Transcriptomic and metabolomic analyses reveal the potential mechanism of waterlogging resistance in cotton (Gossypium hirsutum L.)

Abstract

IntroductionCotton (Gossypium hirsutum L.) is susceptible to long-term waterlogging stress; however, genomic information of cotton response mechanisms toward long days of waterlogging is quite elusive.MethodsHere, we combined the transcriptome and metabolome expression level changes in cotton roots after 10 and 20 days of waterlogging stress treatment pertaining to potential resistance mechanisms in two cotton genotypes.Results and discussionNumerous adventitious roots and hypertrophic lenticels were induced in CJ1831056 and CJ1831072. Transcriptome analysis revealed 101,599 differentially expressed genes in cotton roots with higher gene expression after 20 days of stress. Reactive oxygen species (ROS) generating genes, antioxidant enzyme genes, and transcription factor genes (AP2, MYB, WRKY, and bZIP) were highly responsive to waterlogging stress among the two genotypes. Metabolomics results showed higher expressions of stress-resistant metabolites sinapyl alcohol, L-glutamic acid, galactaric acid, glucose 1-phosphate, L-valine, L-asparagine, and melibiose in CJ1831056 than CJ1831072. Differentially expressed metabolites (adenosine, galactaric acid, sinapyl alcohol, L-valine, L-asparagine, and melibiose) significantly correlated with the differentially expressed PRX52, PER1, PER64, and BGLU11 transcripts. This investigation reveals genes for targeted genetic engineering to improve waterlogging stress resistance to enhance abiotic stress regulatory mechanisms in cotton at the transcript and metabolic levels of study.

Transcriptomic and Metabolomic Analyses Reveal the Response Mechanism of Ophiopogon japonicus to Waterlogging Stress

“…In the context of waterlogging stress, different plant varieties can exhibit significant impacts on metabolic pathways and gene transcription levels. For instance, flood-tolerant onions demonstrated a higher prevalence of downregulated genes [ 37 ], while cotton displayed a robust response involving antioxidant enzyme genes and transcription factor genes after 20 days of waterlogging [ 14 ]. Similarly, waterlogging stress induced notable changes in gene expression and metabolites in CMD.…”

“…For example, onion ( Allium cepa L.) showed significant changes in the phenylalanine metabolic pathway, pathogenesis-related proteins, and energy production after 72 h of waterlogging treatment [ 37 ]. Cotton ( Gossypium hirsutum L.) showed a significant increase in several metabolites including sinapyl alcohol, adenosine, and galactaric acid after 10–20 days of waterlogging [ 14 ]. The mechanisms by which CMD responds to waterlogging stress are different from the literature, but there are similarities.…”

“…Comparatively, metabolomics is used to study alterations in the composition and content of metabolites within specific temporal and spatial contexts to establish connections between metabolites and physiological changes in plants. These powerful analytical tools have been instrumental in investigating diverse aspects of plant biology including the molecular mechanisms underlying plant growth, development, and the synthesis of active compounds [ 3 , 4 , 5 , 6 ], responses to pests and pathogens [ 7 , 8 , 9 , 10 ], and the tolerance mechanisms associated with abiotic stresses [ 11 , 12 , 13 , 14 ]. However, there is limited transcriptomic and metabolomic research on MD under conditions of waterlogging stress.…”

The Transcriptional Regulatory Mechanisms Exploration of Jujube Biological Traits through Multi-Omics Analysis

“…The expression levels of three sucrose phosphate synthase genes (ZjSPS1, scaffold1731.36; ZjSPS2, scaffold19851.46; and ZjSS2, scaffold41823.29) were found to be positively correlated with sucrose content in fruits [43]. [44] identified 19 ZjSWEET genes based on gene family analysis and observed that the expression levels of 2 genes (ZjSWEET11, LOC107404505 and ZjSWEET18, LOC107417626) progressively increased during fruit development, peaking at the full red fruit stage. Several other ZjSWEET genes were found to play vital roles in abiotic stress conditions.…”

“…In recent years, the advent of next-generation sequencing has revolutionized plant biology research, offering a cost-effective solution, even in non-model systems [17]. Secondgeneration sequencing data correlation analysis, particularly, has successfully unraveled molecular mechanisms governing the formation of multiple crop traits and the synthesis of biological components [18][19][20]. These methodologies have found widespread application in jujube studies.…”