Deciphering Ascorbic Acid Regulatory Pathways in Ripening Tomato Fruit Using a Weighted Gene Correlation Network Analysis Approach

Abstract

Genotype is generally determined by the co-expression of diverse genes and multiple regulatory pathways in plants. Gene co-expression analysis combining with physiological trait data provides very important information about the gene function and regulatory mechanism. L-Ascorbic acid (AsA), which is an essential nutrient component for human health and plant metabolism, plays key roles in diverse biological processes such as cell cycle, cell expansion, stress resistance, hormone synthesis, and signaling. Here, we applied a weighted gene correlation network analysis approach based on gene expression values and AsA content data in ripening tomato (Solanum lycopersicum L.) fruit with different AsA content levels, which leads to identification of AsA relevant modules and vital genes in AsA regulatory pathways. Twenty-four modules were compartmentalized according to gene expression profiling. Among these modules, one negatively related module containing genes involved in redox processes and one positively related module enriched with genes involved in AsA biosynthetic and recycling pathways were further analyzed. The present work herein indicates that redox pathways as well as hormone-signal pathways are closely correlated with AsA accumulation in ripening tomato fruit, and allowed us to prioritize candidate genes for follow-up studies to dissect this interplay at the biochemical and molecular level.

Molecular Characterization of a Supergene Conditioning Super-High Vitamin C in Kiwifruit Hybrids

“…This gene is annotated as a component of the dolichol-phosphate mannose synthase complex which mediates mannosylation of glycans[20]. Similar associations between competing carbohydrate metabolic pathway expression and fruit AsA have been reported in studies of tomato interspecific introgressions[21] and ripening[22].…”

Molecular Characterisation of a Supergene Conditioning Super-High Vitamin C in Kiwifruit Hybrids

“…This gene is annotated as a component of the dolichol-phosphate mannose synthase complex which mediates mannosylation of glycans [19]. Similar associations between competing carbohydrate metabolic pathway expression and fruit AsA have been reported in studies of tomato interspecific introgressions [20] and ripening [21].…”

Comparative Transcriptome Analysis of Different Dendrobium Species Reveals Active Ingredients-Related Genes and Pathways

“…Combining the WGCNA method and RNA-Seq data can be used to better mine the genes and transcription factors related to traits. In strawberry, modules related to tissue specificity such as torus were found in strawberry, and 7 hub genes were identified in torus tissue [37]; in tomato, genes related to vitamin C biosynthesis were found [50]; co-expression modules related to acidity and genes related to anthocyanin synthesis were found in apple [33,51]. In addition, specific modules in other tissues such as roots, leaves, flowers, and fruits at other periods can be excavated to find relevant metabolic processes and important genes and potential transcription factors.…”