Gage Joseph L, Romay M Cinta, Buckler Edward S
Department of Crop and Soil Sciences, North Carolina State University, Raleigh, NC 27695.
NC Plant Sciences Initiative, North Carolina State University, Raleigh, NC, 27606.
bioRxiv. 2024 Dec 17:2024.12.16.628400. doi: 10.1101/2024.12.16.628400.
Circadian entrainment and external cues can cause gene transcript abundance to oscillate throughout the day, and these patterns of diel transcript oscillation vary across genes and plant species. Less is known about within-species allelic variation for diel patterns of transcript oscillation, or about how regulatory sequence variation influences diel transcription patterns. In this study, we evaluated diel transcript abundance for 24 diverse maize inbred lines. We observed extensive natural variation in diel transcription patterns, with two-fold variation in the number of genes that oscillate over the course of the day. A convolutional neural network trained to predict oscillation from promoter sequence identified sequences previously reported as binding motifs for known circadian clock genes in other plant systems. Genes showing diel transcription patterns that cosegregate with promoter sequence haplotypes are enriched for associations with photoperiod sensitivity and may have been indirect targets of selection as maize was adapted to longer day lengths at higher latitudes. These findings support the idea that cis-regulatory sequence variation influences patterns of gene expression, which in turn can have effects on phenotypic plasticity and local adaptation.
昼夜节律的同步和外部信号可导致基因转录本丰度在一天中发生振荡，并且这些昼夜转录本振荡模式在不同基因和植物物种间存在差异。关于物种内转录本振荡的昼夜模式的等位基因变异，或者调控序列变异如何影响昼夜转录模式，我们所知甚少。在本研究中，我们评估了24个不同玉米自交系的昼夜转录本丰度。我们观察到昼夜转录模式存在广泛的自然变异，在一天中振荡的基因数量有两倍的差异。一个经过训练可根据启动子序列预测振荡的卷积神经网络识别出了先前在其他植物系统中报道的作为已知生物钟基因结合基序的序列。显示昼夜转录模式且与启动子序列单倍型共分离的基因富含与光周期敏感性的关联，并且在玉米适应高纬度地区更长日照长度的过程中可能是间接的选择目标。这些发现支持了顺式调控序列变异影响基因表达模式的观点，而基因表达模式反过来又可对表型可塑性和局部适应性产生影响。
