Salt stress is one of the important environmental factors that inhibit the normal growth and development of plants. Plants have evolved various mechanisms, including signal transduction regulation, physiological regulation, and gene transcription regulation, to adapt to environmental stress. MicroRNAs (miRNAs) play a role in regulating mRNA expression. Nevertheless, miRNAs related to salt stress are rarely reported in bread wheat (Triticum aestivum L.). In this study, using high−throughput sequencing, we analyzed the miRNA expression profile of wheat under salt stress. We identified 360 conserved and 859 novel miRNAs, of which 49 showed considerable changes in transcription levels after salt treatment. Among them, 25 were dramatically upregulated and 24 were downregulated. Using real−time quantitative PCR, we detected significant changes in the relative expression of miRNAs, and the results showed the same trend as the sequencing data. In the salt−treated group, miR109 had a higher expression level, while miR60 and miR202 had lower expression levels. Furthermore, 21 miRNAs with significant changes were selected from the differentially expressed miRNAs, and 1023 candidate target genes were obtained through the prediction of the website psRNATarget. Gene ontology (GO) analysis of the candidate target genes showed that the expressed miRNA may be involved in the response to biological processes, molecular functions, and cellular components. In addition, the Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis confirmed their important functions in RNA degradation, metabolic pathways, synthesis pathways, peroxisome, environmental adaptation, global and overview maps, and stress adaptation and the MAPK signal pathway. These findings provide a basis for further exploring the function of miRNA in wheat salt tolerance.

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, TaYAK1-2D, 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 TaYAK1-2D, with TaYAK1-2D-Hap2 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.