title: Genome-wide transcriptomic analysis of response to low temperature reveals candidate genes determining divergent cold-sensitivity of maize inbred lines.
abstract: Maize, despite being thermophyllic due to its tropical origin, demonstrates high intraspecific diversity in cold-tolerance. To search for molecular mechanisms of this diversity, transcriptomic response to cold was studied in two inbred lines of contrasting cold-tolerance. Microarray analysis was followed by extensive statistical elaboration of data, literature data mining, and gene ontology-based classification. The lines used had been bred earlier specifically for determination of QTLs for cold-performance of photosynthesis. This allowed direct comparison of present transcriptomic data with the earlier QTL mapping results. Cold-treated (14 h at 8/6 °C) maize seedlings of cold-tolerant ETH-DH7 and cold-sensitive ETH-DL3 lines at V3 stage showed strong, consistent response of the third leaf transcriptome: several thousand probes showed similar, statistically significant change in both lines, while only tens responded differently in the two lines. The most striking difference between the responses of the two lines to cold was the induction of expression of ca. twenty genes encoding membrane/cell wall proteins exclusively in the cold-tolerant ETH-DH7 line. The common response comprised mainly repression of numerous genes related to photosynthesis and induction of genes related to basic biological activity: transcription, regulation of gene expression, protein phosphorylation, cell wall organization. Among the genes showing differential response, several were close to the QTL regions identified in earlier studies with the same inbred lines and associated with biometrical, physiological or biochemical parameters. These transcripts, including two apparently non-protein-coding ones, are particularly attractive candidates for future studies on mechanisms determining divergent cold-tolerance of inbred maize lines.
authors.affiliation: Plant Biochemistry and Physiology Department, Plant Breeding and Acclimatization Institute - National Research Institute, Radzików, 05-870, Błonie, Poland.
authors.forename: Alicja
authors.initials: A
authors.lastname: Sobkowiak
authors.forename: Maciej
authors.initials: M
authors.lastname: Jończyk
authors.forename: Emilia
authors.initials: E
authors.lastname: Jarochowska
authors.forename: Przemysław
authors.initials: P
authors.lastname: Biecek
authors.forename: Joanna
authors.initials: J
authors.lastname: Trzcinska-Danielewicz
authors.forename: Jörg
authors.initials: J
authors.lastname: Leipner
authors.forename: Jan
authors.initials: J
authors.lastname: Fronk
authors.forename: Paweł
authors.initials: P
authors.lastname: Sowiński
mesh_terms: D000222:Adaptation, Physiological; D001947:Breeding; D003080:Cold Temperature; D018506:Gene Expression Regulation, Plant / Q000502:physiology*; D018745:Genome, Plant; D012194:RNA-Directed DNA Polymerase; D060888:Real-Time Polymerase Chain Reaction; D059467:Transcriptome; D003313:Zea mays / Q000235:genetics* / Q000502:physiology*
chemical_list: D012194:RNA-Directed DNA Polymerase