Augmenting tomato functional genomics with a genome-wide induced genetic variation resource

• DOI: 10.3389/fpls.2023.1290937
• Publication Date: 2024-01-24T14:59:34Z
• Authors: Prateek Gupta; Pankaj Singh Dhol...; Kunnappady Princy; Athira Sethu Madh...; Yellamaraju Sreel...; Rameshwar Sharma
• Keywords: Ethyl methanesulfonate; Functional Genomics; Forward genetics

Induced mutations accelerate crop improvement by providing novel disease resistance and yield alleles. However, the alleles with no perceptible phenotype but have an altered function remain hidden in mutagenized plants. The whole-genome sequencing (WGS) of individuals uncovers complete spectrum genome. Genome-wide induced mutation resources can improve targeted breeding tomatoes facilitate functional genomics. In this study, we sequenced 132 doubly ethyl methanesulfonate (EMS)-mutagenized lines tomato detected approximately 41 million 5.5 short InDels not present parental cultivar. Approximately 97% genome had mutations, including genes, promoters, UTRs, introns. More than one-third genes population one or more deleterious predicted Sorting Intolerant From Tolerant (SIFT). Nearly one-fourth mapped on metabolic pathways modulate multiple pathway steps. addition to reported GC>AT transition bias for EMS, our also a substantial number AT>GC transitions. Comparing frequency among synonymous codons revealed that most preferred codon is least mutagenic toward EMS. validation potato leaf-like mutation, reduction carotenoids ζ-carotene isomerase mutant fruits, chloroplast relocation loss phototropin1 validated discovery pipeline. Our database makes large repertoire accessible genomics studies tomatoes.