a challenge.
• Extensive gene editing data in tomato and rice provide a foundation for analyzing trait modification strategies.

Purpose of the Study:

• To analytically overview targeted traits in gene-edited crops, particularly tomato and rice, to understand advancements and bottlenecks.
• To assess the potential of gene editing for de novo domestication, grain quality, fruit color, yield, and stress tolerance by analyzing existing data.

Main Methods:

• Revisiting available gene editing data on allelic values within molecular pathways in tomato and rice.
• Assessing and comparing phenotypes of edits across different genetic backgrounds with resequencing and phenotypic data.
• Evaluating traits including de novo domestication, grain quality, fruit color, yield, and stress tolerance.

Main Results:

• Gene editing effectiveness is significantly influenced by the roles of generated alleles in regulating genetic pathways.
• Phenotypic outcomes of gene editing vary considerably across different genetic backgrounds, with some lines showing desired traits and others exhibiting pleiotropic effects or no expected phenotype.
• The influence of an allele on a trait depends on the trait's nature, gene position in a pathway, and the genetic background.

Conclusions:

• Functional validation of targeted alleles across multiple distinct genetic backgrounds is essential to confirm their utility.
• Prioritizing identification of suitable candidate genes and regulatory motifs is recommended over direct intervention in coding sequences to address challenges in achieving desired phenotypes.
• Gene editing can lead to diverse phenotypic variations, highlighting the critical role of genetic background in trait modification.