Parallel consideration of SSRs and differentially expressed genes under abiotic stress for targeted development of functional markers in almond and related Prunus species

- Extraction of DE genes with SSRs to obtain functional biomarkers.
- RNA-Seq SSR analysis of normal and frost stress treated tissues.
- Calmodulin, trihelix transcription factor GT-1-like and delta-(8)-fatty-acid desaturase as potential markers for MAS.
- High polymorphism of RNA-Seq SSRs in population of P. arabica, P. scoparia and P. haussknechtii as well as P. dulcis.

RNA-Seq approach is widely used to study plant transcriptome responses to different environmental stresses. RNA-Seq datasets have also become valuable resources to develop SSR markers and other types of markers in plant species. However, there are challenges such as the validation of SSR polymorphisms, and translation of these information into a functional approach for plant breeding programs. In our recent work, the first de novo transcriptome assembly of almond have been reported in response to freezing stress, and thousands of differential expression (DE) genes have been identified. Here, for the first time, we have suggested a parallel consideration of genes with DE under frost stress and SSR markers to find functional markers in almond (Prunus dulcis Mill.) and other related Prunus species. The term “RNA-Seq SSR” was used in the current study, replacing the previous term “EST-SSR” (expressed sequence tagged), for the distinction between traditional EST sequencing and the new RNA-Seq methods. Eleven RNA-Seq SSR markers were identified as polymorphic markers. Some of SSR loci were found on genes which are responsive in cold and other abiotic stresses, including calmodulin, trihelix transcription factor GT-1-like and delta-(8)-fatty-acid desaturase. Furthermore, these markers revealed high polymorphism in population of Prunus arabica, Prunus scoparia and Prunus haussknechtii. Our overall results suggest potential application of DE genes carrying SSR sequences as functional markers. The developed workflow and the new findings presented here are likely to open new opportunity for future genetic diversity, association studies and breeding projects of almond and other plants grown under environmental stresses. This workflow can also be applied to targeted validation and development of SNP and/or indel markers.