Abstract
Nitrogen use efficiency (NUE), a critical determinant of crop productivity and agricultural sustainability, varies significantly between indica and japonica subspecies. Here, we identify three coding-region SNPs in OsNLP4 underlying this divergence. These SNPs enhance the binding affinity of OsNLP4indica to nitrate response elements (NREs), amplifying transcriptional activation of nitrogen metabolism and iron homeostasis genes. Introgression of the OsNLP4indica allele into elite japonica cultivar XS134 increases both grain yield and NUE by 12–25% across multi-location field trials under varying nitrogen regimes. Heterologous expression in Arabidopsis increases shoot biomass by 23%, demonstrating possible conservation of function in dicots. Mechanistically, the indica allele’s stronger NRE-binding capacity synergistically modulates downstream pathways. Furthermore, combining OsNLP4indica with balanced nitrogen-iron fertilization boosts NUE by 30–32%. Our findings resolve a critical genetic basis of indica-japonica NUE divergence, provide a validated strategy for improving yield and NUE of commercial japonica varieties, and highlight OsNLP4indica as a cross-species genetic resource for sustainable agriculture. Japonica subspecies has a lower nitrogen use efficiency (NUE) than that of indica rice. Here, the authors show that natural variations in the NIN-like protein 4 (OsNLP4) encoding gene are responsible for the divergence and introgression of the indica OsNLP4 allele into elite japonica cultivar can increase NUE and grain yield.
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Claims 8
Claim · model-written summary
Indica and japonica differ significantly in nitrogen use efficiency.
- Taxon
- rice
Oryza sativat0 - Material
- indica and japonica subspeciese0
- Outcome
- Nitrogen use efficiency (NUE)e0
Not reportedDirection
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Nitrogen use efficiency (NUE), a critical determinant of crop productivity and agricultural sustainability, varies significantly between indica and japonica subspecies.”
t0“rice”
Claim · model-written summary
Three OsNLP4 coding-region SNPs underlie the subspecies divergence.
- Taxon
- riceOryza sativat0
- Gene
- OsNLP4e0
- Outcome
- three coding-region SNPse0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“we identify three coding-region SNPs in OsNLP4 underlying this divergence.”
t0“rice”
Claim · model-written summary
The SNPs enhance binding of OsNLP4indica to nitrate response elements.
- Taxon
- riceOryza sativat0
- Gene
- OsNLP4indicae0
- Outcome
- binding affinitye0
- Direction
- enhancee0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“These SNPs enhance the binding affinity of OsNLP4indica to nitrate response elements (NREs)”
t0“rice”
Claim · model-written summary
The SNPs amplify activation of nitrogen metabolism and iron homeostasis genes.
- Taxon
- riceOryza sativat0
- Gene
- OsNLP4indicae1
- Outcome
- transcriptional activation of nitrogen metabolism and iron homeostasis genese0
- Direction
- amplifyinge0
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“amplifying transcriptional activation of nitrogen metabolism and iron homeostasis genes.”
t0“rice”
e1“These SNPs enhance the binding affinity of OsNLP4indica”
Claim · model-written summary
Introgressing OsNLP4indica into XS134 increased grain yield by 12–25% across field trials.
- Taxon
- riceOryza sativat0
- Material
- XS134e0
- Treatment
- Introgression of the OsNLP4indica allelee0
- Gene
- OsNLP4indicae0
- Outcome
- grain yielde0
- Direction
- increasese0
- Value
- 12–25%e0
- Setting
- multi-location field trialse0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Introgression of the OsNLP4indica allele into elite japonica cultivar XS134 increases both grain yield and NUE by 12–25% across multi-location field trials under varying nitrogen regimes.”
t0“rice”
Claim · model-written summary
Introgressing OsNLP4indica into XS134 increased NUE by 12–25% across field trials.
- Taxon
- riceOryza sativat0
- Material
- XS134e0
- Treatment
- Introgression of the OsNLP4indica allelee0
- Gene
- OsNLP4indicae0
- Outcome
- NUEe0
- Direction
- increasese0
- Value
- 12–25%e0
- Setting
- multi-location field trialse0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Introgression of the OsNLP4indica allele into elite japonica cultivar XS134 increases both grain yield and NUE by 12–25% across multi-location field trials under varying nitrogen regimes.”
t0“rice”
Claim · model-written summary
Heterologous expression in Arabidopsis increased shoot biomass by 23%.
- Taxon
- Arabidopsis
Arabidopsise0 - Treatment
- Heterologous expressione0
- Outcome
- shoot biomasse0
- Direction
- increasese0
- Value
- 23%e0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“Heterologous expression in Arabidopsis increases shoot biomass by 23%, demonstrating possible conservation of function in dicots.”
Claim · model-written summary
Combining OsNLP4indica with balanced nitrogen-iron fertilization raised NUE by 30–32%.
- Taxon
- riceOryza sativat0
- Treatment
- balanced nitrogen-iron fertilizatione0
- Gene
- OsNLP4indicae0
- Outcome
- NUEe0
- Direction
- boostse0
- Value
- 30–32%e0
Not reportedComparator
Organisms pictured · Representative pictures of the matched species, not figures from the paper.
Verbatim
e0“combining OsNLP4indica with balanced nitrogen-iron fertilization boosts NUE by 30–32%.”
t0“rice”
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