Downregulation of three novel candidate genes is important for freezing tolerance of field and laboratory cold acclimated barley

• Published in: Journal of plant physiology 2020-01, Vol.244, p.153049-153049, Article 153049
• Main Authors: Fiust, Anna, Rapacz, Marcin
• Format: Article
• Language: English
• Subjects: Acclimation; Acclimatization; Acclimatization - genetics; Adenosine triphosphatase; Algorithms; Amino acid sequence; Amino acids; Analogies; Annotations; Barley; Bioinformatics; Candidate gene; Cold; Cold acclimation; Cold Temperature; Cold tolerance; Down-Regulation - physiology; Epigenetics; Freezing; Freezing tolerance; Gene Expression Regulation, Plant - physiology; Gene mapping; Gene Ontology; Gene sequencing; Genes; Genotypes; Hordeum - genetics; Hordeum - physiology; Laboratories; Low temperature; Mapping; Markers; Nucleotides; Photosynthesis; Plant growth; Plant Proteins - genetics; Plant Proteins - metabolism; Quantitative trait loci; Signal processing; Signal transduction; Survival
• ISSN: 0176-1617; 1618-1328
• DOI: 10.1016/j.jplph.2019.153049

•DArT markers may be effectively used for the identification of candidate genes.•Hv.ATPase, Hv.DDM1, and Hv.BIG are candidates for freezing tolerance in barley.•Some of these genes may be involved in the control of growth and development.•Downregulation of these genes at low temperature increase freezing survival rate. Diversity arrays technology (DArT) marker sequences for barley were used for identifying new potential candidate genes for freezing tolerance (FT). We used quantitative trait loci (QTL) genetic linkage maps for FT and photosynthetic acclimation to cold for six- and two-row barley populations, and a set of 20 DArT markers obtained using the association mapping of parameters for photosynthetic acclimation to low temperatures in barley for the bioinformatics analyses. Several nucleotide and amino acid sequence, annotation databases and associated algorithms were used to identify the similarities of six of the marker sequences to potential genes involved in plant low temperature response. Gene ontology (GO) annotations based on similarities to database sequences were assigned to these marker sequences, and indicated potential involvement in signal transduction pathways in response to stress factors and epigenetic processes, as well as auxin transport mechanisms. Furthermore, relative gene expressions for three of six of new identified genes (Hv.ATPase, Hv.DDM1, and Hv.BIG) were assessed within four barley genotypes of different FT. A physiological assessment of FT was conducted based on plant survival rates in two field-laboratory and one laboratory experiments. The results suggested that plant survival rate after freezing but not the degree of freezing-induced leaf damage between the tested accessions can be correlated with the degree of low-temperature downregulation of the studied candidate genes, which encoded proteins involved in the control of plant growth and development. Additionally, candidate genes for qRT-PCR suitable for the analysis of cold acclimation response in barley were suggested after validation.