ArticleFrontiers in plant science2017
Root Transcriptomic Analysis Revealing the Importance of Energy Metabolism to the Development of Deep Roots in Rice (
Article in Frontiers in plant science, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 18 papers.
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Who cites it
18 citing papers in PubMed, 38 citations in OpenAlex.
- Molecular and Genetic Regulation of Crop Root System Architecture in Drought Resilience.Plants (Basel, Switzerland) · 2026Review
- CRISPR-Cas9-mediated editing ofGM crops & food · 2025Article
- Flexibility of parental-like or maternal-like gene expression under diverse environments contributes to combined drought avoidance and drought tolerance in a water-saving and drought-resistance rice hybrid.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2024Article
- Comparative transcriptomics identifies genes underlying growth performance of the Pacific black-lipped pearl oyster Pinctada margaritifera.BMC genomics · 2024Article
- Genome- and Transcriptome-wide Association Studies to Discover Candidate Genes for Diverse Root Phenotypes in Cultivated Rice.Rice (New York, N.Y.) · 2023Article
- Overexpression of a novel small auxin-up RNA gene, OsSAUR11, enhances rice deep rootedness.BMC plant biology · 2023Article
- Transcriptome analysis reveals key regulatory genes for root growth related to potassium utilization efficiency in rapeseed (Frontiers in plant science · 2023Article
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- Co-expression analysis to identify key modules and hub genes associated with COVID-19 in platelets.BMC medical genomics · 2022Article
- Proteomics and Co-expression Network Analysis Reveal the Importance of Hub Proteins and Metabolic Pathways in Nicotine Synthesis and Accumulation in Tobacco (Frontiers in plant science · 2022Article
- Combined metabolomic and transcriptomic analysis reveals key components ofFrontiers in plant science · 2022Article
- Root Trait Variation in Lentil (Plants (Basel, Switzerland) · 2021Article
- Hotter, drier, CRISPR: the latest edit on climate change.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2021Review
- Genetics and genomics of root system variation in adaptation to drought stress in cereal crops.Journal of experimental botany · 2021Review
- Article
- Extensive Variation in Drought-Induced Gene Expression Changes Between Loblolly Pine Genotypes.Frontiers in genetics · 2021Article
- Transcriptional analyses reveal the molecular mechanism governing shade tolerance in the invasive plantEcology and evolution · 2020Article
- WGCNA Analysis of Salt-Responsive Core Transcriptome Identifies Novel Hub Genes in Rice.Genes · 2019Article
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Authors and funding
11 authors at 2 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Drought is the most serious abiotic stress limiting rice production, and deep root is the key contributor to drought avoidance. However, the genetic mechanism regulating the development of deep roots is largely unknown. In this study, the transcriptomes of 74 root samples from 37 rice varieties, representing the extreme genotypes of shallow or deep rooting, were surveyed by RNA-seq. The 13,242 differentially expressed genes (DEGs) between deep rooting and shallow rooting varieties (H vs. L) were enriched in the pathway of genetic information processing and metabolism, while the 1,052 DEGs between the deep roots and shallow roots from each of the plants (D vs. S) were significantly enriched in metabolic pathways especially energy metabolism. Ten quantitative trait transcripts (QTTs) were identified and some were involved in energy metabolism. Forty-nine candidate DEGs were confirmed by qRT-PCR and microarray. Through weighted gene co-expression network analysis (WGCNA), we found 18 hub genes. Surprisingly, all these hub genes expressed higher in deep roots than in shallow roots, furthermore half of them functioned in energy metabolism. We also estimated that the ATP production in the deep roots was faster than shallow roots. Our results provided a lot of reliable candidate genes to improve deep rooting, and firstly highlight the importance of energy metabolism to the development of deep roots.
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