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Most plants are sensitive to salt-alkali stress, and the degree of tolerance to salt-alkali stress varies from different species and varieties. In order to explore the salt-alkali stress adaptability of  Brassica napus , we collected the phenotypic data of 505  B. napus  accessions at seedling and mature stages under control, low and high salt-alkali soil stress conditions in Inner Mongolia of China. Six resistant and 5 sensitive materials, respectively, have been identified both in Inner Mongolia and Xinjiang Uygur Autonomous Region of China. Genome-wide association studies (GWAS) for 15 absolute values and 10 tolerance coefficients (TCs) of growth and agronomic traits were applied to investigate the genetic basis of salt-alkali tolerance of  B. napus . We finally mapped 9 significant QTLs related to salt-alkali stress response and predicted 20 candidate genes related to salt-alkali stress tolerance. Some important candidate genes, including  BnABA4, BnBBX14, BnVTI12, BnPYL8 , and  BnCRR1 , were identified by combining sequence variation annotation and expression differences. The identified valuable loci and germplasms could be useful for breeding salt-alkali-tolerant  B.napus  varieties. This study laid a foundation for understanding molecular mechanism of salt-alkali stress adaptation and provides rich genetic resources for the large-scale production of  B. napus  on salt-alkali land in the future.

Genome-Wide Association Studies of Salt-Alkali Tolerance at Seedling and Mature Stages in Brassica napus