ArticleBMC systems biology2016
Clustering and evolutionary analysis of small RNAs identify regulatory siRNA clusters induced under drought stress in rice.
Article in BMC systems biology, 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
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7 citing papers in PubMed, 14 citations in OpenAlex.
- Yield-graph: multi-stage growth-aware maize yield prediction via graph neural networks.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- The Emerging Role of Non-Coding RNAs (ncRNAs) in Plant Growth, Development, and Stress Response Signaling.Non-coding RNA · 2024Review
- Effects of Combined Abiotic Stresses Related to Climate Change on Root Growth in Crops.Frontiers in plant science · 2022Review
- Epigenetic regulation of salinity stress responses in cereals.Molecular biology reports · 2022Review
- Identification and Analysis of Small Interfering RNAs Associated With Heat Stress in Flowering Chinese Cabbage Using High-Throughput Sequencing.Frontiers in genetics · 2021Article
- Understanding epigenomics based on the rice model.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2020Review
- Abiotic and biotic stresses induce a core transcriptome response in rice.Scientific reports · 2019Article
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Authors and funding
7 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
motivationDrought tolerance is an important trait related to growth and yield in crop. Until now, drought related research has focused on coding genes. However, non-coding RNAs also respond significantly to environmental stimuli such as drought stress. Unfortunately, characterizing the role of siRNAs under drought stress is difficult since a large number of heterogenous siRNA species are expressed under drought stress and non-coding RNAs have very weak evolutionary conservation. Thus, to characterize the role of siRNAs, we need a well designed biological and bioinformatics strategy. In this paper, to characterize the function of siRNAs we developed and used a bioinformatics pipeline that includes a genomic-location based clustering technique and an evolutionary conservation tool.
resultsBy comparing the wild type Nipponbare and two drought resistant rice varities, we found that 21 nt and 24 nt siRNAs are significantly expressed in the three rice plants but at different time points under a short-term (0, 1, and 6 hrs) drought treatment. siRNAs were up-regulated in the wild type at an early stage while the up-regulation was delayed in the two drought tolerant plants. Genes targeted by up-regulated siRNAs were related to oxidation reduction and proteolysis, which are well known to be associated with water deficit phenotypes. More interestingly, we found that siRNAs were located in intronic regions as clusters and were of high evolutionary conservation among monocot grass plants. In summary, we show that siRNAs are important respondents to drought stress and regulate genes related to the drought tolerance in water deficit conditions.
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