Comparative transcriptomic analysis of germinating rice seedlings to individual and combined anaerobic and cold stress

Abstract

Background Rice is one of the most important cereals consumed worldwide. Two major abiotic factors affecting rice plants in different growth stages are flooding stress and cold stress. These abiotic stresses can take place independently or simultaneously and significantly affect rice plants during germination and seedling growth. Fortunately, a wide array of phenotypic responses conferring flooding stress and chilling stress tolerance exist within the rice germplasm, indicating the presence of different molecular mechanisms underlying tolerance to these stresses. Understanding these differences may assist in developing improved rice cultivars having higher tolerance to both stresses. In this study, we conducted a comparative global gene expression analysis of two rice genotypes with contrasting phenotypes under cold stress, anaerobic stress, and combined cold and anaerobic stress during germination. Results The differential gene expression analysis revealed that 5571 differentially expressed genes (DEGs), 7206 DEGs, and 13279 DEGs were identified under anaerobic stress, cold stress, and combined stress, respectively. Genes involved in the carbohydrate metabolic process, glucosyltransferase activity, regulation of nitrogen compound metabolic process, protein metabolic process, lipid metabolic process, cellular nitrogen compound biosynthetic process, lipid biosynthetic process, and a microtubule-based process were enriched across all stresses. Notably, the common Gene Ontology (GO) analysis identified three hub genes, namely Os08g0176800 (similar to mRNA-associated protein mrnp 41), Os11g0454200 (dehydrin), and OS10g0505900 (expressed protein). Conclusion A large number of differentially expressed genes were identified under anaerobic, cold conditions during germination and the combination of the two stress conditions in rice. These results will assist in the identification of promising candidate genes for possible manipulation toward rice crops that are more tolerant under flooding and cold during germination, both independently and concurrently.

The Overexpression of Peanut (Arachis hypogaea L.) AhALDH2B6 in Soybean Enhances Cold Resistance

“…Oxidoreductase activity and transcription regulator activity pathway genes were found to be differently expressed in Alfalfa by RNA-seq analysis in response to cold stress [ 29 ]. Another study in rice found that a higher number of genes involved in oxidoreductase activity might contribute to cold tolerance [ 30 ]. Moreover, the identification of DEGs in Pisum sativum using RNA-seq analyses confirmed that oxidoreductase-related genes were enriched after cold treatment [ 29 ].…”

Transcriptional signatures associated with waterlogging stress responses and aerenchyma formation in barley root tissue

“…While aerenchyma is a key trait for waterlogging tolerance (Mustroph, 2018), it can also be formed in response to other abiotic stresses such as drought (Zhu et al, 2010a), mechanical impedance (He et al ., 1996) and nutrient deficiency (Postma & Lynch, 2011). Likewise, a recent study has determined the significant overlap of transcriptomic signatures between anaerobic and cold stresses in rice (Thapa et al, 2023), suggesting that similar regulatory pathway may modulate adaptation to these stresses.…”

Integrated meta-analysis and transcriptomics pinpoint genomic loci and novel candidate genes associated with submergence tolerance in rice

“…A survey of two differentially expressed genes (DEGs) datasets involved in submergence tolerance during seed germination from independent studies [ 43 , 44 ] was explored to validate candidate genes (CGs) found in core MQTL loci. A Venn diagram was employed to compare the common genes regulating submergence tolerance detected by two DEGs studies, and the genes located in MQTL regions.…”