Exploring Novel Genetic Donors of Salt Tolerance across the Tetraploid Cultivated Cotton Germplasm (Gossypium hirsutum) By Transcriptome Profiling and Genetic Network Modeling

Salt stress tolerance is collectively controlled by many functions. The functions are a signaling for ion homeostasis, stomata response, oxidative stress response and post functions are the detoxification, apoptosis, ethylene and senescence, and growth-related functions such as sucrose and plant growth hormones. We performed a comparative analysis of the salt stress response transcriptomes of a minimal comparative panel representing an extreme contrast for salt tolerance across the Gossypium Diversity Reference Set. RNA-seq libraries were constructed from the roots and shoots of highly salt-tolerant and highly salt-sensitive cultivars at day 1, day 2, day 4, day 5, day 7 after mild to moderate levels of salt stress. From these datasets, we identified 1,185 differentially expressed genes (DEGs) with high stringency of over 2 folds difference, including 604 genes in the shoot and 582 genes in root. Among 1,185 DEGs, a subset of 814 were up-regulated in both tolerant and sensitive genotypes. Interestingly the expression increased exponentially across the entire duration of the stress experiment in the sensitive genotype, but only gradual increases were observed in the tolerant genotype with 2-fold to 200-fold difference between genotypes. We dissected 1,185 DEGs into 9 mechanisms to understand how these DEGs contribute to the salt tolerance. The 9 mechanisms are a signaling for ion homeostasis, osmotic stress response, stomata closure, detoxification and anti-oxidants and so on. We propose that under salt stress, the sensitive genotype expends maximum effort to escape the abiotic challenge. This is expressed in terms of over expression of genes conferring tolerance.