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GWAS-Based Mining of Candidate Genes for Low-Nitrogen Tolerance in Maize
Baobao Wang1, Luo Xu1, Ying Huang2
1Shijiazhuang Academy of Agriculture and Forestry Sciences, Shijiazhuang 050041, China.
International Journal of Molecular Sciences
|February 27, 2026
Summary
Researchers identified key genes and maize varieties that enhance nitrogen use efficiency (NUE). This discovery is crucial for developing sustainable agriculture practices and improving crop yields under low nitrogen conditions.
Area of Science:
- Agricultural Science
- Genetics
- Plant Breeding
Background:
- Nitrogen is a critical factor limiting maize yield, impacting sustainable agriculture and environmental health.
- Understanding the genetic underpinnings of nitrogen use efficiency (NUE) in maize is essential but remains incomplete.
Purpose of the Study:
- To conduct a genome-wide association study (GWAS) to identify genetic factors contributing to NUE in maize.
- To pinpoint specific genes and maize inbred lines with enhanced tolerance to low nitrogen conditions.
Main Methods:
- A genome-wide association study (GWAS) was performed on 282 maize inbred lines using the Maize 50K GBTS array (53,162 SNPs).
- Ten NUE-related traits were evaluated under two nitrogen (N) levels.
- Mixed linear models (MLM) were used to control for population structure and kinship.
Main Results:
- GWAS identified 122 significant SNPs associated with low N tolerance.
- Linkage disequilibrium and functional annotation narrowed down 26 candidate genes, with three core genes (Zm00001d027880, Zm00001d034047, Zm00001d010574) identified through enrichment analyses.
- Three maize inbred lines (H1710, 23N272, 23N41) exhibited superior low-nitrogen tolerance.
Conclusions:
- The study identified key genetic loci and candidate genes associated with nitrogen use efficiency in maize.
- Selected maize inbred lines demonstrate potential for breeding programs aimed at enhancing NUE.
- Future research will focus on utilizing these genetic resources to develop improved maize cultivars for sustainable agriculture.
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Genetic screens are tools used to identify genes and mutations responsible for phenotypes of interest. Genetic screens help identify individuals or a group of people at risk of developing genetic diseases and help them with early intervention, targeted therapy, and reproductive options.
Forward genetic screens
Forward or “classical” genetic screens involve creating random mutations in an organism’s DNA using radiation, mutagens, or insertion of additional bases, which result in visible changes...
Forward genetic screens
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01:11Genome-wide Association Studies-GWAS
Genome-wide association studies or GWAS are used to identify whether common SNPs are associated with certain diseases. Suppose specific SNPs are more frequently observed in individuals with a particular disease than those without the disease. In that case, those SNPs are said to be associated with the disease. Chi-square analysis is performed to check the probability of the allele likely to be associated with the disease.
GWAS does not require the identification of the target gene involved in...
GWAS does not require the identification of the target gene involved in...