Abstract
Genetic dissection and molecular breeding of complex traits in crops are entering a precision era driven by genomics and genome-wide association studies (GWAS). This paper provides a systematic discussion centered on four cutting-edge directions: pangenomics, multi-omics integration, genome editing technologies, and gene-environment interactions (G×E). It highlights the critical value of pangenomes in revealing species-level genetic diversity and “dispensable genes,” explores the pivotal role of multi-omics data integration in elucidating genotype–phenotype relationships, analyzes the synergistic potential of GWAS with genome editing tools such as CRISPR/Cas, and examines how environmental factors regulate complex trait formation. By synthesizing recent advances and practical case studies, this paper aims to offer theoretical foundations and technical pathways for building efficient, precise, and intelligent crop breeding systems to support sustainable agriculture in the face of climate change and global food security challenges.
