Genome-wide association study and transcriptome analysis identify candidate genes associated with low...

Area of Science:

• Plant Genetics and Genomics
• Agricultural Science
• Crop Physiology

Background:

• Maize (Zea mays L.) root system is vital for nitrogen acquisition.
• Genetic mechanisms for adaptive root responses to low nitrogen (N) are not well understood.
• Natural variation in root traits under low N across maize subpopulations needs examination.

Purpose of the Study:

• To dissect the genetic basis of low-N-responsive root traits in early-stage maize.
• To investigate the natural variation of these traits across different maize subpopulations.
• To identify candidate genes and genomic regions controlling root plasticity under low-N stress.

Main Methods:

• Evaluated six root and two shoot traits in 387 maize accessions under normal and low N conditions.
• Conducted genome-wide association study (GWAS) using 1.2 million single nucleotide polymorphisms (SNPs).
• Integrated GWAS with transcriptome data from lines with contrasting low-N responses.

Main Results:

• Significant variation in seedling traits observed, with heritability from 0.27 to 0.46.
• Low N altered root morphology, increasing root length, surface area, and root-to-shoot ratio.
• GWAS identified numerous significant SNPs and candidate genes; transcriptome analysis revealed differentially expressed genes (DEGs). Integrated analysis pinpointed four core candidate genes with significant phenotypic differences and enriched favorable haplotypes in the SS subpopulation.

Conclusions:

• Identified key genomic regions and candidate genes controlling root plasticity under low-N stress.
• These findings provide valuable genetic targets for enhancing nitrogen-use efficiency in maize.
• Potential for improving crop performance through molecular breeding strategies.