Identification of important genes involved in priming induced drought tolerance in barley through transcriptomic data mining
Zahra Zinati
A # * and Sima Sazegari B #
+ Author Affiliations
- Author Affiliations
A Department of Agroecology, College of Agriculture and Natural Resources of Darab, Shiraz University, Shiraz, Iran.
B Institute of Biotechnology, Shiraz University, Shiraz, Iran.
* Correspondence to: zahrazinati@shirazu.ac.ir
# These authors contributed equally to this paper
Handling Editor: Enrico Francia
Crop & Pasture Science 73(9) 1011-1025 https://doi.org/10.1071/CP21769
Submitted: 8 July 2021 Accepted: 17 January 2022 Published: 15 March 2022
© 2022 The Author(s) (or their employer(s)). Published by CSIRO Publishing
Abstract
Context and aims: Due to the effect of seed priming on abiotic stress-induced tolerance in plants, this study has been performed to identify the key genes responding to the seed osmo-priming process in a sensitive barley variety under drought stress.
Methods: The microarray data regarding barley expression analysis under drought stress (expression profile of GSE56437) was used to determine differentially expressed probes in time-series data with the BETR package in R. 1388 differentially expressed probes were ranked by 10 attribute weighting approaches in RapidMiner. Also, decision tree models were applied to provide insight into the combination of important probes in a ranked structure.
Key results: Following attribute weighting approaches analysis, 328 differentially probes were identified by at least one attribute weighting approach. The top-ranked genes were HORVU6Hr1G089600 (sugar transporter), HORVU7Hr1G060130 (superoxide dismutase [CU-ZN] 2, Chloroplastic), HORVU4Hr1G076520 (non-specific serine/threonine protein kinase/threonine-specific protein kinase) and HORVU3Hr1G082260 (3-phosphoinositide dependent protein kinase-1).
Conclusions: According to the promoter analysis of key genes, important transcription factor binding sites related to developmental processes, biotic and abiotic stress responses were identified. The most frequent consensus binding sites were related to the vernalisation1 transcription factor. Enriched gene ontology term analysis pointed out processes with a distinguished role in drought tolerance like oxidation–reduction.
Implications: To our awareness, this is the first study for identifying genes involved in priming-induced tolerance via integrating time-series data analysis, various attribute weighting approaches and decision tree models.
Keywords: abiotic stress, attribute weighting approaches, barley, decision tree, genomics, microarray analysis, priming, promoter analysis.
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