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Drought stress is one of the most environmental abiotic stresses affecting seed germination and crop growth. In the present study, the genetic characteristics of seed germination under drought stress in a  Brassica napus  double haploid population were analyzed. Five germination-related indexes, including germination percentage (GP), root length (RL), shoot length (SL), fresh weight (FW), and root-to-shoot length ratio (R/S) under control and drought stress, were calculated, and the drought stress index (DSI), including DSI-GP, DSI-RL, DSI-SL, DSI-FW, and DSI-R/S, was determined using the quantitative trait loci (QTLs) analysis based on high-density genetic linkage map. The phenotypic analysis indicated that the R/S is an effective morphological trait in the determination of drought tolerance in the seedling stage. Thirty-nine identified QTLs were observed for these traits and then integrated into 36 consensus QTLs, in which 18 QTLs were found to affect the DSI of four traits (GP, RL, SL, and R/S). Based on the co-linearity between genetic and physical maps of  B. napus , 256 candidate genes were detected, and 128 genes have single-nucleotidepolymorphisms/insertion–deletion (SNP/InDel) variations between two parents, some of which were associated with the drought stress tolerance (for example,  BnaC03g32780D ,  BnaC03g37030D , and  BnaC09g27300D ). The present results laid insights into drought tolerance and its genetic bases in  B. napus .

QTL Mapping for Seed Germination Response to Drought Stress in Brassica napus