Comparative transcriptome analysis of two maize genotypes with different tolerance to salt stress

A better understanding of the molecular effects of salinity stress is key to improving salt tolerance in Zea mays. In this study, we combined phenotyping with transcript profiling to study genotype-specific differences in salt tolerance in Zea mays. An extensive phenotypic screening identified two genotypes with extreme phenotypic differences in tolerance toward salt stress. De novo RNA-seq analysis of the selected salt-tolerant (R9) and salt-sensitive (S46) genotype was performed to unveil the molecular mechanisms underlying the differences in salt tolerance between the two genotypes. A number of 5884 and 5556 unique transcripts were identified that were uniquely expressed in the R9 and S46 genotypes, respectively. GO enrichment showed that processes such as cellular response to calcium ion, and regulation of secondary metabolites biosynthesis has been highly diverged between the two genotypes at the transcriptome level. Comparing salt treated with control samples for each genotype showed enrichment for salt tolerance related mechanisms, i.e., potassium ion transport and cation/ion transmembrane transport, in the tolerant genotype only. We hypothesized that more efficient potassium uptake and different response to calcium ions can contribute to better ionic hemostasis and subsequently more salt tolerance for the R9 genotype.