ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2023
Mining genes regulating root system architecture in maize based on data integration analysis.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 9 papers.
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9 citing papers in PubMed, 14 citations in OpenAlex.
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- Integrated transcriptomic and proteomic analysis reveals inhibitory effects of naringenin application on soybean roots mainly by interfering with auxin and ROS concentrations.BMC plant biology · 2026Article
- Diversity of root system architecture and root-shoot biomass allocation in industrial hemp (Cannabis sativa L.).PloS one · 2026Article
- Molecular Mechanisms Underlying Salt Tolerance in Maize: A Combined Transcriptome and Metabolome Analysis.Plants (Basel, Switzerland) · 2025Article
- Phenotyping, genome-wide dissection, and prediction of maize root architecture for temperate adaptability.iMeta · 2025Article
- Identification of phenotypic and transcriptomic signatures underpinning maize crown root systems.Plant phenomics (Washington, D.C.) · 2025Article
- Comparative transcriptomic and hormonal analyses reveal potential regulation networks of adventitious root formation in Metasequoia glyptostroboides Hu et Cheng.BMC genomics · 2024Article
- Integrating GWAS with a gene co-expression network better prioritizes candidate genes associated with root metaxylem phenes in maize.The plant genome · 2024Article
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9 authors at 1 institution in 1 country.
Funding
Abstract
key messageA new strategy that integrated multiple public data resources was established to construct root gene co-expression network and mine genes regulating root system architecture in maize. A root gene co-expression network, containing 13,874 genes, was constructed. A total of 53 root hub genes and 16 priority root candidate genes were identified. One priority root candidate was further functionally verified using overexpression transgenic maize lines. Root system architecture (RSA) is crucial for crops productivity and stress tolerance. In maize, few RSA genes are functionally cloned, and effective discovery of RSA genes remains a great of challenge. In this work, we established a strategy to mine maize RSA genes by integrating functionally characterized root genes, root transcriptome, weighted gene co-expression network analysis (WGCNA) and genome-wide association analysis (GWAS) of RSA traits based on public data resources. A total of 589 maize root genes were collected by searching well-characterized root genes in maize or homologous genes of other species. We performed WGCNA to construct a maize root gene co-expression network containing 13874 genes based on public available root transcriptome data, and further discovered the 53 hub genes related to root traits. In addition, by the prediction function of obtained root gene co-expression network, a total of 1082 new root candidate genes were explored. By further overlapping the obtained new root candidate gene with the root-related GWAS of RSA candidate genes, 16 priority root candidate genes were identified. Finally, a priority root candidate gene, Zm00001d023379 (encodes pyruvate kinase 2), was validated to modulate root open angle and shoot-borne roots number using its overexpression transgenic lines. Our results develop an integration analysis method for effectively exploring regulatory genes of RSA in maize and open a new avenue to mine the candidate genes underlying complex traits.
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