Haplotype-rich cis-regulation underlies transcriptomic diversity across the breeding history of maize (Zea mays)

Haplotype-rich cis-regulatory variation explains a significant portion of transcriptomic diversity in maize, with 77.7% of fine-mapped eGenes showing multiple credible sets.

• Why it matters: Understanding gene-expression variation and its link to population differentiation is crucial for crop improvement, yet remains poorly characterized in maize.
• What they did: Researchers integrated leaf RNA-seq and genome variation data from 631 maize inbred lines to identify cis-eQTLs, resolving putative causal variants for over 16,000 genes, and modeled the effects of credible sets.
• The result: Most fine-mapped variants were enriched in transcribed, accessible, and transcription-factor-binding regions, with genes exhibiting higher expression heritability and stronger differential expression associated with increased population differentiation, highlighting the complexity of cis-regulatory loci.