2012 Annual Report 1a.Objectives (from AD-416): Generate a whole cotton transcriptome profile of water deficit stress responsive genes and determine the expression patterns of aquaporin genes across genotypes. 1b.Approach (from AD-416): This project consists of two parts. First, we will use next generation sequencing technology to generate a comprehensive whole transcriptome profile of cotton genes differentially expressed in response to water deficit stress. Leaf and root transcriptomes from a single genotype will be compared between well-watered and water-deficit stressed field treatments. Second, we will use quantitative polymerase chain reaction (PCR) to functionally characterize aquaporin gene expression during cotton growth and development. Tissue and developmental specific gene expression patterns of individual aquaporin genes across different genotypes will be quantitatively measured in response to specific environmental conditions. 3.Progress Report: This project is related to objective 1 of the in-house project: to develop genetic resources and cropping practices that increase cotton water-use efficiency. Water deficit stress is known to be a major inhibitor of environmentally and economically sustainable cotton production systems. The primary objective of this cooperative research project is to identify genes with expression sensitivity to water deficit stress. A single cultivar, reported to be tolerant to water deficit stress, was grown in the field under well watered and water limited conditions. Root and leaf tissue samples were collected from each water treatment during a period of drought and used to prepare RNA libraries. To date, ARS-Florence has worked with Brigham Young University to DNA sequence the expressed portion of the genome for each tissue sample. Analyses are underway to identify sets of genes in roots, leaves, or both that are up or down regulated in response to water deficit stress. This research will provide a vast collection of candidate genes for improving cotton’s water use efficiency and/or performance under water limited conditions.