Comprehensive RNA‐seq analysis revealed molecular pathways and genes associated with drought tolerance in wild soybean (Glycine soja Sieb. and Zucc.)

Abstract

Drought stress at the germination stage is an important environmental stress limiting crop yield. Hence, our study investigated comparative root transcriptome profiles of four contrasting soybean genotypes viz., drought-tolerant (PI342618B/DTP and A214/DTL) and drought-sensitive (NN86-4/DSP and A195/DSL) under drought stress using RNA-Seq approach. A total of 4850 and 6272 differentially expressed genes (DEGs) were identified in tolerant (DTP and DTL) and sensitive (DSP and DSL) genotypes, respectively. Principle component analysis (PCA) and correlation analysis revealed higher correlation between DTP and DTL. Both gene ontology (GO) and MapMan analyses showed that the drought response was enriched in DEGs associated with water and auxin transport, cell wall/membrane, antioxidant activity, catalytic activity, secondary metabolism, signaling and transcription factor (TF) activities.Out of 981 DEGs screened from above terms, only 547 showed consistent opposite expression between contrasting genotypes. Twenty-eight DEGs of 547 were located on Chr.08 rich in QTLs and "Hotspot regions" associated with drought stress, and eight of them showed non-synonymous single nucleotide polymorphism. Hence, 10 genes (including above eight genes plus two hub genes) were predicated as possible candidates regulating drought tolerance, which needs further functional validation. Overall, the transcriptome profiling provided in-depth understanding about the genetic mechanism and candidate genes underlying drought tolerance in soybean.

Whole-Genome Identification of APX and CAT Gene Families in Cultivated and Wild Soybeans and Their Regulatory Function in Plant Development and Stress Response

“…We also selected the four homologous genes each of GmCAT and GsoCAT in cultivated and wild soybean, respectively; the respective homologous genes showed differential expression under drought stress in cultivated and wild soybeans. These results indicate that differential expression of the APX and CAT genes in response to stress conditions among the cultivated and wild soybeans might be responsible for the enhanced resistance of wild soybean against plant stress conditions, as previously reported by Aleem et al [ 78 ]. APX and CAT genes are important components of the plant antioxidant defense system, and their increased gene expression assists in the scavenging of the excess ROS [ 76 ], preventing oxidative damage of plant tissues resulting from the various abiotic stresses [ 79 ].…”

Brassinosteroids induced drought resistance of contrasting drought-responsive genotypes of maize at physiological and transcriptomic levels

“…Pathway advancement examination utilized Omic Share to determine extraordinarily upgraded metabolic pathways or sign transduction pathways in differentially communicated qualities. A hypergeometric test-taking FDR characterized extensively improved pathways in differentially communicated qualities ( Aleem et al., 2021 ).…”

“…Drought is one of the most detrimental environmental conditions, eventually lowering agricultural yields ( Anjum et al., 2016 ). During the vegetative phase, drought stress can limit growth rate, extend the vegetative development stage, and change the distribution of carbohydrates in maize ( Aleem et al., 2021 ).…”

Transcriptome Time-Course Analysis in the Whole Period of Cotton Fiber Development

“…Nowadays, the accumulating evidence supports that the regulation of RNA transcription significantly plays pivotal functions in plant growth and development. To date, RNA-seq has been widely employed in the crops to understand its response to drought, salinity, developmental stages, verticillium wilt, useful to analyze the gene expression and molecular mechanisms underlying various traits ( Shankar et al, 2016 ; Li et al, 2017a ; Aleem et al, 2021 ). Based on the analysis of the transcriptome profiling between drought-tolerant and sensitive soybean genotype, 10 DEGs were recognized as putative candidate genes modifying drought tolerance in soybean ( Aleem et al, 2021 ).…”

“…To date, RNA-seq has been widely employed in the crops to understand its response to drought, salinity, developmental stages, verticillium wilt, useful to analyze the gene expression and molecular mechanisms underlying various traits ( Shankar et al, 2016 ; Li et al, 2017a ; Aleem et al, 2021 ). Based on the analysis of the transcriptome profiling between drought-tolerant and sensitive soybean genotype, 10 DEGs were recognized as putative candidate genes modifying drought tolerance in soybean ( Aleem et al, 2021 ). In rice, transcriptomes comparison of a drought-tolerant (N22) and a salinity-tolerant (Pokkali) rice cultivar revealed some common and exclusive metabolic pathways, which may be important for desiccation and/or salinity stress tolerance ( Shankar et al, 2016 ).…”