Maize inbreds show allelic variation for diel transcription patterns

Area of Science:

• Plant biology
• Genetics
• Chronobiology

Background:

• Gene transcript abundance oscillates daily due to circadian rhythms and environmental cues.
• Understanding allelic variation in these diel (daily) transcription patterns and the role of regulatory sequences is limited.
• Maize (Zea mays) is a globally important crop with diverse genetic resources.

Purpose of the Study:

• To investigate natural variation in diel transcript abundance patterns across diverse maize inbred lines.
• To explore the influence of cis-regulatory (promoter) sequences on diel transcription patterns.
• To identify potential links between circadian gene expression variation, photoperiod sensitivity, and local adaptation in maize.

Main Methods:

• Quantified diel transcript abundance in 24 diverse maize inbred lines.
• Employed a convolutional neural network to predict gene oscillation from promoter sequences.
• Analyzed the co-segregation of diel transcription patterns with promoter sequence haplotypes.

Main Results:

• Observed significant natural variation in diel transcription patterns, with up to a two-fold difference in oscillating genes across lines.
• The predictive model identified known circadian clock gene binding motifs in promoter sequences associated with oscillation.
• Genes with diel patterns linked to promoter haplotypes were enriched for functions related to photoperiod sensitivity.

Conclusions:

• Cis-regulatory sequence variation significantly influences diel gene expression patterns in maize.
• Variation in circadian transcription may contribute to phenotypic plasticity and local adaptation, particularly in response to day length changes.
• This study highlights the importance of regulatory variation in shaping adaptive traits during crop domestication and breeding.