Canola varieties exhibit variation in drought avoidance and drought escape traits, reflecting adaptation to water-deficit environments. Our understanding of underlying genes and their interaction across environments in improving crop productivity is limited. A doubled haploid��population was analysed to identify quantitative trait loci��(QTL) associated with water-use efficiency (WUE) related traits. High WUE in the vegetative phase was associated with low seed yield. Based on the resequenced parental genome data, we developed sequence-capture-based markers and validated their linkage with carbon isotope discrimination (��13C) in an F2 population. RNA��sequencing was performed to determine the expression of candidate genes underlying ��13C QTL. QTL contributing to main and QTL �� environment interaction effects for ��13C and yield were identified. One multiple-trait QTL for ��13C, days to flower, plant height, and seed yield was identified on chromosome A09. Interestingly, this QTL region overlapped with a homoeologous exchange��(HE) event, suggesting its association with the multiple traits. Transcriptome analysis revealed 121 significantly differentially expressed genes underlying ��13C QTL on A09 and C09, including in HE regions. Sorting out the negative relationship��between vegetative WUE and seed yield is a priority. Genetic and genomic resources and knowledge so developed could improve canola WUE and yield.