Candidate Genes for Freezing and Drought Tolerance Selected on the Basis of Proteome Analysis in Doubled Haploid Lines of Barley

Abstract

Plant tolerance to environmental stress is determined by a very complicated network composed of many intra- and extracellular factors. The aim of this study was to select candidate genes involved in responses to freezing and drought in barley on the basis of previous proteomic studies and to analyze changes in their expression caused by application of both stress factors. Six candidate genes for freezing tolerance (namely the genes encoding elongation factor 1 alpha (EF1A), ferredoxin-NADP reductase, a 14-3-3a protein, β-fructofuranosidase, CBF2A and CBF4B) and six for drought tolerance (encoding transketolase, periplasmic serine protease, triosephosphate isomerase, a protein with a co-chaperon region (GroEs), pfam14200 and actin) were chosen arbitrarily on the basis of in silico bioinformatic analyses. The expression levels of these genes were measured under control and stress conditions in six DH (doubled haploid) lines with differing freezing and drought tolerance. The results of gene expression analysis confirmed the roles of the candidate genes preselected in this study on the basis of previous proteome analysis in contributing to the differences in freezing and drought tolerance observed in the studied population of DH lines of winter barley.

Identification of the Genetic Basis of Response to de-Acclimation in Winter Barley

“…The changes observed in the activity of the selected enzymes did not correspond or corresponded only partially to the changes in the number of accumulated transcripts of genes encoding peroxidases and catalase ( Figure 7 and Figure 8 ). As described previously [ 42 ], the number of accumulated transcripts might not comply with the amount of accumulated protein for various reasons. Additional proteomic analysis would be helpful in the future to provide a comprehensive overview of the role of oxidoreductase enzymes in response to mid-winter de-acclimation in barley.…”

Application of Mass Spectrometry-Based Proteomics to Barley Research

“…Different proteomics methods including discovery (shotgun) proteomics and absolute and relative quantitative approaches have been used to broaden the knowledge of barley proteome changes under specific abiotic and biotic stress conditions ( Table 3 ) and to explore impact of post-translational modification (PTMs) and protein interactions. 29 , 36 , 152 , 157 , 168 , 187 , 188 …”

“…It is worth mentioning that SWATH-MS can quantify an unlimited number of target peptides as long as they have been previously observed by shotgun MS. 164,165 Therefore, a "discovery" data-dependent experiment followed by data-independent quantitation by SWATH is a suitable choice when reproducible and accurate quantitation is among the main goals of the project. [164][165][166][167][168]182,183 Application of novel methods such as SWATH-MS has enabled investigation of the beer proteome. For instance, one study used a global untargeted SWATH analysis during beer production revealing protein modifications by protease digestion, glycation, or oxidation during the processing steps.…”

Wheat and Barley: Acclimatization to Abiotic and Biotic Stress

“…The aim of a study by Wójcik-Jagła et al [ 6 ] was to select candidate genes involved in responses to freezing (six genes, encoding elongation factor 1 alpha (EF1A), ferredoxin-NADP reductase, a 14-3-3a protein, β-fructofuranosidase, CBF2A and CBF4B) and drought (six genes, encoding transketolase, periplasmic serine protease, triosephosphate isomerase, a protein with a cochaperone region ( GroEs ), pfam14200 and actin). Their expression in barley under both stress factors was also analyzed.…”