From Association to Causality: Next-Generation GWAS, Pangenomes, and Multi-Omics Driving Gene Discovery and Precision Breeding in Cereal Crops

Abstract

Simple Summary Cereal crops such as rice, wheat, maize, and barley are fundamental to global food security, yet their production is increasingly challenged by climate change, emerging pests and diseases, and environmental stresses. Identifying the genetic basis of traits related to stress tolerance, disease resistance, and nutritional quality is therefore essential for accelerating crop improvement. Genome-wide association studies (GWASs) have contributed substantially to this goal by linking genomic variation with complex phenotypes. However, conventional GWASs often focus primarily on single-nucleotide polymorphisms and may overlook structural variation, while association signals alone do not always reveal the true causal genes. Recent advances in pangenomics, multi-omic integration, and gene-editing technologies are helping to overcome these limitations by improving candidate-gene identification and functional validation. Together, these approaches are moving cereal genomics from statistical association toward biologically validated targets for developing more resilient and nutritious crop varieties.