Genetic dissection of plant height in the CIMMYT elite wheat germplasm through functional Rht allele profiling.

UNLABELLED: Plant height strongly influences wheat yield potential and stability. The causal genes underlying seven reduced height (Rht) loci have already been cloned and gene-specific markers are available for their deployment in wheat breeding. As the birthplace of the wheat Green Revolution, the International Maize and Wheat Improvement Center (CIMMYT) has driven global yield gains through the widespread adoption of the dwarfing genes Rht-B1b and Rht-D1b, and maintains the world's largest open-access wheat germplasm collection. Here, diagnostic markers for the cloned Rht genes were evaluated in a panel of 369 elite wheat lines from CIMMYT's international screening nurseries. A breeder-friendly kompetitive allele-specific PCR (KASP) marker was developed to distinguish Rht24a and Rht24b. Genotyping revealed a strong predominance of Rht-B1b (100% frequency), while Rht24b and Rht25d were present at lower frequencies (13.9% and 6.7%, respectively). By contrast, the widely used Rht-D1b and Rht8b was nearly absent with 0.3% and 1.1%, respectively, and Rht12b were not detected in these CIMMYT wheat lines. Marker-trait association analyses showed no consistent or significant effects of the dwarfing alleles Rht24b and Rht25d on plant height across most of environments. Allelic combinations involving these loci were also rare; the most frequent combinations (Rht-B1b+Rht24b+Rht25d, and Rht-B1b+Rht24b) occurred at only 5.8% and 4.9%, respectively, and confer minimal differences in plant height relative to Rht-B1b alone. These results highlight the overwhelming dominance of Rht-B1b in CIMMYT germplasm and the limited contribution of other functional Rht alleles. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at https://doi.org/10.1007/s11032-026-01715-z.