Characterization and Fine Mapping of ds, a Recessive Dense-Spike Mutant Associated with Shortened Spike Axis and Increased Spikelet Number in Wheat

Spike density is an important component of wheat spike architecture and is determined by the combined effects of spike-axis elongation and spikelet number. In this study, we characterized an ethyl methanesulfonate (EMS)-induced recessive dense-spike mutant, ds, which was obtained from EMS mutagenesis of the wheat cultivar YN21 in 2013 and displays a field-visible compact spike architecture associated with a shortened spike axis, reduced spike internode spacing, and increased spikelet number. Genetic analysis showed that all F1 plants exhibited normal spikes and that segregation in the F2 population fitted a 3:1 ratio, supporting control by a single recessive nuclear gene. Through genome-wide marker-based linkage screening, enlarged-population validation, and fine mapping, ds was delimited to an approximately 864.819 kb interval between ID2B2796 and ID2B7615 on chromosome 2B. This interval contains 11 high-confidence annotated genes, including F-box protein, actin, ubiquitin-conjugating enzyme, ribosomal protein L16, RecX, plant cysteine oxidase, PI4KIIγ, and two adjacent GA3OX-family-related genes. Integrated RNA-seq and RT-qPCR analyses showed that the two adjacent GA3OX-family-related genes were expressed in young spikes and exhibited reduced expression in ds-sib relative to WT-sib. These expression data support their retention as plausible, non-exclusive candidates but do not establish causality. Transcriptome analysis further revealed changes in hormone-related pathways, cell-wall organization, carbohydrate metabolism, and transcription-factor regulation. These results provide a reliable genetic basis for further molecular cloning of ds and suggest that altered hormone- and growth-related transcriptional responses may be associated with dense-spike formation in wheat.