Aims Low nitrogen (LN) strongly limits oat growth. However, the gene networks associated with LN tolerance remain unclear. This study compared the LN-tolerant landrace AS444 with the LN-sensitive cultivar AS7 to identify candidate LN-responsive regulatory networks in oat (Avena sativa L.). Methods AS444 and AS7 were grown under normal nitrogen (1.0 mM N) and LN (0.1 mM N) for 15 days. Growth and physiological traits were measured. RNA sequencing was performed using root tips, young leaves, and upper stems. Weighted gene co-expression network analysis (WGCNA) and reverse transcription quantitative PCR (RT-qPCR) were used to identify and validate candidate genes. Results AS444 was less affected by LN than AS7. Relative to their respective normal-nitrogen controls, plant height and leaf length under LN decreased by approximately 22%-24% in AS444, but by approximately 69%-70% in AS7. AS444 retained about 70% of the control chlorophyll level, whereas AS7 retained about 60%. Total nitrogen content decreased by about 30%-35% in AS444 and about 55% in AS7. Higher chlorophyll retention in AS444 was consistent with better preservation of chloroplast ultrastructure under LN, whereas nitrogen remobilization was not assessed. The root-to-shoot ratio increased only in AS444. Transcriptome analysis showed stronger expression of genes related to nitrogen uptake and assimilation, energy metabolism, and oxidative stress responses in AS444. WGCNA identified trait-associated modules containing four candidate hub transcription factors, NAC11, MYB22, bHLH1, and bHLH2, together with genes related to nitrate uptake and assimilation. Conclusions LN tolerance in oat was associated with root biomass allocation, nitrogen metabolism, carbon metabolism, and stress defence. NAC11, MYB22, bHLH1, and bHLH2 were identified as candidate hub genes in AS444. Their co-expression patterns were associated with root biomass allocation, nitrogen uptake and assimilation, glycolysis-related carbon metabolism, and antioxidant pathways. These findings provide a candidate framework for improving LN adaptation in oat. Graphical Abstract Putative co-expression framework underlying contrasting oat responses to low nitrogen. In the tolerant genotype AS444, candidate hub transcription factors, including NAC11, MYB22, and bHLH1/2, were associated with enhanced nitrogen-related, glycolysis-related, flavonoid-related, and lipid-related responses, together with relatively stable chloroplast structure and stronger root–shoot adjustment. In the sensitive genotype AS7, reduced expression of MYB22 and bHLH1/2 expression, suppressed photosynthesis-related genes, and increased proteasome- and trehalose-related responses were associated with abnormal starch accumulation, chloroplast envelope disruption, and limited root–shoot adjustment. This framework was inferred from DEG, WGCNA, and correlation analyses, and the proposed regulatory relationships require further functional validation.

Multi-tissue transcriptomics reveals candidate co-expression and metabolic networks associated with low-nitrogen adaptation in oat

期刊论文
发表日期：

2026年7月17日

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Chenyue Yang,
Zhongxiang Li,
Muhammad Bilal,
Yunyun Pang,
Mengxin Zhu,
Tao Hu

摘要

Aims

Low nitrogen (LN) strongly limits oat growth. However, the gene networks associated with LN tolerance remain unclear. This study compared the LN-tolerant landrace AS444 with the LN-sensitive cultivar AS7 to identify candidate LN-responsive regulatory networks in oat (Avena sativa L.).

Methods

AS444 and AS7 were grown under normal nitrogen (1.0 mM N) and LN (0.1 mM N) for 15 days. Growth and physiological traits were measured. RNA sequencing was performed using root tips, young leaves, and upper stems. Weighted gene co-expression network analysis (WGCNA) and reverse transcription quantitative PCR (RT-qPCR) were used to identify and validate candidate genes.

Results

AS444 was less affected by LN than AS7. Relative to their respective normal-nitrogen controls, plant height and leaf length under LN decreased by approximately 22%-24% in AS444, but by approximately 69%-70% in AS7. AS444 retained about 70% of the control chlorophyll level, whereas AS7 retained about 60%. Total nitrogen content decreased by about 30%-35% in AS444 and about 55% in AS7. Higher chlorophyll retention in AS444 was consistent with better preservation of chloroplast ultrastructure under LN, whereas nitrogen remobilization was not assessed. The root-to-shoot ratio increased only in AS444. Transcriptome analysis showed stronger expression of genes related to nitrogen uptake and assimilation, energy metabolism, and oxidative stress responses in AS444. WGCNA identified trait-associated modules containing four candidate hub transcription factors, NAC11, MYB22, bHLH1, and bHLH2, together with genes related to nitrate uptake and assimilation.

Conclusions

LN tolerance in oat was associated with root biomass allocation, nitrogen metabolism, carbon metabolism, and stress defence. NAC11, MYB22, bHLH1, and bHLH2 were identified as candidate hub genes in AS444. Their co-expression patterns were associated with root biomass allocation, nitrogen uptake and assimilation, glycolysis-related carbon metabolism, and antioxidant pathways. These findings provide a candidate framework for improving LN adaptation in oat.

Graphical Abstract

Putative co-expression framework underlying contrasting oat responses to low nitrogen. In the tolerant genotype AS444, candidate hub transcription factors, including NAC11, MYB22, and bHLH1/2, were associated with enhanced nitrogen-related, glycolysis-related, flavonoid-related, and lipid-related responses, together with relatively stable chloroplast structure and stronger root–shoot adjustment. In the sensitive genotype AS7, reduced expression of MYB22 and bHLH1/2 expression, suppressed photosynthesis-related genes, and increased proteasome- and trehalose-related responses were associated with abnormal starch accumulation, chloroplast envelope disruption, and limited root–shoot adjustment. This framework was inferred from DEG, WGCNA, and correlation analyses, and the proposed regulatory relationships require further functional validation.