Identification of drought-responsive genes in a drought-tolerant cotton (Gossypium hirsutum L.) cultivar under reduced irrigation field conditions and development of candidate gene markers for drought tolerance

Cotton productivity is affected by water deficit, and little is known about the molecular basis of drought tolerance in cotton. In this study, microarray analysis was conducted to identify drought-responsive genes in the third topmost leaves of the field-grown drought-tolerant cotton (Gossypium hirsutum L.) cultivar Acala 1517-99 under drought stress conditions. Water stress was imposed by withholding irrigation for 9 days in the early squaring stage, which resulted in 10-15 % reduction in plant growth compared to the well-watered plants. A total of 110 drought-responsive genes (0.5 % of the total genes) were identified, 79 % (88 genes) of which were drought-repressed and 21 % (22 genes) were drought-induced. The drought-induced genes were grouped into six functional categories including stress-related (ten genes, nine of which encode heat shock proteins), metabolism (three genes) and one gene each for transcription factor, proline biosynthesis and cellular transport. The drought-repressed genes were classified into 14 functional categories, comprising metabolism (20 genes), cellular transport (12 genes), stress-related (12 genes), regulation of gene expression (nine genes), transcription factor (four genes), signal transduction (seven genes) and two genes each for biosynthesis of secondary compounds, cell wall, fatty acids/lipids and chlorophyll, and protein degradation. Most of the genes have been reported in other plants as drought-tolerant/responsive. The responsiveness of 19 selected drought-responsive genes was validated by quantitative RT-PCR. Furthermore, primers were developed and assayed for all the drought-responsive genes to develop single-strand conformation polymorphic markers, many of which were found to be correlated with drought tolerance. This report represents the first study on integration of a transcriptome analysis to develop molecular markers that are associated with drought tolerance in cotton.