Comparison of genome alterations and phenotypic variations between random mutagenesis and site-directed genome editing in tomato plants

Abstract

The enhancement of crop performance and adaptability in response to the challenges posed by an expanding global population and climate variability is considered pivotal through plant breeding. This study investigates the comparative impacts of ethyl methanesulfonate (EMS) mutagenesis and CRISPR-Cas9 gene editing on tomato plants. EMS, a chemical mutagen known for inducing random mutations, is compared with CRISPR-Cas9, which offers precise, targeted genomic alterations. A purple tomato phenotype monitoring system was established to assess these techniques' mutational and phenotypic effects on transgenic Rubion tomato lines containing the Del/Ros1 gene. Whole genome sequencing revealed that EMS-treated lines exhibited a higher frequency of single nucleotide polymorphisms (SNPs) and insertions/deletions (indels) compared to CRISPR-edited lines, which displayed fewer off-target effects. Phenotypic, nutrient, and phytochemical content analyses indicated no significant differences between EMS and CRISPR treatments, with variations attributed to genetic and environmental factors. This study underscores the complementary roles of EMS and CRISPR in plant breeding, highlighting their respective advantages in inducing genetic diversity and achieving targeted genetic modifications. The findings have significant implications for advancing agricultural innovation and informing regulatory frameworks, ensuring the development of safe, nutritionally enhanced crops. This research contributes to the development of resilient crops, supporting sustainable agricultural practices and addressing global food security challenges.