Transcriptomic and Regulatory Approaches to Candidate Gene Discovery in Plant Development, Phenotypic Variation, and Metabolite Accumulation

Plant development is governed by the coordinated interplay of genetic, transcriptional, post-transcriptional, and metabolic regulatory networks. Despite significant advances in understanding developmental pathways in model organisms, the molecular mechanisms driving phenotypic diversity in growth, organ development, metabolic profiles, and developmental plasticity — particularly in crops and non-model species — remain largely uncharacterized.High-throughput transcriptomics now provides unprecedented resolution for linking gene expression dynamics to metabolite profiles and developmental outcomes across tissues and developmental stages. These approaches enable the systematic identification of candidate genes, transcription factor networks, and metabolic pathways that single-gene analyses cannot reveal. When combined with gene regulatory network inference and post-transcriptional regulatory mechanisms — including alternative splicing — they open concrete paths toward establishing causal genotype–phenotype–metabolite relationships.Developmental regulatory networks act across the full arc of plant growth — from organ specification and vegetative expansion to reproductive transitions and seasonal growth cycles — shaping not only morphological outcomes but also the secondary metabolite profiles that accumulate across tissues and stages. This Research Topic addresses the challenge of identifying candidate genes and regulatory networks underlying plant developmental variation and metabolite accumulation. By combining transcriptomic discovery with gene regulatory network analysis, it aims to advance mechanistic understanding of plant developmental regulation and metabolic control, while supporting translational applications in crop improvement and environmental adaptation.We welcome contributions covering, but not limited to, the following areas:- Transcriptomic approaches linking gene expression dynamics with developmental and metabolic outcomes- Gene regulatory network inference and systems-level analyses of developmental and metabolic pathways- Identification and characterisation of candidate genes controlling developmental traits, phenotypic variation, or metabolite accumulation- Transcriptional and post-transcriptional regulation in plant developmental and metabolic control- Transcription factor characterisation and hormone signalling cross-talk in plant development and secondary metabolism- Developmental plasticity and phenotypic variation in crops and non-model plant species- Translational transcriptomic applications in crop improvement and adaptation to environmental changeOriginal Research, Review, Mini-Review, and Methods articles are all welcome. Studies in both model and non-model species are encouraged, with particular interest in work that connects regulatory discovery to developmental or metabolic phenotypes. Please note that purely transcriptomic studies without functional validation of identified candidate genes fall outside the scope of Frontiers in Plant Science. Topic editors: Keh Chien Lee, Yuqing He Source: https://www.frontiersin.org/research-topics/81198/transcriptomic-and-regulatory-approaches-to-candidate-gene-discovery-in-plant-development-phenotypic-variation-and-metabolite-accumulation