Insights into soybean transcriptome reconfiguration under hypoxic stress: Functional, regulatory, structural, and...

Area of Science:

• Plant Biology
• Molecular Genetics
• Agricultural Science

Background:

• Flooding stress significantly impacts global soybean (Glycine max) production due to reduced oxygen availability in waterlogged soils.
• Oxygen deficiency (hypoxia) is critical in plant tissues, affecting essential processes like mitochondrial aerobic respiration.
• Understanding soybean's response to hypoxia is crucial for developing flood-tolerant varieties and ensuring crop stability.

Purpose of the Study:

• To analyze conserved and divergent root transcriptional responses in flood-tolerant (Embrapa 45) and flood-sensitive (BR 4) soybean cultivars under hypoxic conditions.
• To characterize the structural and compositional evolution of soybean genes responding to hypoxia.
• To investigate the role of specific gene families and regulatory elements in soybean hypoxia tolerance.

Main Methods:

• RNA sequencing (RNA-seq) was employed to compare gene expression profiles between soybean cultivars under hypoxia.
• Quantitative real-time PCR (qRT-PCR) was used to validate RNA-seq findings, particularly for non-symbiotic hemoglobin.
• Structural and compositional analyses of differentially expressed genes, including promoter element frequency and codon usage, were performed.

Main Results:

• The flood-tolerant Embrapa 45 cultivar exhibited fewer up-regulated and more down-regulated genes compared to the sensitive BR 4 cultivar.
• Specific genes like phosphoglucomutase, N-terminal protein myristoylation, protein suppressor of phyA-105, and fibrillin were differentially induced.
• Divergence in gene structure was observed, particularly for non-symbiotic hemoglobin, and promoter analysis revealed differences in TATA box, ABREs, and CRT/DREs frequencies.

Conclusions:

• Soybean cultivars display distinct transcriptional strategies for coping with hypoxic stress, involving differential gene regulation and structural evolution.
• Amino acid metabolism, tRNA modifications, translation efficiency, and endoplasmic reticulum stress are implicated in soybean root responses to hypoxia.
• ABA-responsive elements (ABREs) may mediate gene expression independently of ABA under hypoxia in soybean roots.