Genetic dissection of cold tolerance across developmental stages in sorghum reveals stage-specific haplotypes and potential trade-offs.

key messageCold tolerance in sorghum is largely stage- and environment-specific yet partially shared genetic control allows improvement across developmental stages with mostly modest, trait-specific trade-offs. Cold tolerance is a major constraint to sorghum production in temperate environments, and its improvement is therefore a key breeding objective. However, cold tolerance varies across developmental stages and environments, and selection based on stage-specific phenotypes may overlook shared genetic components. We analysed a diversity panel of 394 sorghum genotypes evaluated across 10 environments representing three developmental stages using multi-environment mixed models, genome-wide haplotype block analysis, and in silico haplotype stacking. Substantial genotype-by-environment interaction was detected, with the strength of GEI varying markedly across traits. Genetic correlations were high within developmental stages but lower and more variable across stages, indicating that the genetic architecture of cold tolerance-relevant traits is largely stage-dependent. Haplotype block analyses identified both stage- and environment-specific regions, as well as regions shared across stages and environments. In silico stacking of favourable haplotypes for early-stage cold tolerance resulted in nonlinear predicted gains, with strong initial responses at low stacking levels followed by diminishing returns. Correlated responses in yield-related traits were generally positive, whereas flowering time was consistently delayed, indicating a potential trait-specific trade-off in cold tolerance improvement. Sorghum cold tolerance can therefore not be treated as a single uniform trait but rather as a combination of stage-specific and shared genetic components, with implications for multi-stage breeding strategies.