Galli Mary, Chen Zongliang, Ghandour Tara, Chaudhry Amina, Gregory Jason, Feng Fan, Li Miaomiao, Schleif Nathaniel, Zhang Xuan, Dong Yinxin, Song Gaoyuan, Walley Justin W, Chuck George, Whipple Clinton, Kaeppler Heidi F, Huang Shao-Shan Carol, Gallavotti Andrea
Waksman Institute of Microbiology, Rutgers University, Piscataway, NJ, USA.
Center for Genomics and Systems Biology, Department of Biology, New York University, New York, NY, USA.
Nat Plants. 2025 Jun;11(6):1205-1219. doi: 10.1038/s41477-025-02007-8. Epub 2025 Jun 12.
Regulatory elements are essential components of plant genomes that have shaped the domestication and improvement of modern crops. However, their identity, function and diversity remain poorly characterized, limiting our ability to harness their full power for agricultural advances using induced or natural variation. Here we mapped transcription factor (TF) binding for 200 TFs from 30 families in two distinct maize inbred lines historically used in maize breeding. TF binding comparison revealed widespread differences between inbreds, driven largely by structural variation, that correlated with gene expression changes and explained complex quantitative trait loci such as Vgt1, an important determinant of flowering time, and DICE, an herbivore resistance enhancer. CRISPR-Cas9 editing of TF binding regions validated the function and structure of regulatory regions at various loci controlling plant architecture and biotic resistance. Our maize TF binding catalogue identifies functional regulatory regions and enables collective and comparative analysis, highlighting its value for agricultural improvement.
调控元件是植物基因组的重要组成部分，它们塑造了现代作物的驯化和改良过程。然而，它们的身份、功能和多样性仍未得到充分表征，这限制了我们利用诱导变异或自然变异充分发挥其潜力以推动农业进步的能力。在此，我们绘制了历史上用于玉米育种的两个不同玉米自交系中30个家族的200个转录因子（TF）的结合图谱。TF结合比较揭示了自交系之间广泛存在的差异，这些差异主要由结构变异驱动，与基因表达变化相关，并解释了复杂的数量性状位点，如控制开花时间的重要决定因素Vgt1和增强食草动物抗性的DICE。对TF结合区域进行CRISPR-Cas9编辑验证了控制植物结构和生物抗性的各个位点调控区域的功能和结构。我们的玉米TF结合目录确定了功能性调控区域，并能够进行集体和比较分析，凸显了其对农业改良的价值。
