Novel insights into expansion and functional diversification of MIR169 family in tomato

Rao, Sombir; Balyan, Sonia; Jha, Sarita; Mathur, Saloni

doi:10.1007/s00425-020-03346-w

Cited by 42 publications

(23 citation statements)

References 92 publications

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“…Diamonds, ellipses, and arrowheads represent the KEGG pathways, target genes, and miRNAs, respectively. Luan et al, 2015;Hanemian et al, 2016;Du et al, 2017;Li et al, 2017;Serivichyaswat et al, 2017;Rao et al, 2020). However, to the best of our knowledge, there are no reports describing the involvement of miR169 in the male sterility of soybean or other plant species.…”

Section: Mir169 May Regulate Pollen Development In Cytoplasmic Male Sterile Soybeanmentioning

confidence: 98%

MicroRNAs Involved in Regulatory Cytoplasmic Male Sterility by Analysis RNA-seq and Small RNA-seq in Soybean

Zhang

Lin

et al. 2021

Front. Genet.

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Cytoplasmic male sterility (CMS) is an important plant characteristic for exploiting heterosis to enhance crop traits during breeding. However, the CMS regulatory network remains unclear in plants, even though researchers have attempted to isolate genes associated with CMS. In this study, we performed high-throughput sequencing and degradome analyses to identify microRNAs (miRNAs) and their targets in a soybean CMS line (JLCMS9A) and its maintainer line (JLCMS9B). Additionally, the differentially expressed genes during reproductive development were identified using RNA-seq data. A total of 280 miRNAs matched soybean miRNA sequences in miRBase, including mature miRNAs and pre-miRNAs. Of the 280 miRNAs, 30, 23, and 21 belonged to the miR166, miR156, and miR171 families, respectively. Moreover, 410 novel low-abundant miRNAs were identified in the JLCMS9A and JLCMS9B flower buds. Furthermore, 303 and 462 target genes unique to JLCMS9A and JLCMS9B, respectively, as well as 782 common targets were predicted based on the degradome analysis. Target genes differentially expressed between the CMS line and the maintainer line were revealed by an RNA-seq analysis. Moreover, all target genes were annotated with diverse functions related to biological processes, cellular components, and molecular functions, including transcriptional regulation, the nucleus, meristem maintenance, meristem initiation, cell differentiation, auxin-activated signaling, plant ovule development, and anther development. Finally, a network was built based on the interactions. Analyses of the miRNA, degradome, and transcriptome datasets generated in this study provided a comprehensive overview of the reproductive development of a CMS soybean line. The data presented herein represent useful information for soybean hybrid breeding. Furthermore, the study results indicate that miRNAs might contribute to the soybean CMS regulatory network by modulating the expression of CMS-related genes. These findings lay the foundation for future studies on the molecular mechanisms underlying soybean CMS.

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Section: Mir169 May Regulate Pollen Development In Cytoplasmic Male Sterile Soybeanmentioning

confidence: 98%

MicroRNAs Involved in Regulatory Cytoplasmic Male Sterility by Analysis RNA-seq and Small RNA-seq in Soybean

Zhang

Lin

et al. 2021

Front. Genet.

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“…The researchers also reported that the over-expression of GmNF-YA3 in Arabidopsis resulted in increased sensitivity to salinity and ABA stresses [40]. Tomato miR169 overexpression lines induced drought stress through its four targets NF-YA1/2/3 and multidrug resistance-associated protein gene 1 (MRP1), which were all down-regulated [42]. Constitutive over-expression of tomato miR169c improved drought stress tolerance as compared to wild-type plants through reduction of leaf water loss, the stomatal opening, and transpiration rate [42].…”

Section: Mirnas In Abiotic Stress Tolerancementioning

confidence: 99%

“…Tomato miR169 overexpression lines induced drought stress through its four targets NF-YA1/2/3 and multidrug resistance-associated protein gene 1 (MRP1), which were all down-regulated [42]. Constitutive over-expression of tomato miR169c improved drought stress tolerance as compared to wild-type plants through reduction of leaf water loss, the stomatal opening, and transpiration rate [42]. The Agrostis stolonifera plants overexpressing a miR319 rice gene Osa-miR319a, increased their wax contents in leaves for the retention of water and reduced their Na + ion uptake.…”

Section: Mirnas In Abiotic Stress Tolerancementioning

confidence: 99%

“…Gene expression analysis indicated that the enhanced abiotic stress tolerance can be attributed to a significant down-regulation of at least four putative turf miR319 target genes, teosinte branched/cycloidea/proliferating factors (TCP) AsPCF5, AsPCF6, AsPCF8, AsTCP14, and a homolog of a rice NAC (NAM, ATAF, and CUC) domain gene AsNAC60 [42][43][44]. Additionally, overexpression of Osa-miR319 enhanced leaf size, enlarged stem size, and reduced the number of tillers of Agrostis stolonifera [43].…”

Section: Mirnas In Abiotic Stress Tolerancementioning

confidence: 99%

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Transgenic Breeding Approaches for Improving Abiotic Stress Tolerance: Recent Progress and Future Perspectives

Anwar

Kim

2020

IJMS

107

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The recent rapid climate changes and increasing global population have led to an increased incidence of abiotic stress and decreased crop productivity. Environmental stresses, such as temperature, drought, nutrient deficiency, salinity, and heavy metal stresses, are major challenges for agriculture, and they lead to a significant reduction in crop growth and productivity. Abiotic stress is a very complex phenomenon, involving a variety of physiological and biochemical changes in plant cells. Plants exposed to abiotic stress exhibit enhanced levels of ROS (reactive oxygen species), which are highly reactive and toxic and affect the biosynthesis of chlorophyll, photosynthetic capacity, and carbohydrate, protein, lipid, and antioxidant enzyme activities. Transgenic breeding offers a suitable alternative to conventional breeding to achieve plant genetic improvements. Over the last two decades, genetic engineering/transgenic breeding techniques demonstrated remarkable developments in manipulations of the genes for the induction of desired characteristics into transgenic plants. Transgenic approaches provide us with access to identify the candidate genes, miRNAs, and transcription factors (TFs) that are involved in specific plant processes, thus enabling an integrated knowledge of the molecular and physiological mechanisms influencing the plant tolerance and productivity. The accuracy and precision of this phenomenon assures great success in the future of plant improvements. Hence, transgenic breeding has proven to be a promising tool for abiotic stress improvement in crops. This review focuses on the potential and successful applications, recent progress, and future perspectives of transgenic breeding for improving abiotic stress tolerance and productivity in plants.

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“…The miR169 family is evolutionarily conserved and reported in several plant species (Guo et al 2020;Sunkar and Jagadeeswaran 2008). In addition, miR169 has also been shown to regulate several developmental, abiotic and biotic stress response pathways, including cold stress (Du et al 2017;Li et al 2008;Lee et al 2010;Rao et al 2020;Song et al 2018;Yu et al 2019;Zhao et al 2011, Zhou et al 2008. miR169 family targets NUCLEAR FACTOR Y (NF-YA), a heterotrimeric transcription factor composed of NF-YA, NF-YB and NF-YC proteins ( Ni et al 2013, Petroni et al 2012.…”

Section: Mir169-nf-ya Module Is Altered In Slr1 Under Low Temperaturementioning

confidence: 99%

Deciphering miRNAs involved in crosstalk between auxin and cold stress in Arabidopsis roots

Aslam

Sakai

Qin

et al. 2020

Preprint

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The phytohormone auxin and microRNA-mediated regulation of gene expressions are key regulators for plant growth and development at both optimal and under low-temperature stress conditions. However, the mechanistic link between microRNA and auxin in regulating plant cold stress response remains elusive. To better understand the role of microRNA in the crosstalk between auxin and cold stress responses, we took advantage of the mutants of Arabidopsis thaliana with altered response to auxin transport and signal. Screening of the mutants for root growth recovery after cold stress at 4°C revealed that the auxin signaling mutant, solitary root 1 ( slr1; mutation in Aux/IAA14), shows a hypersensitive response to cold stress. Genome-wide expression analysis of miRNA in wild-type and slr1 mutant roots using next-generation deep sequencing revealed 180 known and 86 novel cold-responsive microRNAs. Cold stress also increased the abundance of 26nt-31nt small RNA population in slr1 compared with wild-type. Comparative analysis of microRNA expression shows differential expression of 13 miRNAs in slr1 compared with wild-type. Target gene expression analysis of one of the potential candidate miRNAs, miR169 revelaed the possible involvement of miR169- NF-YA module in the auxin-mediated cold stress response. Taken together, these results indicate that SLR/IAA14, a transcriptional repressor of auxin signaling, plays a crucial role in integrating miRNA in auxin and cold responses.

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Novel insights into expansion and functional diversification of MIR169 family in tomato

Abstract: Expansion of MIR169 members by duplication and new mature forms, acquisition of new promoters, differential precursor-miRNA processivity and engaging novel targets increases the functional diversification of MIR169 in tomato. (29/30

Cited by 42 publications

References 92 publications

MicroRNAs Involved in Regulatory Cytoplasmic Male Sterility by Analysis RNA-seq and Small RNA-seq in Soybean

MicroRNAs Involved in Regulatory Cytoplasmic Male Sterility by Analysis RNA-seq and Small RNA-seq in Soybean

Transgenic Breeding Approaches for Improving Abiotic Stress Tolerance: Recent Progress and Future Perspectives

Deciphering miRNAs involved in crosstalk between auxin and cold stress in Arabidopsis roots

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