Abstract
BackgroundLow temperature (LT) often occurs at the seedling stage in the early rice-growing season, especially for direct seeded early-season indica rice, and using flooding irrigation can mitigate LT damage in rice seedlings. The molecular mechanism by which flooding mitigates the damage induced by LT stress has not been fully elucidated. Thus, LT stress at 8 °C, LT accompanied by flooding (LTF) and CK (control) treatments were established for 3 days to determine the transcriptomic, proteomic and physiological response in direct seeded rice seedlings at the seedling stage.ResultsLT damaged chloroplasts, and thylakoid lamellae, and increased osmiophilic bodies and starch grains compared to CK, but LTF alleviated the damage to chloroplast structure caused by LT. The physiological characteristics of treated plants showed that compared with LT, LTF significantly increased the contents of rubisco, chlorophyll, PEPCK, ATP and GA3 but significantly decreased soluble protein, MDA and ABA contents. 4D-label-free quantitative proteomic profiling showed that photosynthesis-responsive proteins, such as phytochrome, as well as chlorophyll and the tricarboxylic acid cycle were significantly downregulated in LT/CK and LTF/CK comparison groups. However, compared with LT, phytochrome, chlorophyllide oxygenase activity and the glucan branching enzyme in LTF were significantly upregulated in rice leaves. Transcriptomic and proteomic studies identified 72,818 transcripts and 5639 proteins, and 4983 genes that were identified at both the transcriptome and proteome levels. Differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) were significantly enriched in glycine, serine and threonine metabolism, biosynthesis of secondary metabolites, glycolysis/gluconeogenesis and metabolic pathways.ConclusionThrough transcriptomic, proteomic and physiological analyses, we determined that a variety of metabolic pathway changes were induced by LT and LTF. GO and KEGG enrichment analyses demonstrated that DEGs and DEPs were associated with photosynthesis pathways, antioxidant enzymes and energy metabolism pathway-related proteins. Our study provided new insights for efforts to reduce the damage to direct seeded rice caused by low-temperature stress and provided a breeding target for low temperature flooding-resistant cultivars. Further analysis of translational regulation and metabolites may help to elucidate the molecular mechanisms by which flooding mitigates low-temperature stress in direct seeded early indica rice at the seedling stage.
Highlights
Low temperature (LT) often occurs at the seedling stage in the early rice-growing season, especially for direct seeded early-season indica rice, and using flooding irrigation can mitigate LT damage in rice seedlings
We identified genes and proteins that were obtained from Illumina-Hiseq and 4D-label-free searching for likely protein identification in Gene Ontology (GO), Kyoto Encyclopedia of Genes and Genomes (KEGG), Klustersof eukaryotic Orthologous Groups (KOG), Swissport and UniProt databases, respectively, and focused on the Differentially expressed genes (DEGs) and differentially expressed proteins (DEPs) involved in the flooding-mediated mitigation of low-temperature stress
Analysis of photosynthesis activity and endogenous hormone content This study showed that the rubisco content of LT was significantly decreased by 26.97% (P < 0.05) compared to that of CK, but there was no significant difference between LT accompanied by flooding (LTF) and CK (Fig. 2a)
Summary
Low temperature (LT) often occurs at the seedling stage in the early rice-growing season, especially for direct seeded early-season indica rice, and using flooding irrigation can mitigate LT damage in rice seedlings. Due to global warming and changes in production habits, sowing dates have become earlier than before, which increases the probability that direct seeded rice will suffer from low temperature to some extent, especially in the seedling stage of direct seeded early rice, resulting in irreversible cold-tolerant growth of seedlings [10, 11]. In 2008 and 2010, due to the low temperature and severe cold stress in China, the emergence rate of direct seeded early rice decreased by 38–55%, and rice yield notably decreased [12]. It is urgently important to perform in-depth research on the response mechanism to low-temperature stress of direct seeded early rice and prevention measures to alleviate this stress and improve the efficiency and stable yield of direct seeded rice
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