Changes in microsatellite motifs in response to abiotic stresses: a case study using wheat and rice RNA-sequencing data

Abstract

Background and Objective: Microsatellites or simple sequence repeat (SSR) markers play an important role in plant breeding projects. While a large number of SSRs in plants has been recently identified, only a few SSRs have been randomly validated in the lab. Therefore, to cope with the large numbers of SSRs, it is suggested that a targeted selection scheme may be more efficient in identifying functional biomarkers than the random selection of SSRs. The aim of this study was to develop a new method for identifying functional SSR markers in plant breeding. Methodology: For this study, in silico analyses of available wheat RNA-seq data under heat SSR stress were conducted and unique SSR patterns were obtained. In addition, alterations of SSRs under other stress conditions were confirmed through RNA-seq data of rice subjected to salt, drought and cold. The Audic and Claverie, R of Stekel and Falciani Fisher and General Chi-squared tests were all applied for comparisons of data. Results: The results of the study revealed that GC/GC and GCC/GGC repeats were significantly more common under stress conditions compared with controls for both wheat and rice samples. Interestingly, genes containing these motifs have been found to participate in abiotic stress responses and to include various heat-shock proteins (HSPs) and DREB/CBF (DRE-binding protein/C-repeat binding factor) proteins. Conclusion: The overall findings of this study suggest the possibility of using genes with altered SSRs as functional markers. The applied workflow and the results presented here are expected to help establish a new paradigm for future studies involving genetic diversity, breeding, molecular biology and association studies of plants grown under adverse environmental conditions.