title: Subtractive hybridization-mediated analysis of genes and in silico prediction of associated microRNAs under waterlogged conditions in sugarcane (Saccharum spp.).
abstract: Sugarcane is an important tropical cash crop meeting 75% of world sugar demand and it is fast becoming an energy crop for the production of bio-fuel ethanol. A considerable area under sugarcane is prone to waterlogging which adversely affects both cane productivity and quality. In an effort to elucidate the genes underlying plant responses to waterlogging, a subtractive cDNA library was prepared from leaf tissue. cDNA clones were sequenced and annotated for their putative functions. Major groups of ESTs were related to stress (15%), catalytic activity (13%), cell growth (10%) and transport related proteins (6%). A few stress-related genes were identified, including senescence-associated protein, dehydration-responsive family protein, and heat shock cognate 70 kDa protein. A bioinformatics search was carried out to discover novel microRNAs (miRNAs) that can be regulated in sugarcane plants subjected to waterlogging stress. Taking advantage of the presence of miRNA precursors in the related sorghum genome, seven candidate mature miRNAs were identified in sugarcane. The application of subtraction technology allowed the identification of differentially expressed sequences and novel miRNAs in sugarcane under waterlogging stress. The comparative global transcript profiling in sugarcane plants undertaken in this study suggests that proteins associated with stress response, signal transduction, metabolic activity and ion transport play important role in conferring waterlogging tolerance in sugarcane.
authors.affiliation: Center for Desert Agriculture, Division of Biological and Environmental Sciences and Engineering, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia ; Division of Crop Improvement, Indian Institute of Sugarcane Research, Rae Bareli Road, P.O. Dilkusha, Lucknow 226002, U.P., India.
authors.forename: Mohammad Suhail
authors.initials: MS
authors.lastname: Khan
authors.affiliation: Center for Genomics and Systems Biology, New York University Abu Dhabi, P.O. Box 129188, Abu Dhabi, United Arab Emirates.
authors.forename: Basel
authors.initials: B
authors.lastname: Khraiwesh
authors.affiliation: Bioscience Core Laboratory, King Abdullah University of Science and Technology, Thuwal 23955-6900, Kingdom of Saudi Arabia.
authors.forename: Ganesan
authors.initials: G
authors.lastname: Pugalenthi
authors.affiliation: Zila Parishad Krishi Mahavidyalata, Banda, India ; Division of Crop Improvement, Indian Institute of Sugarcane Research, Rae Bareli Road, P.O. Dilkusha, Lucknow 226002, U.P., India.
authors.forename: Ram Sagar
authors.initials: RS
authors.lastname: Gupta
authors.affiliation: Division of Crop Improvement, Indian Institute of Sugarcane Research, Rae Bareli Road, P.O. Dilkusha, Lucknow 226002, U.P., India.
authors.forename: Jyotsnendra
authors.initials: J
authors.lastname: Singh
authors.affiliation: Division of Crop Protection, Indian Institute of Sugarcane Research, Rae Bareli Road, P.O. Dilkusha, Lucknow 226002, U.P., India.
authors.forename: Sanjoy Kumar
authors.initials: SK
authors.lastname: Duttamajumder
authors.affiliation: Division of Crop Improvement, Indian Institute of Sugarcane Research, Rae Bareli Road, P.O. Dilkusha, Lucknow 226002, U.P., India.
authors.forename: Raman
authors.initials: R
authors.lastname: Kapur
keywords: ABA, abscisic acid; ADF, actin depolymerizing factor; EST; ESTs, expressed sequence tags; Hsps, heat shock proteins; Novel miRNAs; PTGS, post-transcriptional gene silencing; REMs, remorins; SSA, snow pea pod senescence-associated; SUCEST, sugarcane EST database; Sugarcane; Suppression subtractive hybridization; TGS, transcriptional gene silencing; Waterlogging stress