Integrated Multi-Omics Reveals the Molecular Basis Underlying Wheat Grain Development and Identifies TaYAK1-2D as a Positive Grain Weight Regulator

Grain weight, a highly heritable yield component, is a primary breeding target for enhancing wheat productivity. Unraveling the molecular dynamics underlying grain development is essential for identifying key regulators controlling this trait. In this study, we employed an integrated multi-omics approach to analyze transcriptomic and proteomic profiles in developing grains using pairwise near-isogenic lines with contrasting grain weight across four grain developmental stages. Our analysis revealed that early grain development, particularly at 7 days post-anthesis, serves as a critical window during which differential regulation of genes and proteins involved in carbohydrate biosynthesis and metabolic pathways establishes the final grain weight. By combining weighted gene co-expression network analysis (WGCNA) and K-means clustering, we identified a grain weight-associated module and pinpointed four high-confidence candidate genes. Among these, <i>TaYAK1-2D</i>, which encodes a YAK family protein kinase, was functionally validated as a positive regulator of grain weight through mutational analysis. Sequence analysis revealed two major natural haplotypes of <i>TaYAK1-2D</i>, with <i>TaYAK1-2D-Hap2</i> being significantly associated with higher grain weight across multiple environments. Our findings not only delineate a crucial metabolic window governing grain weight but also provide both a novel genetic target and a practical haplotype marker for molecular breeding aimed at yield improvement in wheat.