Mapping regulatory variants controlling gene expression in drought response and tolerance in maize

Area of Science:

• Plant Genomics
• Molecular Biology
• Drought Stress Physiology

Background:

• Gene expression variation is crucial for cellular responses and links genetic diversity to phenotypic changes.
• Identifying regulatory variants controlling gene expression under drought is vital for developing drought-tolerant crops.
• Drought poses a significant threat to global crop production, necessitating research into plant resilience.

Purpose of the Study:

• To unravel the genetic architecture of gene expression in maize under drought conditions.
• To identify regulatory variants that control constitutive and drought-dynamic gene expression.
• To build a drought-responsive gene regulatory network and prioritize candidate genes for drought tolerance.

Main Methods:

• Performed 627 RNA-sequencing analyses across 224 diverse maize accessions under three water regimes.
• Detected 73,573 expression quantitative trait loci (eQTLs) for approximately 30,000 genes using high-density genome-wide single nucleotide polymorphisms.
• Constructed a drought-responsive transcription factor network and employed Mendelian randomization to prioritize drought-associated genes.

Main Results:

• A comprehensive and dynamic genetic architecture of gene expression in response to drought was revealed.
• Identified constitutive and drought-dynamic regulatory variants controlling gene expression.
• Prioritized 97 genes associated with drought tolerance, including Abscisic acid 8'-hydroxylase, which was verified to negatively impact drought tolerance.

Conclusions:

• Genetic variants significantly influence gene expression dynamics during drought response in maize.
• This research enhances understanding of genetic effects on gene expression and phenotypic plasticity.
• Prioritized genes offer targets for functional investigation and allelic mining to improve crop drought tolerance.