QTL mapping and candidate gene analysis for sclerotinia stem rot resistance in rapeseed cultivar Zhongshuang 11 by linkage, bulk segregant, and transcriptome analysis

Sclerotinia stem rot (SSR) is an important disease in rapeseed production caused by Sclerotinia sclerotiorum . Zhongshuang11(ZS11) is an elite double-low (low glucosinolate and low erucic acid) rapeseed cultivar with moderate SSR resistance. Identifying SSR resistance loci in ZS11 is of great significance for improving the SSR resistance of new double-low rapeseed varieties. In this study, 12 quantitative trait loci were mapped in the doubled haploid (DH) population, constructed using the resistant line ZS11 and susceptible line 19514 A, through linkage analysis. In the same population, seven intervals were identified using bulked segregant analysis sequencing. Among these, qDIA3–1 , qDIA4–1 , and qDIC4–1 could be identified by both methods and were considered as stable loci. Transcriptome analysis results revealed that a series of identical response pathways were induced in both ZS11 and 19514 A after infection. Furthermore, ZS11 produced a more pronounced response in the microtubule-associated and ribosome-associated pathways, which may partially explain the stronger resistance of ZS11 over 19514 A. Finally, a list of candidate genes of qDIA3–1 , qDIA4–1 , and qDIC4–1 were predicted by putative functions and expression levels. This research contributes to the advancement of knowledge regarding the genetic underpinnings and regulatory pathways of resistance to SSR in rapeseed, especially the explanation of the high resistance of ZS11, and provides a reference for the application of ZS11 for SSR resistance improvement. • 12 quantitative trait loci to Sclerotinia stem rot were mapped by linkage analysis. • 7 linkage intervals were mapped by bulk segregant analysis sequencing. • qDIA3–1 , qDIA4–1 , and qDIC4–1 were identified by both methods.