The integration of genomics and phenomics represents one of the most consequential developments in modern crop science. High-throughput genotyping platforms, including genotyping-by-sequencing (GBS), SNP arrays, and whole-genome resequencing, now generate molecular data at scale across diverse germplasm, while advances in field and controlled-environment phenotyping enable precise, multidimensional characterization of plant performance across environments and developmental stages. Translating this dual capacity into measurable breeding outcomes has become a defining challenge and opportunity for the field.
Quantitative trait locus (QTL) mapping, genome-wide association studies (GWAS), and fine-mapping approaches have substantially advanced our understanding of the genetic architecture underlying complex agronomic traits, including yield, biotic and abiotic stress tolerance, and grain quality, across major crop groups such as cereals, pulses, and oilseeds. Combined with marker-assisted selection (MAS), marker-assisted backcrossing, and genomic prediction, these methods now support coherent pipelines from gene discovery to the introgression of key alleles into elite germplasm, pipelines that have already contributed to the commercial release of improved varieties with enhanced resistance and productivity.
Yet critical gaps remain. The genotype-to-phenotype relationship in complex, variable environments is still poorly resolved, and the polygenic architecture of many target traits limits the predictive power of current models. Phenotyping throughput and precision remain bottlenecks in many programs, particularly for underserved crop species. The functional validation of QTLs and candidate genes, increasingly addressed through multi-omics dissection and targeted genome editing, is not yet routine. This Research Topic brings together empirical and methodological contributions that advance the connection between genomic data and breeding outcomes, with an emphasis on studies that move beyond association discovery toward functional insight or translational application.
To gather further insights into the genomics–phenomics interface in crop improvement, we welcome articles addressing, but not limited to, the following themes:
• QTL mapping, GWAS, and fine-mapping for biotic stress resistance, abiotic stress tolerance, and agronomic traits in cereals, pulses, oilseeds, and other crop species
• Marker-assisted selection, backcross introgression, and the deployment of molecular markers in elite breeding programs, including case studies of varietal release
• Genomic prediction and selection models for complex polygenic traits, including genotype-by-environment (G×E) interactions and multi-environment trial analyses
• High-throughput phenotyping and its computational integration with genome-scale datasets for trait dissection
• Functional characterization of QTLs and candidate genes through multi-omics approaches or genome editing, linking molecular variation to phenotypic outcomes
Article types and fees
This Research Topic accepts the following article types, unless otherwise specified in the Research Topic description:
Brief Research Report
Data Report
Editorial
FAIR² Data
General Commentary
Hypothesis and Theory
Methods
Mini Review
Opinion
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Article types
This Research Topic accepts the following article types, unless otherwise specified in the Research Topic description:
Important note: All contributions to this Research Topic must be within the scope of the section and journal to which they are submitted, as defined in their mission statements. Frontiers reserves the right to guide an out-of-scope manuscript to a more suitable section or journal at any stage of peer review.
