Differential expression of micro<scp>RNA</scp>s and other small <scp>RNA</scp>s in barley between water and drought conditions

Hackenberg, Michael; Gustafson, Perry; Langridge, Peter; Shi, Bu‐Jun

doi:10.1111/pbi.12220

Cited by 151 publications

(133 citation statements)

References 56 publications

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“…The abundance of small RNA reads in the control libraries of the two species was comparable to those reported in Lagenaria siceraria, Cucurbita moschata, Cucurbita pepo and watermelon (Jagadeeswaran et al 2012). However, control and drought stress libraries of Medicago truncatula and Hordeum vulgare were reported to show the highest peak of small RNA reads at 24-nt and second highest reads for 21-nt size class Hackenberg et al 2015). Similar kind of size distribution of drought stressed small RNA libraries of the two species in this study have been observed with the highest peak of total small RNA reads at 24-nt followed by 21-nt size class (Figs.…”

Section: Resultssupporting

confidence: 75%

MicroRNA dynamics in a wild and cultivated species of Convolvulaceae exposed to drought stress

Ghorecha

Zheng

Liu

et al. 2017

Physiol Mol Biol Plants

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Agricultural productivity is severely hampered by drought in many parts of the globe. It is well-known that wild plant species can tolerate drought better when compared with their closely related cultivated plant species. Better drought adaptation of wild species over cultivated ones is accounted for their ability to differentially regulate gene expression. miRNAs, known to regulate gene expression at the post-transcriptional level, are admitted to play an important role in plant adaptation to stresses. This study aims at evaluating miRNA dynamics in a droughttolerant wild Ipomoea campanulata L. and drought-sensitive cultivated Jacquemontia pentantha (Jacq.) of the family Convolvulaceae under ex situ drought. Sequencing profiles revealed that 34 conserved miRNA families were analogous between the two species. Drought altered expression levels of several of these miRNAs in both the species. Drought-tolerant I. campanulata showed upregulation of miR398, miR168, miR858, miR162 and miR408, while miR394 and miR171 were downregulated. Droughtsensitive J. pentantha showed upregulation of miR394, miR156, miR160, miR164, miR167, miR172, miR319, miR395, miR396, miR403 and downregulation of miR157. Basal miRNA levels and their drought mediated regulation were very different between the two species. Differential drought sensitivities of these two plant species can be attributed to these innate variations in miRNA levels and their expression.

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Section: Resultssupporting

confidence: 75%

MicroRNA dynamics in a wild and cultivated species of Convolvulaceae exposed to drought stress

Ghorecha

Zheng

Liu

et al. 2017

Physiol Mol Biol Plants

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“…In general, low-count miRNAs are considered to have weak or low biological importance or mRNA degradation effect [51], because these low-count miRNAs have a quick turnover in evolution [52]. In our study sRNA turnover or degradation may better explain why few and low abundance transgene-derived reads were obtained in the libraries of the transformed peanut lines.…”

Section: Discussionmentioning

confidence: 84%

Characterization of small RNA populations in non-transgenic and aflatoxin-reducing-transformed peanut

et al. 2017

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Power, Imana L.; Dang, Phat M.; Sobolev, Victor S.; Orner, Valerie; Powell, Joseph L.; Lamb, Marshall C.; and Arias, Renée S., "Characterization of small RNA populations in non-transgenic andaflatoxin-reducing-transformed peanut" (2017 t r a c tAflatoxin contamination is a major constraint in food production worldwide. In peanut (Arachis hypogaea L.), these toxic and carcinogenic aflatoxins are mainly produced by Aspergillus flavus Link and A. parasiticus Speare. The use of RNA interference (RNAi) is a promising method to reduce or prevent the accumulation of aflatoxin in peanut seed. In this study, we performed high-throughput sequencing of small RNA populations in a control line and in two transformed peanut lines that expressed an inverted repeat targeting five genes involved in the aflatoxin-biosynthesis pathway and that showed up to 100% less aflatoxin B 1 than the controls. The objective was to determine the putative involvement of the small RNA populations in aflatoxin reduction. In total, 41 known microRNA (miRNA) families and many novel miRNAs were identified. Among those, 89 known and 10 novel miRNAs were differentially expressed in the transformed lines. We furthermore found two small interfering RNAs derived from the inverted repeat, and 39 sRNAs that mapped without mismatches to the genome of A. flavus and were present only in the transformed lines. This information will increase our understanding of the effectiveness of RNAi and enable the possible improvement of the RNAi technology for the control of aflatoxins.

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“…During the last few years, an emerging number of drought-related miRNAs have been reported in several crop plants, such as barley (Hordeum vulgare; Hackenberg et al, 2015), rice (Oryza sativa; Zhou et al, 2010;BarreraFigueroa et al, 2012), cotton (Xie et al, 2015), potato (Solanum tuberosum; Zhang et al, 2014), maize (Zea mays; Li et al, 2013b), tomato (Candar-Cakir et al, 2016), cowpea (Vigna unguiculata; Barrera-Figueroa et al, 2011), peach (Prunus persica; Eldem et al, 2012), and poplar Ren et al, 2012). Recently, Sun et al (2015) described changes in grape miRNA abundance induced by cold stress and Pantaleo et al (2016) characterized novel miRNAs in virus-infected grapevine contemporaneously subjected to water stress.…”

Section: Conserved and Novel Grapevine Mirnas Respond To Ds In The Twmentioning

confidence: 99%

The Accumulation of miRNAs Differentially Modulated by Drought Stress Is Affected by Grafting in Grapevine

et al. 2017

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Grapevine (Vitis vinifera) is routinely grafted, and rootstocks inducing drought tolerance represent a source for adapting vineyards to climate change in temperate areas. Our goal was to investigate drought stress effects on microRNA (miRNA) abundance in a drought-resistant grapevine rootstock, M4 (Vitis vinifera 3 Vitis berlandieri), compared with a commercial cultivar, Cabernet Sauvignon, using their autografts and reciprocal grafts. RNA extracted from roots and leaves of droughted and irrigated plants of different graft combinations was used to prepare cDNA libraries for small RNA sequencing and to analyze miRNAs by quantitative real-time polymerase chain reaction (RT-qPCR). Measurements of leaf water potential, leaf gas exchange, and root hydraulic conductance attested that, under irrigation, M4 reduced water loss in comparison with cultivar Cabernet Sauvignon mostly through nonhydraulic, root-specific mechanisms. Under drought, stomatal conductance decreased at similar levels in the two genotypes. Small RNA sequencing allowed the identification of 70 conserved miRNAs and the prediction of 28 novel miRNAs. Different accumulation trends of miRNAs, observed upon drought and in different genotypes and organs, were confirmed by RT-qPCR. Corresponding target transcripts, predicted in silico and validated by RT-qPCR, often showed opposite expression profiles than the related miRNAs. Drought effects on miRNA abundance differed between the two genotypes. Furthermore, the concentration of drought-responsive miRNAs in each genotype was affected by reciprocal grafting, suggesting either the movement of signals inducing miRNA expression in the graft partner or, possibly, miRNA transport between scion and rootstock. These results open new perspectives in the selection of rootstocks for improving grapevine adaptation to drought.

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Differential expression of microRNAs and other small RNAs in barley between water and drought conditions

Cited by 151 publications

References 56 publications

MicroRNA dynamics in a wild and cultivated species of Convolvulaceae exposed to drought stress

MicroRNA dynamics in a wild and cultivated species of Convolvulaceae exposed to drought stress

Characterization of small RNA populations in non-transgenic and aflatoxin-reducing-transformed peanut

The Accumulation of miRNAs Differentially Modulated by Drought Stress Is Affected by Grafting in Grapevine

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