Prateek Gupta, Pankaj Singh Dholaniya, Kunnappady Princy, Athira Sethu Madhavan, Yellamaraju Sreelakshmi, Rameshwar Sharma

Front Plant Sci.; 2024 Jan 24: 14:1290937. doi: 10.3389/fpls.2023.1290937.

Abstract

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 mutagenized individuals uncovers the complete spectrum of mutations in the genome. Genome-wide induced mutation resources can improve the targeted breeding of tomatoes and facilitate functional genomics. In this study, we sequenced 132 doubly ethyl methanesulfonate (EMS)-mutagenized lines of tomato and detected approximately 41 million novel mutations and 5.5 million short InDels not present in the parental cultivar. Approximately 97% of the genome had mutations, including the genes, promoters, UTRs, and introns. More than one-third of genes in the mutagenized population had one or more deleterious mutations predicted by Sorting Intolerant From Tolerant (SIFT). Nearly one-fourth of deleterious genes mapped on tomato metabolic pathways modulate multiple pathway steps. In addition to the reported GC>AT transition bias for EMS, our population also had a substantial number of AT>GC transitions. Comparing mutation frequency among synonymous codons revealed that the most preferred codon is the least mutagenic toward EMS. The validation of a potato leaf-like mutation, reduction in carotenoids in ζ-carotene isomerase mutant fruits, and chloroplast relocation loss in phototropin1 mutant validated the mutation discovery pipeline. Our database makes a large repertoire of mutations accessible to functional genomics studies and breeding of tomatoes.

See https://pubmed.ncbi.nlm.nih.gov/38328621/

Figure 1: The spectrum of nucleotides changes in the mutagenized population. (A) The magnitude of changes in the different nucleotides in the mutagenized population. (B, C) The percent nucleotide changes in the whole genome (B) and coding sequence (CDS) (C). (D) The flanking sequence (20 bp) on either side of the mutations in the genome. The 0 bp represents the site of mutation. The bars depict the percent nucleotides at a given position in the sequence. The colors represent the individual nucleotides with annotations indicated below the graph.