Functional description and development of polymorphic EST-SSR markers in bread wheat and their gene interactions network

The tolerance of abiotic stress is considered to be one of the key features of crop breeding under climate changes. For any crop improvement program, the selection of suitable gene pools among the germplasms is first needed. Drought and salinity traits are the most difficult ones to monitor for being polygenic. Bread wheat (Triticum aestivum) is the most commonly grown cereal grain. To predict new EST-SSR markers, 6717 expressed sequence tags (ESTs) expressed in drought and salinity stress conditions were collected from the National Center for Biotechnology Information (NCBI) then clustered and assembled. Simple sequence repeats (SSRs) have been researched from all unigenes, and then characterization and functional annotation (GO, KEGG, enzymes, TFs, and conserved motifs) for SSR-containing unigenes have been achieved. Fifty primer pairs were selected and synthesized. A polymorphism comparison between the in-silico and real PCR results was conducted. High drought and salinity-tolerant genotypes were grouped in cluster B. Interaction networks between the predicted genes were explored. Out of the polymorphic primer pairs, two primers were identified as unique primers, which may be more related to drought and salinity tolerance and could be further used in quantitative trait locus (QTLs) mapping and marker-assisted selection (MAS). The transferability of the EST-SSR markers for related wheat species ranged between 90% in some Triticum L. species and 50% in Hordeum vulgare L. In addition, some SSR-containing unigenes were highly conserved with the Zea mays genome. •A set of functional annotations (GO, KEGG, enzymes, TFs, and conserved motifs)•A polymorphism comparison between the in silico and real PCR results•Two unique EST-SSR primers•Exploration of interactions network between the predicted genes•The transferability of the EST-SSR markers in some related wheat species