Development of molecular markers associated with saline-alkali tolerance in rapeseed (Brassica napus L.)

Salt-tolerant rapeseed ( Brassica napus L.) plays a pivotal role in the sustainable utilization and improvement of saline-alkaline soils. However, current breeding of highly tolerant cultivars still relies largely on conventional hybridization combined with phenotype-based selection, which is strongly influenced by environmental variation, labor-intensive, and low-throughput, thereby limiting breeding efficiency. To address these challenges, a total of 1,281 candidate genes previously reported across rice, maize, wheat, sorghum, and Arabidopsis were compiled. Subsequent candidate gene-based association analysis identified 483 significantly associated genes, 355 of which harbored favorable haplotypes. Molecular markers were efficiently developed for 275 genes, including 746 KASP and 201 InDel marker pairs. Four marker pairs were randomly selected for validation, and the results demonstrated their effectiveness in classifying germplasm based on tolerance levels. Given the relatively small effect of individual saline–alkaline tolerance loci in rapeseed, these markers enable efficient pyramiding of favorable alleles into parental lines, thereby accelerating the development of highly tolerant varieties. This study provides essential tools for early-generation evaluation and marker-assisted selection (MAS) and lays a solid foundation for the molecular design breeding of saline–alkaline-tolerant rapeseed