A role for heritable transcriptomic variation in maize adaptation to temperate environments.

Area of Science:

• Plant genetics and genomics
• Molecular biology
• Crop adaptation

Background:

• Maize (Zea mays) originated in tropical regions and has adapted to temperate environments.
• Understanding transcriptional regulation is key to bridging genetic information and observable traits (phenotypes).

Purpose of the Study:

• To investigate how alterations in transcriptional regulation facilitate maize adaptation to temperate climates.
• To identify genetic factors influencing gene expression and splicing in maize roots.

Main Methods:

• Generated 572 RNA-sequencing datasets from 340 maize genotypes.
• Performed expression genome-wide association studies (eGWAS) and GWAS for alternative splicing.
• Utilized independent component analysis to identify co-expression modules.
• Analyzed gene expression variation between tropical and temperate maize lines.

Main Results:

• Identified 19,602 expression quantitative trait loci (eQTLs) for 11,444 genes and 49,897 splicing QTLs (sQTLs) for 7614 genes.
• Genes related to anti-oxidation showed higher expression heritability; core process genes showed lower heritability.
• Genes with both cis-eQTLs and cis-sQTLs often encode transcription factors or respond to stress.
• Discovered loci regulating co-expression modules involved in stress responses and biogenesis.
• Identified candidate genes overlapping with regions under selection during temperate adaptation.

Conclusions:

• Transcriptional regulatory networks in maize enable adaptation to temperate regions.
• Genetic variation in gene expression and splicing plays a crucial role in maize adaptation.