Decoding Gene Regulation in Crops: From Evolutionary Dynamics to Agronomic Innovation

Gene regulatory networks in crops reflect hundreds of millions of years of plant evolution and thousands of years of domestication. From wild progenitors to modern cultivars, selective bottlenecks, gene duplication, polyploidization, and cis-regulatory changes have shaped gene-function partitioning, stress-response pathways, and the genetic architecture of agronomic traits. However, many functional studies remain focused on individual cultivated species and do not fully consider the evolutionary history of regulatory networks. This limits our understanding of the adaptive origins, functional plasticity, and improvement potential of crop traits. Integrating evolutionary history into gene-regulation research is therefore essential for addressing climate volatility, emerging stresses, and the need to increase agricultural productivity sustainably.This Research Topic aims to examine how the evolutionary trajectories of crop gene regulatory networks have influenced stress tolerance, yield components, phenology, and other agronomic traits. Recent advances in pan-genomics, ancient-DNA analysis, selective-sweep detection, comparative genomics, and single-cell transcriptomics provide new opportunities to trace the origin, diversification, and functional switching of regulatory elements. We welcome studies that integrate evolutionary biology, functional genomics, and breeding to identify causal regulatory variation, clarify the effects of gene duplication and polyploidization, and assess the contributions of wild and ancestral alleles to crop performance. The Research Topic will also explore how these insights can support precision genome editing, regulatory-element design, and evolution-informed breeding strategies.To gather further insights into the evolutionary basis and practical applications of gene regulation in crop plants, we welcome original research, review, and methodological contributions addressing, but not limited to, the following themes:o Signatures of regulatory-sequence selection during domestication and crop diversification, including the identification of adaptive regulatory elements retained or lost during domestication bottlenecks.o Evolutionary mining of stress-responsive regulatory modules in wild relatives, including phylogenetic approaches to identify ancestral circuits associated with drought, salinity, disease resistance, heat, and other stresses.o The effects of gene duplication, subfunctionalization, and neofunctionalization on the regulation of agronomic traits, including the functional divergence of paralogous genes.o Evolutionary dynamics and functional switching of cis-regulatory elements, using DNase-seq, ATAC-seq, comparative genomics, and related approaches to investigate changes in regulatory activity and phenotype.o Convergent and divergent evolution of environmental stress-response networks across crops, wild relatives, and contrasting ecotypes.o Evolution-informed gene-function annotation and causal-variant identification through the integration of evolutionary conservation, selection signals, and phenotype–genotype associations.o Reconstruction of regulatory sequences from ancient DNA and historical specimens to investigate regulatory changes during domestication and crop improvement.o Evolution-guided precision genome editing and synthetic-biology design, including ancestral-sequence reconstruction and the identification of convergent evolutionary sites.o Regulatory imbalance among homoeologous genes in polyploid crops, including cotton, rapeseed, wheat, and other polyploid species, and its consequences for subgenome dominance and agronomic traits.o Evolution-informed breeding frameworks that incorporate evolutionary parameters into selection indices and evaluate their effectiveness in developing resilient crop varieties.---------------------We welcome contributions from researchers across the field and are happy to support you as you prepare your submission. If you would like initial feedback on whether your planned manuscript aligns with the scope of this Research Topic, please reach out to us at plantscience@frontiersin.org before submitting. Early input can help ensure your work is a strong fit and save you time later in the process. To take part, click “Participate in this topic” at the top right of this page, and then confirm through the “Participate” link in the follow-up email. This lets us know to expect your contribution, keeps you informed of key deadlines, and gives you access to resources that guide you through submission. We look forward to your participation and to building a vibrant, cohesive Research Topic together.” Topic editors: Cheng Song, Irfan Ali Sabir, Yunpeng Cao, Muhammad Abdullah Source: https://www.frontiersin.org/research-topics/85044/decoding-gene-regulation-in-crops-from-evolutionary-dynamics-to-agronomic-innovation