Subtractive hybridization-mediated analysis of genes and in silico prediction of associated microRNAs under waterlogged conditions in sugarcane (Saccharum spp.)

Handle URI:
http://hdl.handle.net/10754/334607
Title:
Subtractive hybridization-mediated analysis of genes and in silico prediction of associated microRNAs under waterlogged conditions in sugarcane (Saccharum spp.)
Authors:
Khan, Mohammad Suhail; Khraiwesh, Basel; Pugalenthi, Ganesan; Gupta, Ram Sagar; Singh, Jyotsnendra; Duttamajumder, Sanjoy Kumar; Kapur, Raman
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. © 2014 The Authors.
Citation:
Khan MS, Khraiwesh B, Pugalenthi G, Gupta RS, Singh J, et al. (2014) Subtractive hybridization-mediated analysis of genes and in silico prediction of associated microRNAs under waterlogged conditions in sugarcane (Saccharum spp.). FEBS Open Bio 4: 533-541. doi:10.1016/j.fob.2014.05.007.
Publisher:
Elsevier
Journal:
FEBS Open Bio
Issue Date:
9-Jun-2014
DOI:
10.1016/j.fob.2014.05.007
PubMed ID:
25009768
PubMed Central ID:
PMC4087145
Type:
Article
ISSN:
22115463
Appears in Collections:
Articles

Full metadata record

DC FieldValue Language
dc.contributor.authorKhan, Mohammad Suhailen
dc.contributor.authorKhraiwesh, Baselen
dc.contributor.authorPugalenthi, Ganesanen
dc.contributor.authorGupta, Ram Sagaren
dc.contributor.authorSingh, Jyotsnendraen
dc.contributor.authorDuttamajumder, Sanjoy Kumaren
dc.contributor.authorKapur, Ramanen
dc.date.accessioned2014-11-11T14:31:48Z-
dc.date.available2014-11-11T14:31:48Z-
dc.date.issued2014-06-09en
dc.identifier.citationKhan MS, Khraiwesh B, Pugalenthi G, Gupta RS, Singh J, et al. (2014) Subtractive hybridization-mediated analysis of genes and in silico prediction of associated microRNAs under waterlogged conditions in sugarcane (Saccharum spp.). FEBS Open Bio 4: 533-541. doi:10.1016/j.fob.2014.05.007.en
dc.identifier.issn22115463en
dc.identifier.pmid25009768en
dc.identifier.doi10.1016/j.fob.2014.05.007en
dc.identifier.urihttp://hdl.handle.net/10754/334607en
dc.description.abstractSugarcane 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. © 2014 The Authors.en
dc.language.isoenen
dc.publisherElsevieren
dc.rightsThis is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/3.0/).en
dc.rights.urihttp://creativecommons.org/licenses/by-nc-nd/3.0/en
dc.titleSubtractive hybridization-mediated analysis of genes and in silico prediction of associated microRNAs under waterlogged conditions in sugarcane (Saccharum spp.)en
dc.typeArticleen
dc.identifier.journalFEBS Open Bioen
dc.identifier.pmcidPMC4087145en
dc.eprint.versionPublisher's Version/PDFen
dc.contributor.affiliationKing Abdullah University of Science and Technology (KAUST)en
kaust.authorKhan, Mohammad Suhailen
kaust.authorGanesan, Pugalenthien

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