Drought responsive microRNAs in two barley cultivars differing in their level of sensitivity to drought stress

Fard, Ehsan Mohseni; Oghan, Hassan Amiri; Keshavarznia, Reza; Nikpay, Nava; Shahbazi, Maryam; Salekdeh, Ghasem Hosseini

doi:10.1016/j.plaphy.2017.06.007

Cited by 38 publications

(17 citation statements)

References 49 publications

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“…Contrasting evidence was observed for IAA-related genes in response to salinity; while IAA-resistant leucine 1, PIN-FORMED 5 (PIN5), AFB2 , and Non-phototrophic hypocotyl (NPH4) were commonly repressed among the analyzed studies, UGT75B1, CAND1, JAR1 , AIR9 were upregulated. These data partially agree with previous findings showing an involvement of AIR9 and JAR1 in drought responses in barley through the action of miR2406 [ 26 ]. UGT75B1 is an auxin-related gene that controls cellular ABA content and activity through glycosylation.…”

Section: Discussionsupporting

confidence: 93%

Gaining Insight into Exclusive and Common Transcriptomic Features Linked to Drought and Salinity Responses across Fruit Tree Crops

Benny

Marchese

Giovino

et al. 2020

Plants

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The present study aimed at identifying and mapping key genes expressed in root tissues involved in drought and salinity tolerance/resistance conserved among different fruit tree species. Twenty-six RNA-Seq samples were analyzed from six published studies in five plant species (Olea europaea, Vitis riparia Michx, Prunus mahaleb, Prunus persica, Phoenix dactylifera). This meta-analysis used a bioinformatic pipeline identifying 750 genes that were commonly modulated in three salinity studies and 683 genes that were commonly regulated among three drought studies, implying their conserved role in resistance/tolerance/response to these environmental stresses. A comparison was done on the genes that were in common among both salinity and drought resulted in 82 genes, of which 39 were commonly regulated with the same trend of expression (23 were upregulated and 16 were downregulated). Gene set enrichment and pathway analysis pointed out that pathways encoding regulation of defense response, drug transmembrane transport, and metal ion binding are general key molecular responses to these two abiotic stress responses. Furthermore, hormonal molecular crosstalk plays an essential role in the fine-tuning of plant responses to drought and salinity. Drought and salinity induced a different molecular “hormonal fingerprint”. Dehydration stress specifically enhanced multiple genes responsive to abscisic acid, gibberellin, brassinosteroids, and the ethylene-activated signaling pathway. Salt stress mostly repressed genes encoding for key enzymes in signaling proteins in auxin-, gibberellin-(gibberellin 2 oxidase 8), and abscisic acid-related pathways (aldehyde oxidase 4, abscisic acid-responsive element-binding protein 3). Abiotic stress-related genes were mapped into the chromosome to identify molecular markers usable for the improvement of these complex quantitative traits. This meta-analysis identified genes that serve as potential targets to develop cultivars with enhanced drought and salinity resistance and/or tolerance across different fruit tree crops in a biotechnological sustainable way.

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Section: Discussionsupporting

confidence: 93%

Gaining Insight into Exclusive and Common Transcriptomic Features Linked to Drought and Salinity Responses across Fruit Tree Crops

Benny

Marchese

Giovino

et al. 2020

Plants

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“…In the past two decades, extensive studies revealed that, apart from their role in plant development, miRNAs also orchestrate plant innate immunity, leading to antiviral immunity or viral pathogenesis [36]. In barley, roles have been identified for miRNAs for plant development [37,38] and responses to abiotic stresses, such as drought [39][40][41][42][43], heat [44], phosphorus deficiency [45,46], and boron [47]. To our knowledge, our study is the first to identify miRNAs that change in response to a biotic stress.…”

Section: Discussionmentioning

confidence: 99%

Analysis of Small RNAs of Barley Genotypes Associated with Resistance to Barley Yellow Dwarf Virus

Jarošová

Singh

Chrpová

et al. 2020

Plants

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Barley yellow dwarf virus (BYDV) causes an often-devastating disease of cereals that is most effectively controlled by using plant genotypes that are resistant or tolerant to the virus. New barley lines Vir8:3 and Vir13:8, with pyramided resistance genes against different pathogens and resistance gene Ryd2 against BYDV, are currently being tested. Because microRNAs (miRNAs) are associated with antiviral plant defense, here we compared the miRNA profiles in these lines and in cultivar Wysor (carrying one resistance gene, Ryd2), with and without BYDV infection and after feeding by virus-free aphids, to determine whether the miRNA profile in the resistant variety bear similarities with the newly developed lines. The BYDV titer for each group was also determined and compared to the titer in sensitive cultivar Graciosa. Among 746 miRNAs identified in barley, 66 were known miRNAs, and 680 were novel. The expression of 73 miRNAs differed significantly after BYDV infection, including the strong, specific upregulation of novel miRNA10778 that was conserved across all the barley genotypes. This miRNA belongs to the H box and ACA box (H/ACA) snoR14 family of RNAs (Rf01280) and is associated with pseudourydilation. The expression of 48 miRNAs also differed depending on the barley genotype. The profile of miRNAs expressed in Vir8:3 and Vir13:8 in response to BYDV was similar and differed from that of Wysor. Insights into the expression patterns of miRNAs in response to BYDV in barley provided here will benefit further studies toward understanding the resistance mechanisms and developing novel strategies against virus infections.

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“…Widely-known examples include modules like miR167 and ARF (auxin response factors), regulating auxin signaling; miR156 and SPL (Squamosa promoter binding protein-like) transcription factors, regulating flowering time; miR398 and superoxide dismutases, regulating ROS scavenging; miR164 and HSPs, regulating cellular protein conformation [ 37 , 38 , 39 , 40 ]. Studies in cereals have also reported contrasting regulatory patterns of miRNA-mRNA modules between stress-tolerant and -sensitive genotypes [ 18 , 41 , 42 , 43 ]. The molecular functions of these modules have been linked to physiological and yield performance, confirming that miRNAs are promising candidates for crop improvement.…”

Section: Introductionmentioning

confidence: 99%

Integrated Analysis of Small RNA, Transcriptome, and Degradome Sequencing Reveals the Water-Deficit and Heat Stress Response Network in Durum Wheat

Liu

Able

2020

IJMS

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Water-deficit and heat stress negatively impact crop production. Mechanisms underlying the response of durum wheat to such stresses are not well understood. With the new durum wheat genome assembly, we conducted the first multi-omics analysis with next-generation sequencing, providing a comprehensive description of the durum wheat small RNAome (sRNAome), mRNA transcriptome, and degradome. Single and combined water-deficit and heat stress were applied to stress-tolerant and -sensitive Australian genotypes to study their response at multiple time-points during reproduction. Analysis of 120 sRNA libraries identified 523 microRNAs (miRNAs), of which 55 were novel. Differentially expressed miRNAs (DEMs) were identified that had significantly altered expression subject to stress type, genotype, and time-point. Transcriptome sequencing identified 49,436 genes, with differentially expressed genes (DEGs) linked to processes associated with hormone homeostasis, photosynthesis, and signaling. With the first durum wheat degradome report, over 100,000 transcript target sites were characterized, and new miRNA-mRNA regulatory pairs were discovered. Integrated omics analysis identified key miRNA-mRNA modules (particularly, novel pairs of miRNAs and transcription factors) with antagonistic regulatory patterns subject to different stresses. GO (Gene Ontology) and KEGG (Kyoto Encyclopedia of Genes and Genomes) enrichment analysis revealed significant roles in plant growth and stress adaptation. Our research provides novel and fundamental knowledge, at the whole-genome level, for transcriptional and post-transcriptional stress regulation in durum wheat.

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Drought responsive microRNAs in two barley cultivars differing in their level of sensitivity to drought stress

Cited by 38 publications

References 49 publications

Gaining Insight into Exclusive and Common Transcriptomic Features Linked to Drought and Salinity Responses across Fruit Tree Crops

Gaining Insight into Exclusive and Common Transcriptomic Features Linked to Drought and Salinity Responses across Fruit Tree Crops

Analysis of Small RNAs of Barley Genotypes Associated with Resistance to Barley Yellow Dwarf Virus

Integrated Analysis of Small RNA, Transcriptome, and Degradome Sequencing Reveals the Water-Deficit and Heat Stress Response Network in Durum Wheat

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