Integrated Analysis of Metabolome and Transcriptome Reveals Insights for Cold Tolerance in Rapeseed (Brassica napus L.)

Abstract

Rapeseed (Brassica napus L.) is an important oilseed crop in the world. Its productivity is significantly influenced by numerous abiotic stresses, including cold stress (CS). Consequently, enhancement in CS tolerance is becoming an important area for agricultural investigation and crop improvement. Therefore, the current study aimed to identify the stress-responsive genes, metabolites, and metabolic pathways based on a combined transcriptome and metabolome analysis to understand the CS responses and tolerance mechanisms in the cold-tolerant (C18) and cold-sensitive (C6) rapeseed varieties. Based on the metabolome analysis, 31 differentially accumulated metabolites (DAMs) were identified between different comparisons of both varieties at the same time points. From the transcriptome analysis, 2,845, 3,358, and 2,819 differentially expressed genes (DEGs) were detected from the comparison of C6-0 vs. C18-0, C6-1 vs. C18-1, and C6-7 vs. C18-7. By combining the transcriptome and metabolome data sets, we found that numerous DAMs were strongly correlated with several differentially expressed genes (DEGs). A functional enrichment analysis of the DAMs and the correlated DEGs specified that most DEGs and DAMs were mainly enriched in diverse carbohydrates and amino acid metabolisms. Among them, starch and sucrose metabolism and phenylalanine metabolism were significantly enriched and played a vital role in the CS adaption of rapeseed. Six candidate genes were selected from the two pathways for controlling the adaption to low temperature. In a further validation, the T-DNA insertion mutants of their Arabidopsis homologous, including 4cl3, cel5, fruct4, ugp1, axs1, and bam2/9, were characterized and six lines differed significantly in levels of freezing tolerance. The outcome of the current study provided new prospects for the understanding of the molecular basis of CS responses and tolerance mechanisms in rapeseed and present a set of candidate genes for use in improving CS adaptability in the same plant.

Comprehensive In Silico Characterization and Expression Profiling of TCP Gene Family in Rapeseed

“…Rapeseed is an allotetraploid crop that practices broad genome replication and combination activities ( Song et al, 2020 ). Nevertheless, rapeseed yield is pretentious by numerous environmental factors such as cold, heat, drought, salinity, and heavy metals toxicity ( Raza et al, 2021a ; Raza et al, 2021b ; He et al, 2021 ; Raza, 2021 ; Su et al, 2021 ). The TCP TFs are antique plant-specific proteins ( Cubas et al, 1999 ).…”

Phenylalanine Ammonia-Lyase (PAL) Genes Family in Wheat (Triticum aestivum L.): Genome-Wide Characterization and Expression Profiling

“…Phenylalanine ammonia-lyase (PAL) produces precursors of various secondary metabolites, including lignin, phytoalexin, and phenolic compounds. This gene family is also associated with the production of the first enzyme of the phenylpropanoid pathway [1][2][3]. PAL genes have a molecular mass in the range of 270-330 kilodalton (kDa) and are present in higher plants, yeast, some bacteria, and fungi.…”

Advances in “Omics” Approaches for Improving Toxic Metals/Metalloids Tolerance in Plants

“…The term transcriptomics refers to a set of techniques that are used to study the RNA transcripts in an organism. Several transcriptomic techniques are widely used to measure the abundance of the transcripts of interest ( Lowe et al, 2017 ; Mehmood et al, 2021 ; Raza et al, 2021c ). Studies have shown that stress-induced changes in gene expression may lead to the synthesis of novel proteins, stress mediating metabolic compounds, or encode transcription factors (TFs), which help to regulate the stress-responsive genes ( Table 4 ).…”