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Sclerotinia stem rot is a broad-spectrum threat to rapeseed production, and Brassica juncea contains abundant genetic resources for resistance against Sclerotinia sclerotiorum. Therefore, it is of great significance to carry out screening, localization, and exploration of resistance loci for sclerotinia stem rot in Brassica juncea germplasm resources for the breeding of Sclerotinia-resistant rapeseed. In this study, the S. sclerotiorum resistance of Brassica juncea germplasm resources collected from various regions in Yunnan Province was evaluated under three different growth environments, and a whole-genome association analysis of S. sclerotiorum resistance loci was conducted based on the resequencing data of 91 Brassica juncea germplasm materials. According to the results of leaf identification under in vitro conditions in the three growth environments, one highly resistant germplasm material J7667 and one relatively resistant germplasm material J047 were selected. The resequencing data of the 91 materials were aligned to the reference genome of Brassica juncea for variation detection analysis, resulting in the detection of 11 337 871 SNPs and 40 170 Indels distributed on the 18 chromosomes of Brassica juncea. After data filtering, 403 211 high-quality SNPs were obtained. The phenotypic data of in vitro leaves, in vitro stems, and stem resistance to S. sclerotiorum of the 91 materials under the three growth environments were subjected to whole-genome association analysis using two analysis software, Emmax and Tassel. In the in vitro leaves, both analysis methods identified a total of 62 significantly associated SNP loci with resistance in the three different growth environments, including 23 and 39 significantly associated SNP loci in the Luoping winter sowing and Xiaoshao winter sowing environments, respectively, while no resistance loci were detected in the Xiaoshao summer sowing environment. In the stem of Luoping winter sowing, both methods detected 3 significantly associated SNP loci with resistance, while no significant SNP was detected in the stem of Xiaoshao summer sowing. In the Tassel method, closely located resistance SNP loci were detected on chromosomes A2, A8, and B2 in Luoping winter sowing and Xiaoshao winter sowing, while in the Emmax method, closely located resistance SNP loci were detected on chromosomes B5 and B8 in Luop-ing winter sowing and Xiaoshao winter sowing. In addition, this study mapped the previously identified S. sclerotio-rum resistance QTL loci and the resistance loci identified in this study to the reference genome of Brassica juncea. It was found that the resistance QTL intervals identified in this study (XLRA2-2, XLRA1-4) overlapped with the reported resistance QTL loci Sll2 and qsr10-1, respectively. [ABSTRACT FROM AUTHOR]