Integrative transcriptomic and metabolomic data provide insights into gene networks associated with lignification in postharvest Lei bamboo shoots under low temperature

Hou, Dan; Lu, Hai‐Wen; Zhao, Zhongyu; Pei, Jialong; Yang, Huqing; Wu, Ai‐Min; Yu, Xiao Fang; Lin, Xinchun

doi:10.1016/j.foodchem.2021.130822

Cited by 31 publications

(19 citation statements)

References 39 publications

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“…The upregulated C4H expression is crucial. C4H greatly affects lignin synthesis and plays an important regulatory role in early lignin G/S differentiation ( Hou et al., 2022 ). The downregulated HCT expression and 1-caffeoylquinic acid accumulation were also well demonstrated.…”

Section: Resultsmentioning

confidence: 99%

Transcriptome and metabolome analyses reveal phenotype formation differences between russet and non-russet apples

Wang

Huo

et al. 2022

Front. Plant Sci.

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The apple is an economically important fruit, and fruit russeting is not conducive to its appearance. Although studies have examined fruit russeting, its mechanism remains unclear. Two apple strains of the F1 hybrid population derived from ‘Fuji’ and ‘Golden Delicious’ were used in this study. We found that the skin of russet apples was rough and fissured, while that of non-russet apples was smooth and waxy. Chemical staining, LC- and GC-MS showed that both lignin and suberin were increased in russet apple skin. Meanwhile, genes involved in lignin and suberin synthetic pathways were upregulated in russet apple skin. Additionally, we found many differentially expressed genes (DEGs1) involved in hormone biosynthesis and signaling and stress responses in the two apple strains. We found that WRKY13 may influence russeting by regulating lignin synthesis. Our study identified several candidate metabolites and genes, which will provide a good foundation for further research.

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Section: Resultsmentioning

confidence: 99%

Transcriptome and metabolome analyses reveal phenotype formation differences between russet and non-russet apples

Wang

Huo

et al. 2022

Front. Plant Sci.

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“…Similarly, the homologous genes of OsNAP and OsNAC10 are six and three in moso bamboo [ 209 , 210 , 211 ]. It is also noted that moso bamboo presented more duplication events during genome evolution than rice; many genes display a specific function such as floral organ development-related genes in bamboo, and their respective high homology genes in rice, lignin, jasmonic acid, and stress-responsive genes [ 212 ] have been reported in bamboo ( Figure 4 ). Bamboo growth requires indispensable energy resources and the integrity of the cell wall to perform normal physiochemical processes for maintaining bamboo’s fast growth ( Figure 4 ) [ 211 ].…”

Section: Understanding the Bamboos’ Tolerance Using Ngs And Metabolomementioning

confidence: 99%

Entailing the Next-Generation Sequencing and Metabolome for Sustainable Agriculture by Improving Plant Tolerance

Hou

Hussain

Imran

et al. 2022

IJMS

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Crop production is a serious challenge to provide food for the 10 billion individuals forecasted to live across the globe in 2050. The scientists’ emphasize establishing an equilibrium among diversity and quality of crops by enhancing yield to fulfill the increasing demand for food supply sustainably. The exploitation of genetic resources using genomics and metabolomics strategies can help generate resilient plants against stressors in the future. The innovation of the next-generation sequencing (NGS) strategies laid the foundation to unveil various plants’ genetic potential and help us to understand the domestication process to unmask the genetic potential among wild-type plants to utilize for crop improvement. Nowadays, NGS is generating massive genomic resources using wild-type and domesticated plants grown under normal and harsh environments to explore the stress regulatory factors and determine the key metabolites. Improved food nutritional value is also the key to eradicating malnutrition problems around the globe, which could be attained by employing the knowledge gained through NGS and metabolomics to achieve suitability in crop yield. Advanced technologies can further enhance our understanding in defining the strategy to obtain a specific phenotype of a crop. Integration among bioinformatic tools and molecular techniques, such as marker-assisted, QTLs mapping, creation of reference genome, de novo genome assembly, pan- and/or super-pan-genomes, etc., will boost breeding programs. The current article provides sequential progress in NGS technologies, a broad application of NGS, enhancement of genetic manipulation resources, and understanding the crop response to stress by producing plant metabolites. The NGS and metabolomics utilization in generating stress-tolerant plants/crops without deteriorating a natural ecosystem is considered a sustainable way to improve agriculture production. This highlighted knowledge also provides useful research that explores the suitable resources for agriculture sustainability.

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“…In addition, NAC, bHLH, bZIP, MYB, and WRKY were identified as critical TFs for shoot postharvest senescence, in which PheNAP2 and PheNAP3 were found to promote leaf senescence in Arabidopsis (Li X. et al, 2019). The expression of jasmonic acid (JA) biosynthesis related genes was highly consistent with that of lignin precursor biosynthesis genes under low temperature (LT), indicating a LT-lignification or LT-JA-lignification regulatory pathway existed in Lei bamboo shoots (Hou et al, 2022). However, the molecular mechanism affecting edible quality associated with carbohydrates in postharvest shoots is still unclear.…”

Section: Introductionmentioning

confidence: 99%

Multifaceted analyses reveal carbohydrate metabolism mainly affecting the quality of postharvest bamboo shoots

Yang

et al. 2022

Front. Plant Sci.

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Bamboo shoot is one of nutritious vegetables in China. However, the edible quality of fresh bamboo shoots deteriorates easily after harvest. Here, morphological, physiological, transcriptomic and microRNA sequencing analyses were conducted to investigate the postharvest characteristics of moso bamboo (Phyllostachys edulis) shoots. Rapid decreases of soluble sugars, structural polysaccharides and hydrolyzed tannins, and increases of lignin and condensed tannins were observed in the postharvest bamboo shoots. Differentially expressed genes (DEGs) and miRNAs with opposite trends were mainly enriched in structural polysaccharide metabolism, starch and sucrose metabolism and glycolysis pathways, which were consistent with the changes of carbohydrates. A co-expression network of carbohydrate metabolism was constructed, which was verified by qPCR and yeast one-hybrid (Y1H) assay. Furthermore, the function of one hub glycosyltransferase gene was validated in Arabidopsis, which confirmed that it was involved in xylan biosynthesis. These results are of great significance for revealing the carbohydrate metabolism mechanisms of postharvest bamboo shoots and provide a potential candidate gene for molecular breeding related to xylan in the future.

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Integrative transcriptomic and metabolomic data provide insights into gene networks associated with lignification in postharvest Lei bamboo shoots under low temperature

Cited by 31 publications

References 39 publications

Transcriptome and metabolome analyses reveal phenotype formation differences between russet and non-russet apples

Transcriptome and metabolome analyses reveal phenotype formation differences between russet and non-russet apples

Entailing the Next-Generation Sequencing and Metabolome for Sustainable Agriculture by Improving Plant Tolerance

Multifaceted analyses reveal carbohydrate metabolism mainly affecting the quality of postharvest bamboo shoots

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