ISSN 1392-3196 Zemdirbyste-Agriculture Vol. 107, No. 4 (2020) 329 ISSN 1392-3196 / e-ISSN 2335-8947 Zemdirbyste-Agriculture, vol. 107, No. 4 (2020), p. 329–336 DOI 10.13080/z-a.2020.107.042 Transcriptome changes triggered by a short-term low temperature stress in winter wheat Andrius ALELIŪNAS, Kristina JAŠKŪNĖ, Gražina STATKEVIČIŪTĖ, Gabija VAITKEVIČIŪTĖ, Gintaras BRAZAUSKAS, Rita ARMONIENĖ Lithuanian Research Centre for Agriculture and Forestry, Institute of Agriculture Instituto 1, Akademija, Kėdainiai distr., Lithuania E-mail: andrius.aleliunas@lammc.lt Abstract Abiotic stresses alter the expression of multiple genes in plants allowing them to accommodate to hostile environmental conditions. Exposure to low temperatures in the autumn prior to winter is a crucial environmental factor determining an increase in freezing tolerance and winter hardiness in temperate plants. The objective of this study was to evaluate transcriptome changes under a short-term low temperature stress using an RNA-Seq approach in winter wheat (Triticum aestivum L.). Signifcant alterations were observed for nuclear transcriptome of winter wheat, whereas the expression profles of organellar genes were much less responsive to low temperature stress. In total, there were 15,042 nuclear genes with signifcantly (FDR < 0.05) altered expression profles caused by exposure to low temperature. From this number, a total of 2,466 genes had a substantially (log 2 FC > 2 or log 2 FC < −2) afected expression profle. The highest number of upregulated genes was observed from chromosomes in homoeologous group 5, followed by group 2. Diferentially expressed genes (DEGs) with the most extreme upregulation encompassed CBFIIId-12.1, WRKY transcription factor 55-like, and a group of genes related to jasmonate signalling pathway. Key words: cold stress, diferentially expressed genes, jasmonate signalling, RNA-Seq, transcription factors, Triticum aestivum. Introduction Bread wheat (Triticum aestivum L.) has undergone a complex history of spread, adaptation and selection since domestication ~8,000–10,000 years ago in the Fertile Crescent and has become one of the most widely cultivated crops in the world (Pont et al., 2019). Today, bread wheat is cultivated in 6 continents and occupies more than 220 million hectares, providing 20% of the protein and caloric intake of humans. Bread wheat is allohexaploid (2n = 6x = 42, AABBDD) with three closely related subgenomes originated from diferent species by two polyploidization events (Feldman, Levy, 2012). Complex bread wheat genome of about 16 Gbp has a very high content of long terminal repeat retrotransposons and displays high levels of similarity between the homologous gene sets on the three subgenomes. Recently, a fully annotated reference sequence of the bread wheat genome in the form of 21 chromosome-like sequence assemblies with access to 107,891 high-confdence genes was made publicly available by The International Wheat Genome Sequencing Consortium (IWGSC, 2018). Most of the world’s wheat is cultivated in temperate climate, where it is exposed to a wide range of fuctuating environmental conditions. Two main types of wheat, difering in their vernalization requirement – spring wheat (no vernalization required) and winter wheat (vernalization required), are cultivated. Winter wheat has higher yield potential; however, a lack of adequate freezing tolerance is still the main limiting factor in some regions (Fowler, Limin, 1997). Freezing tolerance of winter cereals develops through the process of cold acclimation, which is triggered by upregulation or downregulation of hundreds to thousands of cold regulated (COR) genes after exposure of plants to low but non-freezing temperature for certain periods of time (Laudencia-Chingcuanco, Fowler, 2012; Li et al., 2018). Transcriptional cascade of Inducer of CBF Expression (ICE)-C-Repeat-Binding Factors (CBF)- COR is the only well-characterized cold acclimation signalling pathway, which is suggested to be functionally conserved in diferent plant species. In this pathway, CBFs are rapidly induced by inducer of ICE1 during cold stress and bind to the promoter regions of COR genes, known as the CBF regulon, to activate their transcription (Chinnusamy et al., 2007). Although the CBF-dependent pathway plays a crucial role in cold acclimation, only 10– Please use the following format when citing the article: Aleliūnas A., Jaškūnė K., Statkevičiūtė G., Vaitkevičiūtė G., Brazauskas G., Armonienė R. 2020. Transcriptome changes triggered by a short-term low temperature stress in winter wheat. Zemdirbyste-Agriculture, 107 (4): 329–336. DOI 10.13080/z-a.2020.107.042