Dr Naser Aliye Feto (Senior Lecturer & Leader, OMICS Research Group & Facility, Department of Biotechnology, Faculty of Applied & Computer Sciences, Vaal University of Technology) obtained his BSc in Plant Sciences on July 07 2001 & MSc in Phytopathology (Phytobacteriology) on July 07 2007 from Haramaya University (Haramaya, Ethiopia) and PhD in Biology (Biotechnology) on July 18, 2012 from University of Camerino (Camerino, Italy). Dr Feto authored two books, co-edited a book and has been publishing a number of research articles & book chapters. He is the recipient of Vaal University’s Faculty Research Achievement Award for 2015 and a recipient of Vice Chancellor’s “Wow” Award for 2016. His areas of research interest are microbial Metagenomics, Metatranscriptomics, Proteomics and Metabolomics (OMICS) and transgenic crop development. Currently, two postdocs and a number of postgraduate students are researching at the State-of the-art OMICS Research Facility under his direct supervision.
Previous studies highlighted the impact of simple sequence repeats (SSR) markers in genetic diversity, association studies as well as comparative and functional genomics analysis. Despite detection of a large number of SSRs in plants through high-throughput RNA sequencing (RNA-seq) techniques, a few numbers of them were randomly validated in the lab. To cope with the large amounts of detected SSRs, we suggest a targeted selection scheme for SSRs, instead of random selection of these markers. The term “RNA-seq SSR” was used in the current study, replacing the previous term “EST-SSRs” (expressed sequence tagged), for the distinction between traditional EST sequencing and the new RNA-seq methods. In silico SSR analyses of available wheat RNA-seq data indicate unique SSR patterns under heat stress. Alternations of SSRs in other stress conditions were also confirmed by RNA-seq data obtained from rice under salt, drought and cold stress conditions. Our findings showed that GC/GC and GCC/GGC repeats were significantly abundant under stress conditions when compared to control samples in both wheat and rice. Interestingly, genes containing these motifs are found to participate in abiotic stress responses and include different heat shocked proteins (HSPs) and transcription factors. Our overall results suggest the potential application of responsive genes with SSRs as functional markers. In conclusion, the developed workflow and the findings presented here are likely to open a new paradigm for future genetic diversity, breeding and molecular biology research as well as association studies of plants grown under adverse environmental conditions. Besides, this workflow can also be applied for targeted validation and development of SNP and/or indel markers.
Keywords: Genetic diversity; Heat shocked proteins; RNA-seq SSR