Transcriptomic profiling of germinating seeds under cold stress and characterization of the cold-tolerant gene LTG5 in rice

Abstract

Background: Low temperature is a limiting factor of rice productivity and geographical distribution. Wild rice (Oryza rufipogon Griff.) is an important germplasm resource for rice improvement. It has superior tolerance to many abiotic stresses, including cold stress, but little is known about the mechanism underlying its resistance to cold. Results: This study elucidated the molecular genetic mechanisms of wild rice in tolerating low temperature. Comprehensive transcriptome profiles of two rice genotypes (cold-sensitive ce 253 and cold-tolerant Y12-4) at the germinating stage under cold stress were comparatively analyzed. A total of 42.44-68.71 million readings were obtained, resulting in the alignment of 29,128 and 30,131 genes in genotypes 253 and Y12-4, respectively. Many common and differentially expressed genes (DEGs) were analyzed in the cold-sensitive and cold-tolerant genotypes. Results showed more upregulated DEGs in the cold-tolerant genotype than in the cold-sensitive genotype at four stages under cold stress. Gene ontology enrichment analyses based on cellular process, metabolic process, response stimulus, membrane part, and catalytic activity indicated more upregulated genes than downregulated ones in the cold-tolerant genotype than in the cold-sensitive genotype. Quantitative real-time polymerase chain reaction was performed on seven randomly selected DEGs to confirm the RNA Sequencing (RNA-seq) data. These genes showed similar expression patterns corresponding with the RNA-Seq method. Weighted gene co-expression network analysis (WGCNA) revealed Y12-4 showed more positive genes than 253 under cold stress. We also explored the cold tolerance gene LTG5 (Low Temperature Growth 5) encoding a UDP-glucosyltransferase. The overexpression of the LTG5 gene conferred cold tolerance to indica rice. Conclusion: Gene resources related to cold stress from wild rice can be valuable for improving the cold tolerance of crops.

The Role of Membrane Transporters in Plant Growth and Development, and Abiotic Stress Tolerance

“…Comparative transcriptome profiling can provide millions of treatment-dependent reads that can be aligned with reference genomes (if available) and de novo (if not) and ultimately will provide thousands of novel transcripts/genes. For example, in rice, mRNA sequencing of two contrasting cultivars, i.e., Y12–4 (cold-tolerant) and 253 (cold-sensitive) showed that a total of 42.44–68.71 million reads were obtained and later on aligned to nearly 30 and 29 thousand genes, respectively [ 93 ]. In the results, a majority of cold tolerant DEGs were found in tolerant genotype.…”

Integrated Transcriptomics and Metabolomics Analysis Reveal Key Metabolism Pathways Contributing to Cold Tolerance in Peanut

“…Transcriptomic analysis has been a highly efficient way to reveal cold-responsive genes in many crops, such as maize ( Li et al, 2019 ), rice ( Pan et al, 2020 ), Brassica napus ( Mehmood et al, 2021 ) and Brassica juncea ( Sinha et al, 2015 ). Microarray analysis of peanut leaves subjected to low temperature got a number of cold-regulated genes and provided some useful insights into cold signal transduction pathways in peanut ( Chen et al, 2014 ).…”

Transcriptome Analysis of Near-Isogenic Lines Provides Novel Insights into Genes Associated with Seed Low-Temperature Germination Ability in Maize (Zea mays L.)

“…Many studies have been published to show the effectiveness of transcriptome analysis in identification of new genes or regulatory pathways for plant response to low temperature stress [ 18 , 19 ]. By comparing cold-responsive transcriptomes of wild type and mutants or cultivars of contrasting cold tolerance, a number of genes involved in multiple biology processes, such as cell cycle, zeatin biosynthesis, hormone signal transduction, membrane part, and response stimulus, have been found to be regulated by cold stress in rice [ 20 , 21 , 22 ]. When cold stress was imposed on seedlings of maize, numerous cold-stress-related genes were also identified, and these genes fall into similar functional categories as rice research indicated [ 1 , 23 , 24 , 25 , 26 , 27 , 28 , 29 ].…”