Integrated germination related traits and transcriptomic analysis elucidate the potential mechanism of rapeseed under drought stress

Drought is a critical factor affecting rapeseed seed germination, leading to poor stability of direct seeding rapeseed cultivation in the Yangtze River Basin region of China. Identifying the key mechanisms and gaining a comprehensive understanding of drought related plant responses can improve the selection of desirable phenotypes of drought tolerance. Therefore, we aimed to identify important compounds that could work as stress responsive biomarkers. Herein, 22 rapeseed varieties were used in pot experiment with different levels of soil moisture contents during the seed germination stage. Among 22 varieties, Qingyou 3 (Q3) and Qinyou 7 (Q7) were selected to assess the decomposition of storage substances, hormone levels, and antioxidant enzyme activity besides transcriptome analysis during the germination stage under drought stress conditions. Our study revealed that drought stress significantly prolonged seed germination time to 60 h with significant differences in drought tolerance among varieties. Additionally, during the germination process, degradation of storage substances (sugar, protein, and lipid) was delayed under drought stress conditions. Sugar content was decreased by 19.80% (Q3) and 15.46% (Q7) during 36–72 h of seed germination; whereas, protein degradation occurred earlier in Q3 resulting in a 17.62% reduction as compared to Q7 at 96 h of seed germination. Moreover, drought treatment increased ABA while reducing GA content in seeds versus normal conditions, which significantly decreased the GA/ABA ratio that was higher in Q3 as compared to Q7. Furthermore, SOD and POD activities were higher, whereas MDA content was lower in roots and leaves of Q3 compared to Q7 under drought stress conditions. Transcriptome analysis revealed that drought tolerance during germination primarily focused on sugar, amino acids, antioxidants and hormones pathways related genes. GO enrichment pathway analysis showed significant differences in ion transport, peroxisomes, and proteasome complexes related genes. Studied varieties exhibited similar enrichment patterns under both conditions, particularly in the pathways associated with antioxidant activity, nutrient library activity, and cysteine peptidase activity. KEGG analysis found that the metabolism of vitamin B6 (B6) and riboflavin (B2) had an important role in drought tolerance and their priming application (400 μmol/L) improved the stress tolerance during the germination stage in Q7. Besides, their application