Using RNA-Seq Transcriptome Profiling in support of Field Based Strategies to improve Cotton Productivity under Water Deficit Stress

In the face of changing climatic conditions, water deficit stress is one of the most challenging agricultural issues limiting sustainable cotton production. In this research, our objective was to construct a transcriptome profile of cotton under field water deficit stress. Using RNA-seq and the newly published diploid D₅ Gossypium raimondii sequence, we constructed a profile of genes expressed in tetraploid cotton after being exposed to water deficit stress during flowering. Using innovative sequence analysis techniques, transcripts were putatively localized to A_T or D_T genomes. This study represents one of the first to use RNA-seq techniques and whole genome sequence resources for tetraploid cotton transcriptomics. These data will facilitate efforts to understand the complex responses governing transcriptomic regulatory mechanisms and to identify candidate genes that may benefit applied plant breeding programs.