Contrasting cDNA-AFLP profiles between crown and leaf tissues of cold-acclimated wheat plants indicate differing regulatory circuitries for low temperature tolerance Seedhabadee Ganeshan • Pallavi Sharma • Lester Young • Ashwani Kumar • D. Brian Fowler • Ravindra N. Chibbar Received: 9 November 2010 / Accepted: 9 January 2011 / Published online: 26 January 2011 Ó Springer Science+Business Media B.V. 2011 Abstract Low-temperature (LT) tolerance in winter wheat (Triticum aestivum L.) is an economically important but complex trait. Four selected wheat genotypes, a winter hardy cultivar, Norstar, a tender spring cultivar, Manitou and two near-isogenic lines with Vrn-A1 (spring Norstar) and vrn-A1 (winter Manitou) alleles of Manitou and Nor- star were cold-acclimated at 6°C and crown and leaf tissues were collected at 0, 2, 14, 21, 35, 42, 56 and 70 days of cold acclimation. cDNA-AFLP profiling was used to determine temporal expression profiles of transcripts dur- ing cold-acclimation in crown and leaf tissues, separately to determine if LT regulatory circuitries in crown and leaf tissues could be delineated using this approach. Screening 64 primer combinations identified 4,074 and 2,757 differ- entially expressed transcript-derived fragments (TDFs) out of which 38 and 16% were up-regulated as compared to 3 and 6% that were down-regulated in crown and leaf tissues, respectively. DNA sequencing of TDFs revealed sequences common to both tissues including genes coding for DEAD- box RNA helicase, choline-phosphate cytidylyltransferase and delta-1-pyrroline carboxylate synthetase. TDF specific to crown tissues included genes coding for phospahtidyli- nositol kinase, auxin response factor protein and brassi- nosteroid insensitive 1-associated receptor kinase. In leaf, genes such as methylene tetrahydrofolate reductase, NADH-cytochrome b5 reductase and malate dehydroge- nase were identified. However, 30 and 14% of the DNA sequences from the crown and leaf tissues, respectively, were hypothetical or unknown proteins. Cluster analysis of up-, down-regulated and unique TDFs, DNA sequence and real-time PCR validation, infer that mechanisms operating in crown and leaf tissue in response to LT are differently regulated and warrant further studies. Keywords Transcriptome profiling Á Winter wheat Á Low temperature Introduction Cold acclimation and reproductive phase transition are intricately inter-connected in temperate plants as a result of environmental dicta including temperature and light (for reviews see Bernier and Perilleux 2005; Franklin and Whitelam 2004; Winfield et al. 2010). Plants respond to temperature, light quality and quantity variably in various cell-types, tissues and organs due to juxtaposition of can- opy density and plant architecture. Consequently, variable gene expression patterns are triggered thereby affecting development, adaptation, function and response of plants to environmental stimuli. In wheat, differential expression Seedhabadee Ganeshan and Pallavi Sharma contributed equally to this manuscript. Electronic supplementary material The online version of this article (doi:10.1007/s11103-011-9734-8) contains supplementary material, which is available to authorized users. S. Ganeshan Á P. Sharma Á D. B. Fowler Á R. N. Chibbar (&) Department of Plant Sciences, College of Agriculture and Bioresources, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada e-mail: ravi.chibbar@usask.ca L. Young Food and Bioproduct Sciences, College of Agriculture and Bioresources, University of Saskatchewan, 51 Campus Drive, Saskatoon, SK S7N 5A8, Canada A. Kumar Centre for Rural Development and Technology, Indian Institute of Technology, Delhi, Hauz Khas, New Delhi, India 123 Plant Mol Biol (2011) 75:379–398 DOI 10.1007/s11103-011-9734-8