21Drought stress especially at the reproductive stage is a major limiting factor that 22 compromises the productivity and profitability of canola in many regions of the world. 23 Improved genetics for drought tolerance would enable the identification and 24 development of resilient varieties, resulting in increased canola production. The main 25 objective of this study was to dissect the genetic basis of seed yield under water-limited 26 conditions in canola. A doubled haploid population derived from a cross between two 27 Australian parental lines, RP04 and Ag-Outback, was evaluated to identify the genetic 28 variation in fractional normalised deviation vegetative index (NDVI), above ground shoot 29 biomass accumulation, flowering time, and plasticity in seed yield under irrigated and 30 rainfed field conditions in two consecutive years. An irrigation treatment was applied at 31 the 50% flowering stage and an incremental drought tolerance index (DTI) was 32 estimated for seed yield. By utilising a genetic linkage map based on 18,851 genome-33 wide DArTseq markers, we identified 25 genomic regions significantly associated with 34 different traits (LOD ≥ 3), accounting for 5.5 to 22.3% of the genotypic variance. Three 35 significant genomic regions on chromosome A06, A10 and C04 were associated with 36 DTI for seed yield. Some of the QTL were localised in the close proximity of candidates 37 genes involved in traits contributing to drought escape and drought avoidance 38 mechanisms, including FLOWERING LOCUS T (FT) and FLOWERING LOCUS C 39 (FLC). Trait-marker associations identified herein can be validated across diverse 40 environments, and the sequence based markers may be used in a marker assisted 41 selection breeding strategy to enhance drought tolerance in canola breeding 42 germplasm. 43 44 45 46 47 48 Key words: Brassica napus, QTL mapping, early vigour, NDVI, Biomass, response to 49 drought 50 51 Oilseed rape (Brassica napus L) is one of the major crops grown for vegetable oil 52 production and is grown on 57 million hectares worldwide. Climate change 53 accompanied by the prevalence of elevated temperatures and variation in weather 54 patterns poses a great challenge to canola production and profitability. It is estimated 55 that 30% more oil crop production is required by 2050 to meet growing demands for 56 vegetable oil, biodiesel and stock feed markets [1]. This projected increase in 57 productivity has to come largely from improved genetics, advanced genetic selection 58 technologies and improved agronomic practices on farm. In Australia, canola is grown 59 over ~2.5 million ha, however the area sown depends upon seasonal rainfall and global 60 price index (www.australianoilseeds.com/). It is sown in autumn (March-May) and 61 harvested in early summer months (November-Dec). During the 7 month crop season, 62 provision of an adequate water supply (either by rainfall or irrigation) is critical for canola 63 growth, especially at the flowering and pod filling stages. Drought stress at these stages 64...