Gamma ray induced significant phenotypic and metabolite changes in sugarcane variants derived through in vitro mutagenesis

Sugarcane is an economically important polyploid crop whose genetic complexity and limited fertility poses a challenge for crop improvement programs. Gamma radiation-induced mutagenesis is an alternate approach for generating a diverse array of agronomically useful mutants, accelerating varietal development in a long-duration crop like sugarcane. To develop agronomically useful mutants of a commercial sugarcane genotype Co 99004, gamma ray induced in vitro mutagenesis was carried out. The phenotypic variants of Co 99004 in V1 generation could be categorized into five distinct phenotypically scorable classes, including three chlorophyll mutants (albina, chlorina and chlorina pigmented) and two green mutants like wild type control. SRAP marker analyses indicated distinct genomic variation among the phenotypic mutants and control plants, with the polymorphic information content (PIC) ranging from 0 to 0.472. Further, the phylogenetic dendrogram derived from the SRAP marker data grouped the mutants into four distinct clusters clearly differentiating the phenotypic classification. Sequencing of selected SRAP amplicons indicated deletion/insertion of gene specific fragments. Interestingly, the loss of chlorophyll in albina and chlorina mutants showed gamma irradiation-induced deletions in the gene encoding FAR1-RELATED SEQUENCE 5-like protein, which is involved in chlorophyll biosynthesis. GC-MS based metabolome profiling showed alteration in tetrapyrrole biosynthesis, MEP (Methylerythritol Phosphate), and fatty acid biosynthesis pathways, indicating a significant metabolic variation in the chlorophyll mutants. Further characterization of the genetically distinct, non-lethal green wild type mutants can lead to the identification of agronomically useful mutants. In addition, the loss-of-function chlorophyll mutants can serve as a good source for comparative genomics studies aimed at gene-trait association.