ArticleBMC plant biology2023
Combining GS-assisted GWAS and transcriptome analysis to mine candidate genes for nitrogen utilization efficiency in Populus cathayana.
Article in BMC plant biology, 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, 11 citations in OpenAlex.
- Genome-wide association study and KASP development for growth and leaf traits in Populus deltoides.BMC genomics · 2026Article
- Advances in tea breeding in Japan: from traditional methods to genomic approaches.Breeding science · 2026Article
- Integrative machine learning approach for identifying genes associated with quantitative traits: A soybean (Glycine max) yield case study.The plant genome · 2026Article
- Leveraging GWAS-Identified Markers in Combination with Bayesian and Machine Learning Models to Improve Genomic Selection in Soybean.International journal of molecular sciences · 2025Article
- Physiologic, Genetic and Epigenetic Determinants of Water Deficit Tolerance in Fruit Trees.Plants (Basel, Switzerland) · 2025Review
- Genetic Variation Analysis and Development of KASP Marker for Leaf Area and Hight in Southern-TypePlants (Basel, Switzerland) · 2025Article
- Genetic architecture and genomic prediction of vase life in carnation.Frontiers in plant science · 2025Article
- Optimizing nitrogen use efficiency in forest plantations: mechanistic insights fromForestry research · 2025Review
- Transcriptomic and Phenotypic Analyses Reveal the Molecular Mechanism of Dwarfing in TetraploidInternational journal of molecular sciences · 2024Article
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7 authors at 3 institutions in 1 country.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundForest trees such as poplar, shrub willow, et al. are essential natural resources for sustainable and renewable energy production, and their wood can reduce dependence on fossil fuels and reduce environmental pollution. However, the productivity of forest trees is often limited by the availability of nitrogen (N), improving nitrogen use efficiency (NUE) is an important way to address it. Currently, NUE genetic resources are scarce in forest tree research, and more genetic resources are urgently needed.
resultsHere, we performed genome-wide association studies (GWAS) using the mixed linear model (MLM) to identify genetic loci regulating growth traits in Populus cathayana at two N levels, and attempted to enhance the signal strength of single nucleotide polymorphism (SNP) detection by performing genome selection (GS) assistance GWAS. The results of the two GWAS analyses identified 55 and 40 SNPs that were respectively associated with plant height (PH) and ground diameter (GD), and 92 and 69 candidate genes, including 30 overlapping genes. The prediction accuracy of the GS model (rrBLUP) for phenotype exceeds 0.9. Transcriptome analysis of 13 genotypes under two N levels showed that genes related to carbon and N metabolism, amino acid metabolism, energy metabolism, and signal transduction were differentially expressed in the xylem of P. cathayana under N treatment. Furthermore, we observed strong regional patterns in gene expression levels of P. cathayana, with significant differences between different regions. Among them, P. cathayana in Longquan region exhibited the highest response to N. Finally, through weighted gene co-expression network analysis (WGCNA), we identified a module closely related to the N metabolic process and eight hub genes.
conclusionsIntegrating the GWAS, RNA-seq and WGCNA data, we ultimately identified four key regulatory genes (PtrNAC123, PtrNAC025, Potri.002G233100, and Potri.006G236200) involved in the wood formation process, and they may affect P. cathayana growth and wood formation by regulating nitrogen metabolism. This study will provide strong evidence for N regulation mechanisms, and reliable genetic resources for growth and NUE genetic improvement in poplar.
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