<i>SWP1</i>negatively regulates lateral root initiation and elongation in Arabidopsis

Singh, Sharmila; Singh, Archita; Roy, Shradha; Sarkar, Ananda K.

doi:10.4161/psb.22099

Cited by 34 publications

(17 citation statements)

References 27 publications

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“…Within the dataset were 86 loci encoding protein kinases and components of protein phosphorylation activity that include BRL1 , involved in brassinosteroid-mediated regulation of root development 29 , BAM3 , a receptor-like kinase influencing root meristem growth 30 , and RPK2 , a modulator of cell proliferation in the root meristem 31 . Another 22 DMGs were involved in the regulation of root development, including TIR1 , an auxin receptor 32 , LDL1 , a histone modifier 33 , the auxin-regulated transcription factor NPH4 34 , and the receptor-like kinase CRINKLY4 ( ACR4 ) 35 . At least ten identified loci participate in basipetal auxin transport, including D6 PROTEIN KINASE-LIKE 2 ( D6PKL2 ) and ABCB3 , 6 , 11 , 12 , 14 , 19 , and 20 , a series of ABC B-family transporters of auxin 36 .…”

Section: Resultsmentioning

confidence: 99%

MSH1-induced heritable enhanced growth vigor through grafting is associated with the RdDM pathway in plants

et al. 2020

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Plants transmit signals long distances, as evidenced in grafting experiments that create distinct rootstock-scion junctions. Noncoding small RNA is a signaling molecule that is graft transmissible, participating in RNA-directed DNA methylation; but the meiotic transmissibility of graft-mediated epigenetic changes remains unclear. Here, we exploit the MSH1 system in Arabidopsis and tomato to introduce rootstock epigenetic variation to grafting experiments. Introducing mutations dcl2, dcl3 and dcl4 to the msh1 rootstock disrupts siRNA production and reveals RdDM targets of methylation repatterning. Progeny from grafting experiments show enhanced growth vigor relative to controls. This heritable enhancement-through-grafting phenotype is RdDM-dependent, involving 1380 differentially methylated genes, many within auxin-related gene pathways. Growth vigor is associated with robust root growth of msh1 graft progeny, a phenotype associated with auxin transport based on inhibitor assays. Large-scale field experiments show msh1 grafting effects on tomato plant performance, heritable over five generations, demonstrating the agricultural potential of epigenetic variation.

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Section: Resultsmentioning

confidence: 99%

MSH1-induced heritable enhanced growth vigor through grafting is associated with the RdDM pathway in plants

et al. 2020

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“…A modified procedure for RNA ligase-mediated rapid amplification of cDNA ends (5′ RACE) was followed with the GeneRacer Kit (ThermoFisher Scientific/Invitrogen, CA, USA) as described previously 10 . Total RNA was isolated using modified TRIzol ® Reagent (ThermoFischer Scientific/Ambion, USA) from the apple twig ( Malus domestica , cultivar Vance) and Glycine max (hybrid cultivar JS-335xUPSM-534) shoot and root tissues 60 . Plant material from the sequenced cultivars of Md m (Golden delicious) and Gma, which was used for sequence analysis, could not be availed.…”

Section: Methodsmentioning

confidence: 99%

Coevolution Pattern and Functional Conservation or Divergence of miR167s and their targets across Diverse Plant Species

Barik

Kumar

Das

et al. 2015

Sci Rep

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microRNAs (miRNAs), a class of endogenously produced small non-coding RNAs of 20–21 nt length, processed from precursor miRNAs, regulate many developmental processes by negatively regulating the target genes in both animals and plants. The coevolutionary pattern of a miRNA family and their targets underscores its functional conservation or diversification. The miR167 regulates various aspects of plant development in Arabidopsis by targeting ARF6 and ARF8. The evolutionary conservation or divergence of miR167s and their target genes are poorly understood till now. Here we show the evolutionary relationship among 153 MIR167 genes obtained from 33 diverse plant species. We found that out of the 153 of miR167 sequences retrieved from the “miRBase”, 27 have been annotated to be processed from the 3′ end, and have diverged distinctively from the other miR167s produced from 5′ end. Our analysis reveals that gma-miR167h/i and mdm-miR167a are processed from 3′ end and have evolved separately, diverged most resulting in novel targets other than their known ones, and thus led to functional diversification, especially in apple and soybean. We also show that mostly conserved miR167 sequences and their target AUXIN RESPONSE FACTORS (ARFs) have gone through parallel evolution leading to functional diversification among diverse plant species.

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“…To investigate if the isolated RNA is good enough for gene expression studies, we synthesized cDNA from amplified LCM-derived RNA obtained from embryonic RAMs. Since several genes, phytohormones, epigenetic factors, and miRNAs have been implicated in plant root development, few candidate genes and miRNAs were selected for their expression in Arabidopsis RAM 20 21 22 . Expression of constitutively expressed genes such as ACTIN4 (ACT4), TONOPLAST INTRINSIC PROTEIN (TIP41), ELONGATION FACTOR1α (EF1α) and At2g28390 , and tissue specific WUSCHEL RELATED HOMEOBOX5 (WOX5) and SHOOT MERISTEMLESS (STM) genes were studied using RT-PCR analysis.…”

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confidence: 99%

An Efficient LCM-Based Method for Tissue Specific Expression Analysis of Genes and miRNAs

Gautam

Singh

et al. 2016

Sci Rep

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Laser Capture Microdissection (LCM) is a powerful tool to isolate and study gene expression pattern of desired and less accessible cells or tissues from a heterogeneous population. Existing LCM-based methods fail to obtain high quality RNA including small RNAs from small microdissected plant tissue and therefore, are not suitable for miRNA expression studies. Here, we describe an efficient and cost-effective method to obtain both high quality RNA and miRNAs from LCM-derived embryonic root apical meristematic tissue, which is difficult to access. We have significantly modified and improved the tissue fixation, processing, sectioning and RNA isolation steps and minimized the use of kits. Isolated RNA was checked for quality with bioanalyzer and used for gene expression studies. We have confirmed the presence of 19-24 nucleotide long mature miRNAs using modified stem-loop RT-PCR. This modified LCM-based method is suitable for tissue specific expression analysis of both genes and small RNAs (miRNAs).

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SWP1negatively regulates lateral root initiation and elongation in Arabidopsis

Cited by 34 publications

References 27 publications

MSH1-induced heritable enhanced growth vigor through grafting is associated with the RdDM pathway in plants

MSH1-induced heritable enhanced growth vigor through grafting is associated with the RdDM pathway in plants

Coevolution Pattern and Functional Conservation or Divergence of miR167s and their targets across Diverse Plant Species

An Efficient LCM-Based Method for Tissue Specific Expression Analysis of Genes and miRNAs

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