Department of Plant and Microbial Biology, University of Minnesota, Saint Paul, United States.
Crop and Soil Sciences, North Carolina State University, Raleigh, United States.
Elife. 2020 Sep 30;9:e58993. doi: 10.7554/eLife.58993.
An important challenge of crop improvement strategies is assigning function to paralogs in polyploid crops. Here we describe the circadian transcriptome in the polyploid crop . Strikingly, almost three-quarters of the expressed genes exhibited circadian rhythmicity. Genetic redundancy resulting from whole genome duplication is thought to facilitate evolutionary change through sub- and neo-functionalization among paralogous gene pairs. We observed genome-wide expansion of the circadian expression phase among retained paralogous pairs. Using gene regulatory network models, we compared transcription factor targets between and Arabidopsis circadian networks to reveal evidence for divergence between paralogs that may be driven in part by variation in conserved non-coding sequences (CNS). Additionally, differential drought response among retained paralogous pairs suggests further functional diversification. These findings support the rapid expansion and divergence of the transcriptional network in a polyploid crop and offer a new approach for assessing paralog activity at the transcript level.
作物改良策略的一个重要挑战是为多倍体作物中的同源基因赋予功能。在这里，我们描述了多倍体作物 中的昼夜转录组。引人注目的是，几乎四分之三的表达基因表现出昼夜节律性。全基因组加倍导致的遗传冗余被认为通过同源基因对之间的亚功能化和新功能化促进了进化变化。我们观察到保留的同源基因对之间的昼夜表达相位在全基因组范围内扩展。使用基因调控网络模型，我们比较了 和拟南芥昼夜网络中的转录因子靶标，以揭示 同源基因的分化证据，这可能部分是由保守非编码序列 (CNS) 的变异驱动的。此外，保留的同源基因对之间的差异干旱响应表明进一步的功能多样化。这些发现支持了多倍体作物中转录网络的快速扩展和分化，并为评估转录水平上同源基因的活性提供了一种新方法。
