miRNAs for crop improvement

Raza, Ali; Charagh, Sidra; Karikari, Benjamin; Sharif, Rahat; Yadav, Vivek; Mubarik, Muhammad Salman; Habib, Madiha; Zhuang, Yuhui; Zhang, Chong; Chen, Hua; Varshney, Rajeev K.; Zhuang, Weijian

doi:10.1016/j.plaphy.2023.107857

Cited by 22 publications

(11 citation statements)

References 301 publications

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“…During recent years, due to the advance in epigenetics and sequencing technologies, people start to realize that small RNAs play important roles as post-transcriptional regulators and could be used for crop genetic improvement ( Navarro, 2016 ; Tang and Chu, 2017 ; Raza et al., 2023 ). In the current study, we used high-through-put sequencing and degradome to investigate changes on both transcript levels and microRNAs.…”

Section: Discussionmentioning

confidence: 99%

Multiomics analysis of a resistant European turnip ECD04 during clubroot infection reveals key hub genes underlying resistance mechanism

Zhou,

Zhong,

et al. 2024

Front. Plant Sci.

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The clubroot disease has become a worldwide threat for crucifer crop production, due to its soil-borne nature and difficulty to eradicate completely from contaminated field. In this study we used an elite resistant European fodder turnip ECD04 and investigated its resistance mechanism using transcriptome, sRNA-seq, degradome and gene editing. A total of 1751 DEGs were identified from three time points after infection, among which 7 hub genes including XTH23 for cell wall assembly and two CPK28 genes in PTI pathways. On microRNA, we identified 17 DEMs and predicted 15 miRNA-target pairs (DEM-DEG). We validated two pairs (miR395-APS4 and miR160-ARF) by degradome sequencing. We investigated the miR395-APS4 pair by CRISPR-Cas9 mediated gene editing, the result showed that knocking-out APS4 could lead to elevated clubroot resistance in B. napus. In summary, the data acquired on transcriptional response and microRNA as well as target genes provide future direction especially gene candidates for genetic improvement of clubroot resistance on Brassica species.

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Section: Discussionmentioning

confidence: 99%

Multiomics analysis of a resistant European turnip ECD04 during clubroot infection reveals key hub genes underlying resistance mechanism

Zhou,

Zhong,

et al. 2024

Front. Plant Sci.

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“…The miRNAs which are a class of small non-coding RNAs regulate gene expression through post-transcriptional modifications such as mRNA cleavage or translational inhibition, and they play critical roles in plant basic development and defense responses to environmental signals ( Raza et al, 2023 ). In this study, six different miRNAs were predicted to target 17 ARFs (7 SpapARFs and 10 SpnpARFs ).…”

Section: Discussionmentioning

confidence: 99%

Identification of ARF transcription factor gene family and its defense responses to bacterial infection and salicylic acid treatment in sugarcane

Lin,

Ali,

Chu

et al. 2023

Front. Microbiol.

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Auxin response factor (ARF) is a critical regulator in the auxin signaling pathway, involved in a variety of plant biological processes. Here, gene members of 24 SpapARFs and 39 SpnpARFs were identified in two genomes of Saccharum spontaneum clones AP85-441 and Np-X, respectively. Phylogenetic analysis showed that all ARF genes were clustered into four clades, which is identical to those ARF genes in maize (Zea mays) and sorghum (Sorghum bicolor). The gene structure and domain composition of this ARF family are conserved to a large degree across plant species. The SpapARF and SpnpARF genes were unevenly distributed on chromosomes 1–8 and 1–10 in the two genomes of AP85-441 and Np-X, respectively. Segmental duplication events may also contribute to this gene family expansion in S. spontaneum. The post-transcriptional regulation of ARF genes likely involves sugarcane against various stressors through a miRNA-medicated pathway. Expression levels of six representative ShARF genes were analyzed by qRT-PCR assays on two sugarcane cultivars [LCP85-384 (resistant to leaf scald) and ROC20 (susceptible to leaf scald)] triggered by Acidovorax avenae subsp. avenae (Aaa) and Xanthomonas albilineans (Xa) infections and salicylic acid (SA) treatment. ShARF04 functioned as a positive regulator under Xa and Aaa stress, whereas it was a negative regulator under SA treatment. ShARF07/17 genes played positive roles against both pathogenic bacteria and SA stresses. Additionally, ShARF22 was negatively modulated by Xa and Aaa stimuli in both cultivars, particularly LCP85-384. These findings imply that sugarcane ARFs exhibit functional redundancy and divergence against stressful conditions. This work lays the foundation for further research on ARF gene functions in sugarcane against diverse environmental stressors.

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“…Metabolomics investigations uncover the complicated metabolic changes that are essential for HMs' tolerance (Table 5). MicroRNAs are 21 nucleotides long non-coding RNAs that play a crucial role in plant growth and development and regulate gene expression at the post-transcriptional stage (Ding et al, 2020;Raza et al, 2023a).…”

Section: Understanding the Stress Responses And Tolerance Mechanisms ...mentioning

confidence: 99%

Unveiling Innovative Approaches to Mitigate Metals/Metalloids Toxicity for Sustainable Agriculture

Charagh,

Hui,

Wang

et al. 2024

Physiologia Plantarum

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Due to anthropogenic activities, environmental pollution of heavy metals/metalloids (HMs) has increased and received growing attention in recent decades. Plants growing in HM‐contaminated soils have slower growth and development, resulting in lower agricultural yield. Exposure to HMs leads to the generation of free radicals (oxidative stress), which alters plant morpho‐physiological and biochemical pathways at the cellular and tissue levels. Plants have evolved complex defense mechanisms to avoid or tolerate the toxic effects of HMs, including HMs absorption and accumulation in cell organelles, immobilization by forming complexes with organic chelates, extraction via numerous transporters, ion channels, signaling cascades, and transcription elements, among others. Nonetheless, these internal defensive mechanisms are insufficient to overcome HMs toxicity. Therefore, unveiling HMs adaptation and tolerance mechanisms is necessary for sustainable agriculture. Recent breakthroughs in cutting‐edge approaches such as phytohormone and gasotransmitters application, nanotechnology, omics, and genetic engineering tools have identified molecular regulators linked to HMs tolerance, which may be applied to generate HMs‐tolerant future plants. This review summarizes numerous systems that plants have adapted to resist HMs toxicity, such as physiological, biochemical, and molecular responses. Diverse adaptation strategies have also been comprehensively presented to advance plant resilience to HMs toxicity that could enable sustainable agricultural production.

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miRNAs for crop improvement

Cited by 22 publications

References 301 publications

Multiomics analysis of a resistant European turnip ECD04 during clubroot infection reveals key hub genes underlying resistance mechanism

Multiomics analysis of a resistant European turnip ECD04 during clubroot infection reveals key hub genes underlying resistance mechanism

Identification of ARF transcription factor gene family and its defense responses to bacterial infection and salicylic acid treatment in sugarcane

Unveiling Innovative Approaches to Mitigate Metals/Metalloids Toxicity for Sustainable Agriculture

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