Integrated transcriptome and metabolome analyses of biochar-induced pathways in response to Fusarium wilt infestation in pepper

Zhu, Quanyong; Chen, Limin; Chen, Tingting; Qian, Xu; He, Tianjun; Wang, Yikun; Deng, Xianjun; Zhang, Sihai; Pan, Yiming; Jin, Aiwu

doi:10.1016/j.ygeno.2021.04.031

Cited by 17 publications

(9 citation statements)

References 73 publications

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“…Similarly, pepper plants in soils amended with bamboo biochar showed an improvement in plant photosynthesis, energy production, enhanced stress signaling pathways, as well as plant defenses, among others. These effects were tightly coordinated with the differential expression of genes and accumulation of metabolites involved in plant–pathogen interactions, photosynthesis, phenylpropanoid biosynthesis, and protein processing in the endoplasmic reticulum ( Zhu et al, 2021 ). Future research should contribute to increasing this mentioned knowledge in cereal crops.…”

Section: Biochar From Barleymentioning

confidence: 99%

Overview of the use of biochar from main cereals to stimulate plant growth

2022

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The total global food demand is expected to increase up to 50% between 2010 and 2050; hence, there is a clear need to increase plant productivity with little or no damage to the environment. In this respect, biochar is a carbon-rich material derived from the pyrolysis of organic matter at high temperatures with a limited oxygen supply, with different physicochemical characteristics that depend on the feedstock and pyrolysis conditions. When used as a soil amendment, it has shown many positive environmental effects such as carbon sequestration, reduction of greenhouse gas emissions, and soil improvement. Biochar application has also shown huge benefits when applied to agri-systems, among them, the improvement of plant growth either in optimal conditions or under abiotic or biotic stress. Several mechanisms, such as enhancing the soil microbial diversity and thus increasing soil nutrient-cycling functions, improving soil physicochemical properties, stimulating the microbial colonization, or increasing soil P, K, or N content, have been described to exert these positive effects on plant growth, either alone or in combination with other resources. In addition, it can also improve the plant antioxidant defenses, an evident advantage for plant growth under stress conditions. Although agricultural residues are generated from a wide variety of crops, cereals account for more than half of the world’s harvested area. Yet, in this review, we will focus on biochar obtained from residues of the most common and relevant cereal crops in terms of global production (rice, wheat, maize, and barley) and in their use as recycled residues to stimulate plant growth. The harvesting and processing of these crops generate a vast number and variety of residues that could be locally recycled into valuable products such as biochar, reducing the waste management problem and accomplishing the circular economy premise. However, very scarce literature focused on the use of biochar from a crop to improve its own growth is available. Herein, we present an overview of the literature focused on this topic, compiling most of the studies and discussing the urgent need to deepen into the molecular mechanisms and pathways involved in the beneficial effects of biochar on plant productivity.

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Section: Biochar From Barleymentioning

confidence: 99%

Overview of the use of biochar from main cereals to stimulate plant growth

2022

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“…Principal component analysis (PCA) and Pearson correlation were computed using the fragments per kilobase of transcript per million fragments mapped (FPKM) values in R with the packages corrplot and ggbiplot , respectively (R Core Team, 2018). To identify the differentially expressed genes (DEGs), a stringent threshold of log2 foldchange ǀlog2FCǀ ≥1 and false discovery rate (FDR) ≤ 0.05 ( Zhu et al, 2021 ) were adopted using DESeq2 package in R ( Love et al, 2014 ) ( Figure 1 ).…”

Section: Methodsmentioning

confidence: 99%

Transcriptome sequencing of Cocos nucifera leaves in response to Rhynchophorus ferrugineus infestation

2023

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Red palm weevil (RPW, Rhynchophorus ferrugineus) is an invasive pest of palms. In China, coconut (Cocos nucifera) production is being significantly affected by the RPW attack. To develop a long-term RPW control strategy, host-plant resistance is the most sustainable option. In this regard, the availability of transcriptome sequencing data from RPW-infected coconut plants can be highly useful. Therefore, the present study assessed coconut leaf physiological responses and transcriptional changes after different days of RPW attack i.e., 5, 10, 15, 20, and 25 days after infestation (DAI). A comparison of physiological data indicated that populations with the higher number of RPW insects i.e., population C (15 males +21 females) and D (20 males +28 females) triggered higher antioxidant enzyme activities. We used this data to study the transcriptomic responses on 5 and 20 DAI. Of the 38,432 detected transcripts, 3,984, 1,981, 3,925, and 2,257 were differentially expressed in CK (control/no RPW)_vs._C (5 DAI), CK_vs._D (5 DAI), CK_vs._C (20 DAI), and CK_vs._D (20 DAI), respectively. These transcripts were enriched in plant-pathogen interaction, phenylpropanoid/flavonoid biosynthesis, amino sugar and nucleotide sugar metabolism, plant hormone signal transduction, mitogen-activated protein kinase, and reactive oxygen scavenging pathway. We discuss these results and present several candidate genes to be manipulated for developing a sustainable strategy to control RPW attack regarding host-plant resistance. Furthermore, these findings provide a basis for developing effective early and late RPW attack detection strategies.

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“…Data quality and reproducibility were assessed by Pearson correlation and principal component analysis (PCA). The differentially accumulated metabolites (DAMs) were detected by application of partial least squares-discriminant analysis (PLSDA) with a threshold of log2FC ≥ 1 and variable importance of the projection (VIP) ≥ 1 [ 79 ].…”

Section: Methodsmentioning

confidence: 99%

“…The detected genes were annotated to a translation of the European Molecular Biology Laboratory (TrEMBL) [ 82 ], non-redundant (Nr) [ 83 ], EuKaryotic Orthologous Group (KOG) [ 84 ], gene ontology (GO) [ 85 ], protein families (Pfam) [ 86 ], SwissProt [ 87 ], Kyoto Encyclopedia of Genes and Genomes (KEGG) [ 88 ], and Plant transcription factors database (PlantTFDB) 3.0 [ 89 ]. Thresholds of log2 foldchange (log2FC) ≥ 1 and false discovery rate (FDR) ≤ 0.05 [ 79 ] were used to detect differentially expressed genes (DEGs) with the DESeq2 package in R [ 90 ]. Pearson correlation and principal components analyses were conducted in R with the packages corrplot and ggbiplot, respectively (R Core Team, 2018).…”

Section: Methodsmentioning

confidence: 99%

Combined Transcriptome and Metabolome Profiling Provide Insights into Cold Responses in Rapeseed (Brassica napus L.) Genotypes with Contrasting Cold-Stress Sensitivity

Liu

Wei

Tian

et al. 2022

IJMS

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Low temperature is a major environmental factor, which limits rapeseed (Brassica napus L.) growth, development, and productivity. So far, the physiological and molecular mechanisms of rapeseed responses to cold stress are not fully understood. Here, we explored the transcriptome and metabolome profiles of two rapeseed genotypes with contrasting cold responses, i.e., XY15 (cold-sensitive) and GX74 (cold-tolerant). The global metabolome profiling detected 545 metabolites in siliques of both genotypes before (CK) and after cold-stress treatment (LW). The contents of several sugar metabolites were affected by cold stress with the most accumulated saccharides being 3-dehydro-L-threonic acid, D-xylonic acid, inositol, D-mannose, D-fructose, D-glucose, and L-glucose. A total of 1943 and 5239 differentially expressed genes were identified from the transcriptome sequencing in XY15CK_vs_XY15LW and GX74CK_vs_GX74LW, respectively. We observed that genes enriched in sugar metabolism and biosynthesis-related pathways, photosynthesis, reactive oxygen species scavenging, phytohormone, and MAPK signaling were highly expressed in GX74LW. In addition, several genes associated with cold-tolerance-related pathways, e.g., the CBF-COR pathway and MAPK signaling, were specifically expressed in GX74LW. Contrarily, genes in the above-mentioned pathways were mostly downregulated in XY15LW. Thus, our results indicate the involvement of these pathways in the differential cold-stress responses in XY15 and GX74.

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Integrated transcriptome and metabolome analyses of biochar-induced pathways in response to Fusarium wilt infestation in pepper

Cited by 17 publications

References 73 publications

Overview of the use of biochar from main cereals to stimulate plant growth

Overview of the use of biochar from main cereals to stimulate plant growth

Transcriptome sequencing of Cocos nucifera leaves in response to Rhynchophorus ferrugineus infestation

Combined Transcriptome and Metabolome Profiling Provide Insights into Cold Responses in Rapeseed (Brassica napus L.) Genotypes with Contrasting Cold-Stress Sensitivity

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