The present work is a pioneer study specifically addressing the aquaporin transcripts in sugarcane transcriptomes. Representatives of the four aquaporin subfamilies (PIP, TIP, SIP, and NIP), already described for higher plants, were identified. Forty-two distinct aquaporin isoforms were expressed in four HT-SuperSAGE libraries from sugarcane roots of drought-tolerant and -sensitive genotypes, respectively. At least 10 different potential aquaporin isoform targets and their respective unitags were considered to be promising for future studies and especially for the development of molecular markers for plant breeding. From those 10 isoforms, four (SoPIP2-4, SoPIP2-6, OsPIP2-4, and SsPIP1-1) showed distinct responses towards drought, with divergent expressions between the bulks from tolerant and sensitive genotypes, when they were compared under normal and stress conditions. Two targets (SsPIP1-1 and SoPIP1-3/PIP1-4) were selected for validation via RT-qPCR and their expression patterns as detected by HT-SuperSAGE were confirmed. The employed validation strategy revealed that different genotypes share the same tolerant or sensitive phenotype, respectively, but may use different routes for stress acclimation, indicating the aquaporin transcription in sugarcane to be potentially genotype-specific. 1. Introduction Sugarcane (Saccharum spp.) is a valuable crop once it accumulates high levels of sucrose in the stems [1, 2]. In 2011, the twenty largest sugarcane producers generated about 1.7 billion tons of sucrose worldwide, valued about 52.5 billion dollars [3]. However, abiotic stresses can reduce the potential yield of these cultivated plants by 70%, with drought being the most dangerous one [4]. Water deficit, and its influence onto a variable number of morphological and functional characters in plants, eventually becomes one of the main obstacles to sustainable agricultural production worldwide [5]. The reduction of the water content in a plant cell provokes a complex network of molecular responses, involving stress perception, signal transmission in a transduction cascade and physiological, cellular, and morphological changes [6], including stomatal closure, suppression of cell growth and photosynthesis, and activation of cellular respiration. Plants under drought still respond to it and adapt by accumulating specific osmolytes and proteins for stress tolerance [7]. Genes expressed during drought can be classified into two functional groups. The first group encodes proteins that increase plant tolerance to stress, such as water channels proteins
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