Molecular Karyotyping and Exome Analysis of Salt‐Tolerant Rice Mutant from Somaclonal Variation

Abstract

LPT123‐TC171 is a salt‐tolerant (ST) and drought‐tolerant (DT) rice line that was selected from somaclonal variation of the original Leuang Pratew 123 (LPT123) rice cultivar. The objective of this study was to identify the changes in the rice genome that possibly lead to ST and/or DT characteristics. The genomes of LPT123 and LPT123‐TC171 were comparatively studied at the four levels of whole chromosomes (chromosome structure including telomeres, transposable elements, and DNA sequence changes) by using next‐generation sequencing analysis. Compared with LPT123, the LPT123‐TC171 line displayed no changes in the ploidy level, but had a significant deficiency of chromosome ends (telomeres). The functional genome analysis revealed new aspects of the genome response to the in vitro cultivation condition, where exome sequencing revealed the molecular spectrum and pattern of changes in the somaclonal variant compared with the parental LPT123 cultivar. Mutation detection was performed, and the degree of mutations was evaluated to estimate the impact of mutagenesis on the protein functions. Mutations within the known genes responding to both drought and salt stress were detected in 493 positions, while mutations within the genes responding to only salt stress were found in 100 positions. The possible functions of the mutated genes contributing to salt or drought tolerance were discussed. It was concluded that the ST and DT characteristics in the somaclonal variegated line resulted from the base changes in the salt‐ and drought‐responsive genes rather than the changes in chromosome structure or the large duplication or deletion in the specific region of the genome.