Time Series RNA-seq in Pigeonpea Revealed the Core Genes in Metabolic Pathways under Aluminum Stress

Gao, Zhaoxu; Dong, Biying; Cao, Hongyan; He, Hang; Meng, Dong; Fu, Yujie

doi:10.3390/genes11040380

Cited by 9 publications

(7 citation statements)

References 48 publications

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“…Recent evidence showed that metabolic change plays an important role for cells to adapt to Al stress. Genome-wide transcriptional profiling revealed that a substantial amount of differentially expressed genes in response to Al stress are associated with metabolisms ( Fan et al, 2014 ; Xu et al, 2017 ; Gao et al, 2020 ). In rice bean ( Vigna umbellata ), Al-induced formate accumulation is responsible for Al toxicity, and VuFDH is a gene encoding formate dehydrogenase that catalyzes formate degradation, thereby conferring Al tolerance ( Lou et al, 2016a ).…”

Section: Introductionmentioning

confidence: 99%

The Tomato Transcription Factor SlNAC063 Is Required for Aluminum Tolerance by Regulating SlAAE3-1 Expression

Jin

Zhu

et al. 2022

Front. Plant Sci.

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Aluminum (Al) toxicity constitutes one of the major limiting factors of plant growth and development on acid soils, which comprises approximately 50% of potentially arable lands worldwide. When suffering Al toxicity, plants reprogram the transcription of genes, which activates physiological and metabolic pathways to deal with the toxicity. Here, we report the role of a NAM, ATAF1, 2 and CUC2 (NAC) transcription factor (TF) in tomato Al tolerance. Among 53 NAC TFs in tomatoes, SlNAC063 was most abundantly expressed in root apex and significantly induced by Al stress. Furthermore, the expression of SlNAC063 was not induced by other metals. Meanwhile, the SlNAC063 protein was localized at the nucleus and has transcriptional activation potentials in yeast. By constructing CRISPR/Cas9 knockout mutants, we found that slnac063 mutants displayed increased sensitivity to Al compared to wild-type plants. However, the mutants accumulated even less Al than wild-type (WT) plants, suggesting that internal tolerance mechanisms but not external exclusion mechanisms are implicated in SlNAC063-mediated Al tolerance in tomatoes. Further comparative RNA-sequencing analysis revealed that only 45 Al-responsive genes were positively regulated by SlNAC063, although the expression of thousands of genes (1,557 upregulated and 636 downregulated) was found to be affected in slnac063 mutants in the absence of Al stress. The kyoto encyclopedia of genes and genomes (KEGG) pathway analysis revealed that SlNAC063-mediated Al-responsive genes were enriched in “phenylpropanoid metabolism,” “fatty acid metabolism,” and “dicarboxylate metabolism,” indicating that SlNAC063 regulates metabolisms in response to Al stress. Quantitative real-time (RT)-PCR analysis showed that the expression of SlAAE3-1 was repressed by SlNAC063 in the absence of Al. However, the expression of SlAAE3-1 was dependent on SlNAC063 in the presence of Al stress. Taken together, our results demonstrate that a NAC TF SlNAC063 is involved in tomato Al tolerance by regulating the expression of genes involved in metabolism, and SlNAC063 is required for Al-induced expression of SlAAE3-1.

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Section: Introductionmentioning

confidence: 99%

The Tomato Transcription Factor SlNAC063 Is Required for Aluminum Tolerance by Regulating SlAAE3-1 Expression

Jin

Zhu

et al. 2022

Front. Plant Sci.

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“…Pigeon pea grows in tropical and subtropical regions; acidic soil is widespread in these regions. Aluminum (Al) toxicity and drought are two major constraints on plant growth in acidic soil (Ahmed et al, 2018; Gao, Dong, et al, 2020). Drought can alleviate aluminum toxicity.…”

Section: Discussionmentioning

confidence: 99%

Genome‐wide identification and expression analysis of MYB gene family in Cajanus cajan and CcMYB107 improves plant drought tolerance

Yang

et al. 2023

Physiologia Plantarum

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MYB transcription factor (TF) is one of the largest superfamilies that play a vital role in multiple plant biological processes. However, the MYB family has not been comprehensively identified and functionally verified in Cajanus cajan, which is the sixth most important legume crop. Here, 170 CcR2R3‐MYBs were identified and divided into 43 functional subgroups. Segmental and tandem duplications and alternative splicing events were found and promoted the expansion of the CcR2R3‐MYB gene family. Functional prediction results showed that CcR2R3‐MYBs were mainly involved in secondary metabolism, cell fate and identity, developmental processes, and responses to abiotic stress. Cis‐acting element analysis of promoters revealed that stress response elements were widespread in the above four functional branches, further suggesting CcR2R3‐MYBs were extensively involved in abiotic stress response. The transcriptome data and qRT‐PCR results indicated that most of the CcR2R3‐MYB genes responded to various stresses, of which the expression of CcMYB107 was significantly induced by drought stress. Overexpression of CcMYB107 enhanced antioxidant enzyme activity and increased proline and lignin accumulation, thus improving the drought resistance of C. cajan. Furthermore, Overexpression of CcMYB107 up‐regulated the expression of stress‐related genes and lignin biosynthesis genes after drought stress. Our findings established a strong foundation for the investigation of biological function of CcR2R3‐MYB TFs in C. cajan.

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“…Pigeon pea (Cajanus cajan, Fabaceae) is widely cultivated for its nutritional and medicinal value in tropical and subtropical regions of Asia and Africa (Gao et al 2020). Pigeon pea is the second pulse crop in India and fourth in world in terms of area, yield, and production (FAOSTAT 2018).…”

Section: Introductionmentioning

confidence: 99%

Deciphering miRNA‐lncRNA‐mRNA interaction through experimental validation of miRNAs, lncRNAs, and miRNA targets on mRNAs in Cajanus cajan

Chowdhury,

Chatterjee,

Ghosh

et al. 2024

Plant Biol J

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Pigeon pea (Cajanus cajan) is widely cultivated for its nutritional and medicinal value yet remains an orphan crop as productivity has not been improved because of a lack of genome and non‐coding genome information. Non‐coding RNAs, like miRNAs and long non‐coding RNAs (lncRNAs), are involved in regulation of growth, metabolism, development, and stress response, and have a critical role in post‐transcriptional gene regulation (PTGR). We attempted to elucidate the roles of miRNAs and lncRNAs in pigeon pea through experimental validation of computationally predicted miRNAs and lncRNAs and targets of miRNAs on mRNAs. We experimentally validated 20 miRNAs and 11 lncRNAs. We predicted cleavage sites of three miRNA targets: serine/threonine‐protein kinase, polygalacturonase, beta‐galactosidase. We identified 469 targets of 265 miRNAs and their functional annotations using computational methods. We built a miRNA‐mRNA‐lncRNA network model, with the miRNAs targeting both mRNAs and lncRNAs, to obtain information on the interplay of these three molecules. A confirmed interaction through experimental validation was established between miRNA, namely cca‐miR1535a targeting the mRNA for beta‐galactosidase, as well as the lncRNA cca‐lnc‐020033. Our findings increase knowledge of the non‐coding genome of pigeon pea and their roles in PTGR and in improving agronomic traits of this pulse crop.

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Time Series RNA-seq in Pigeonpea Revealed the Core Genes in Metabolic Pathways under Aluminum Stress

Cited by 9 publications

References 48 publications

The Tomato Transcription Factor SlNAC063 Is Required for Aluminum Tolerance by Regulating SlAAE3-1 Expression

The Tomato Transcription Factor SlNAC063 Is Required for Aluminum Tolerance by Regulating SlAAE3-1 Expression

Genome‐wide identification and expression analysis of MYB gene family in Cajanus cajan and CcMYB107 improves plant drought tolerance

Deciphering miRNA‐lncRNA‐mRNA interaction through experimental validation of miRNAs, lncRNAs, and miRNA targets on mRNAs in Cajanus cajan

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