Somaclonal Variation in Rice: Retrotransposon Tos17 and Structural Variation with NGS Analysis

Phenotypic changes in regenerated plants observed from early times of the development of tissue culture methods in 1960s and 1970s, was termed somaclonal variation in 1981. The causes for these changes have been a long-standing interest among plant biologists. In early 1990s, transposition events of endogenous retrotransposon Tos17 were found in regenerated plants from cultured cells of japonica rice cultivar Nipponbare. The transposition of Tos17 was recognized as one cause for somaclonal variation. Tos17 prefers genic regions for their transposition. However, contribution of Tos17 transposition for somaclonal variation is estimated to be less than 5% of total phenotypic changes. Next generation sequencing (NGS) technology enables whole genome sequence analysis of rice individuals. Analysis of genome sequence from regenerated plants by the recently developed software PED (2019) now enables analysis of somaclonal variations appearing as genomic changes of large duplications and deletions and frequent single base mutations, as well as transpositions of Tos17. Because we now are able to know the genomic changes at the nucleotide sequence level using the new genomic analysis tools, detection of high frequency changes of genome in somaclones will contribute significantly to breeding and functional genomics of rice.