Allele-specific Expression Reveals Multiple Paths to Highland Adaptation in Maize

Area of Science:

• Plant genetics
• Evolutionary biology
• Genomics

Background:

• Maize is a vital crop for high-altitude farmers, with adaptation occurring independently in Mexican and South American highlands.
• Understanding the genetic basis of this adaptation is crucial for crop improvement and food security.

Purpose of the Study:

• To investigate the mechanistic basis of maize adaptation to highland environments.
• To identify genes and regulatory mechanisms involved in convergent evolution of highland maize.

Main Methods:

• Crossed highland and lowland maize landraces with inbred line B73 to create F1 hybrids.
• Grew hybrids in highland and lowland Mexican sites for comparative analysis.
• Utilized a novel allele-specific expression pipeline to detect divergent cis-regulatory variation.

Main Results:

• Identified thousands of genes with divergent expression between highland and lowland maize populations.
• Discovered hundreds of genes with convergent cis-regulation between Mexican and South American highland adaptations.
• Found evidence for multiple regulatory mechanisms contributing to convergent evolution in highland maize.

Conclusions:

• Convergent evolution plays a significant role in highland maize adaptation at the gene expression and regulatory levels.
• While most adaptive changes are region-specific, gene regulation shows notable convergence.
• Findings provide insights into the genetic architecture of adaptation in staple crops.