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

Abstract

Soybean (Glycine max) is one of the major crops worldwide and flooding stress affects the production and expansion of cultivated areas. Oxygen is essential for mitochondrial aerobic respiration to supply the energy demand of plant cells. Because oxygen diffusion in water is 10,000 times lower than in air, partial (hypoxic) or total (anoxic) oxygen deficiency is important component of flooding. Even when oxygen is externally available, oxygen deficiency frequently occurs in bulky, dense or metabolically active tissues such as phloem, meristems, seeds, and fruits. In this study, we analyzed conserved and divergent root transcriptional responses between flood-tolerant Embrapa 45 and flood-sensitive BR 4 soybean cultivars under hypoxic stress conditions with RNA-seq. To understand how soybean genes evolve and respond to hypoxia, stable and differentially expressed genes were characterized structurally and compositionally comparing its mechanistic relationship. Between cultivars, Embrapa 45 showed less up- and more down-regulated genes, and stronger induction of phosphoglucomutase (Glyma05g34790), unknown protein related to N-terminal protein myristoylation (Glyma06g03430), protein suppressor of phyA-105 (Glyma06g37080), and fibrillin (Glyma10g32620). RNA-seq and qRT-PCR analysis of non-symbiotic hemoglobin (Glyma11g12980) indicated divergence in gene structure between cultivars. Transcriptional changes for genes in amino acids and derivative metabolic process suggest involvement of amino acids metabolism in tRNA modifications, translation accuracy/efficiency, and endoplasmic reticulum stress in both cultivars under hypoxia. Gene groups differed in promoter TATA box, ABREs (ABA-responsive elements), and CRT/DREs (C-repeat/dehydration-responsive elements) frequency. Gene groups also differed in structure, composition, and codon usage, indicating biological significances. Additional data suggests that cis-acting ABRE elements can mediate gene expression independent of ABA in soybean roots under hypoxia.

RNA-Seq reveals novel genes and pathways associated with hypoxia duration and tolerance in tomato root

“…NO production during hypoxia increases through different pathways including coordinated activity of the root-specific plasma membrane-bound nitrate reductase (PM-NR) and nitrite:NO reductase (NI-NOR) 51 , nitrate reductase (NR) and the mitochondrial electron transport chain 31,52 . The induction of NO after hypoxia in the root occurs rapidly, within minutes, and therefore it has been suggested to be involved in hypoxic stress response in the root 53 .…”

Systems protobiology: origin of life in lipid catalytic networks

“…Thus, a compositional assembly may contain sequential molecules, such as peptides. By the same token, the set of all mRNAs in a cell is often dealt with compositionally, as in the realm of transcriptome analyses [ 101 ]. So in a final account all biomolecules embody both sequential and compositional information, with different functional readouts for each information type.…”

Advances in Transcriptome Analyses Using RNA Sequencing Technology in Soybean Plants [Glycine max]

“…Song et al (2020) performed a genome-wide analysis of AS events in soybean roots grown under various drought conditions and identified 385, 989, 1 429, and 465 AS events that were significantly differentially spliced under very mild drought stress, mild drought stress, severe drought stress, and recovery after severe drought conditions, respectively. Nakayama et al (2017) analyzed root transcriptional responses between flood-tolerant (Embrapa 45) and flood-sensitive (BR4) soybean cultivars under hypoxic stress conditions with RNA-seq. Between cultivars, Embrapa 45 showed less up-and more down-regulated genes.…”