Marker-trait association analysis revealed loci linked to salinity tolerance in a worldwide collection of safflower

The present investigation was designed to identify molecular marker loci linked to essential agronomic traits and oil content under contrasting salinity regimes, and to evaluate the stability of these associations within a globally representative safflower (Carthamus tinctorius L.) germplasm collection. Over two successive years, 100 accessions were evaluated, generating 341 polymorphic amplified fragment length polymorphism (AFLP) markers using 10 EcoRI/MseI primer combinations. These markers were subsequently employed in association mapping analyses encompassing 17 agronomic traits and their derived indices. Population structure assessment revealed three genetically distinct subgroups within the panel. Mixed linear model (MLM) analysis facilitated the identification of 140 significant MTAs under non-saline conditions and 128 MTAs under salinity stress. Several loci exhibited associations with multiple traits, suggesting either pleiotropic regulatory functions or tight genetic linkage. Markers M61/E37-1, M61/E37-16, M62/E41-15, M60/E38-9, M51/E41-31, M61/E40-20, and M47/E37-9 were consistently associated with salinity tolerance across environments. After confirmation, these MTAs represent valuable resources for marker-assisted selection and for the targeted introgression of favorable alleles into safflower breeding programs adapted to both optimal and saline conditions. Furthermore, the results provide a critical framework for fine-scale genetic mapping and the eventual isolation of causal genes and quantitative trait loci (QTLs) that confer salinity tolerance.