Development and validation of a KASP marker for a domestication-associated stem diameter allele in sorghum.

Abstract

Stem diameter is a key agronomic trait in sorghum (Sorghum bicolor L.), influencing biomass accumulation and stalk strength. It also affects practical outcomes such as mechanical harvesting efficiency and end-use quality. Despite its importance, the genetic basis of this trait remains unclear. To address this, we performed a genome-wide association study (GWAS) on a diverse panel, which identified a candidate locus containing Sobic.010G085400 (SbMADS52), a gene encoding a MADS-box transcription factor. Within this gene, we identified a putative functional G185S substitution associated with both stem thickness and plant height, suggesting a role in stalk architecture. To leverage this variant for breeding, we developed and validated a putative functional KASP marker. Population genetic analyses further revealed that the favorable allele has been under selection since domestication but is less frequent in modern breeding, highlighting an underused genetic resource. Collectively, our study characterizes a candidate regulator of stem morphology and provides a practical marker that may be used for sorghum breeding.