Comprehensive characterization of the rye dwarfism locus (dw10) on chromosome 5R: Phenotypic and molecular insights

Plant height is a critical determinant of yield stability in cereals, with dwarfing alleles reducing lodging risk. We present the first molecular characterization of dw10 , a gibberellin (GA)-insensitive recessive dwarfing locus in rye ( Secale cereale L.). Using Near-Isogenic Lines (NILs), high-resolution DArTseq mapping, and RNA-seq profiling, dw10 was fine-mapped to chromosome 5 R and shown to be distinct from known loci ( Ddw1 , dw8 ). The allele reduced internode length without affecting thousand-grain weight, with incomplete dominance in F₁ hybrids. GA₃ treatment partially restored elongation, indicating altered GA signaling. Transcriptome analysis revealed 125 differentially expressed genes (DEGs) on 5 R, including four within the dw10 interval: IBH1-LIKE (a BR signaling repressor), an FAD/NAD(P)-binding protein, a TolB-like protein, and a cyclin-like protein. Co-expression analysis implicated brassinosteroid-related regulatory modules and protease-mediated remodeling in height control. Variant analysis identified a missense mutation in TRYPTOPHAN SYNTHASE ALPHA ( TSA ) with upregulation of paralogues, suggesting functional compensation. These results define the genetic and molecular framework of dw10 , provide tightly linked markers for breeding, and highlight hormone signaling and cell wall processes as targets for height modulation in rye and related cereals. • A gibberellin-insensitive recessive dwarfing locus ( dw10) was characterized in rye. • The dw10 was fine-mapped to chromosome 5 R using high-resolution DArTseq. • Transcriptome analysis revealed four DEGs within the dw10 mapping interval. • Co-expression analysis associated brassinosteroids and proteases to height control. • A missense mutation in TSA and upregulation of paralogues suggests functional compensation.