Identification of DEGs Under Drought Stress Treatment
RNA-seq was used to detect DEGs in the soybean roots of DTP, DSP, DTL & DSL genotypes subjected to drought stress at germination stage. By comparing the genes showing differential expression under drought stress, a total of 2325, 3060, 2525 and 3212 DEGs (including both up- and down-) were found in the pairwise comparisons of DTP, DSP, DTL and DSL, respectively under drought treatment vs. control by using log2FC≥2 and q value ≤ 0.05 (Fig. 2A). Hence, Sensitive genotypes viz., DSP and DSL showed higher number of DEGs as compared to tolerant genotypes DTP & DTL (Fig. 2A). Moreover, in sensitive genotypes there are more number of down-regulated genes compared to tolerant genotypes. By comparing the transcriptome profiles of four genotypes, it was observed that total of 676, 493, 510 and 700 DEGs were uniquely and uniformly expressed in DTP, DSP, DTL and DSL, respectively under drought stress treatment (Fig. 2B ). In addition, 775 DEGs were common among all four genotypes.
Further, we analyzed overlapping DEGs among 12 different combinations of four genotypes under drought and control conditions using Circos software (Fig. 2C). This analysis indicates that a major fraction of DEGs were unique under stress condition compared to control in all 12 combinations. Highest number of common DEGs (1950) among all genotype combination were found between tolerant genotypes combination under stress and control conditions (DTP-T vs DTL-T & DTP-C vs DTL-C), whereas it was only 550 between sensitive genotypes under stress and control conditions (DSP-T vs DSL-T & DSP-C vs DSL-C). In addition, higher number of unique DEGs (2847) were found in sensitive genotypes under drought stress (DSP-T vs DSL-T) compared to only 2095 in tolerant genotypes (DTP-T vs DTL-T). These findings are in agreement with DEG data and venn-diagram analysis, and revealed that sensitive genotypes are more influenced by drought stress compared to tolerant genotypes at the transcriptomic/gene expression level.