Excess fertilizer responsive miRNAs revealed in Linum usitatissimum L

Melnikova, N. V.; Dmitriev, Alexey A.; Belenikin, Maxim S.; Speranskaya, A.S.; Krinitsina, A.A.; Rachinskaia, Olga A.; Lakunina, V. A.; Krasnov, George S.; Snezhkina, Anastasiya V.; Садритдинова, А. Ф.; Урошлев, Л. А.; Koroban, N. V.; Samatadze, Tatiana E.; Amosova, Аlexandra V.; Zelenin, A. V.; Muravenko, Olga V.; Bolsheva, Nadezhda L.; Kudryavtseva, Anna V.

doi:10.1016/j.biochi.2014.11.017

Cited by 34 publications

(28 citation statements)

References 38 publications

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“…Under different types of abiotic stress (drought, salinity, cold, UV, mechanical, and heat stress), up-regulation of miR168 expression (Bej and Basak, 2014;Sunkar, 2010) has been observed. The expression alterations of lusmiR168 under the excessive use of fertilizers have been studied extensively (Melnikova et al, 2014). Because the record of miRNA sequencing of Silybum marianum is not known and the study of these molecules in the genomes of medicinal plants is not very common as in crop plants, we decided to use further primer findings from the study of Hypericum perforatum.…”

Section: Characterisation Of Selected Mirnamentioning

confidence: 99%

Application of the RAPD and miRNA markers in the genotyping of Silybum marianum (L.) Gaertn.

Ražná¹,

Hlavačková

Bežo

et al. 2015

Acta fytotechn zootechn

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Two types of molecular markers based on randomly amplified DNA by RAPD-based assay and amplified microRNA by miRNA-based assay were applied for the genotyping of five accessions of Silybum marianum (L.) Gaertn. It was also verified the effectiveness of the isolation of genomic DNA by three commercially available isolation kits and two similar complex methods and their applicability for this medicinal herb. None of the commercial isolation kits provided the genomic DNA of sufficient quality and quantity. Applied originally designed CTAB method and modified CTAB method for purpose of DNA isolation from medicinal plants allowed to isolate DNA of required quality and of sufficient yield. RAPD-based DNA fingerprints, allowed to distinguish the individual genotypes of Silybum marianum. MicroRNA-based markers showed the cross-genera transferability potential and displayed sufficient level of polymorphism. Both types of molecular markers could be used as suitable tool for genotyping of milk thistle. However, because of the size of miRNA amplicons is the efficiency of miRNA-based markers PCR amplifications preferred and consequently less DNA quality-dependent which may be advantageous in view of the content of undesirable secondary metabolites in medicinal plants.

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Section: Characterisation Of Selected Mirnamentioning

confidence: 99%

Application of the RAPD and miRNA markers in the genotyping of Silybum marianum (L.) Gaertn.

Ražná¹,

Hlavačková

Bežo

et al. 2015

Acta fytotechn zootechn

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“…All the calculations were performed using the Analysis of Transcription of Genes software (Krasnov et al, 2011). For the evaluation of expression levels,

Δ C_{t}^{e f f}

and

Δ Δ C_{t}^{e f f}

values were calculated (Melnikova et al, 2015, 2016). …”

Section: Methodsmentioning

confidence: 99%

Glutathione S-transferases and UDP-glycosyltransferases Are Involved in Response to Aluminum Stress in Flax

et al. 2016

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About 30% of the world's ice-free land area is occupied by acid soils. In soils with pH below 5, aluminum (Al) releases to the soil solution, and becomes highly toxic for plants. Therefore, breeding of varieties that are resistant to Al is needed. Flax (Linum usitatissimum L.) is grown worldwide for fiber and seed production. Al toxicity in acid soils is a serious problem for flax cultivation. However, very little is known about mechanisms of flax resistance to Al and the genetics of this resistance. In the present work, we sequenced 16 transcriptomes of flax cultivars resistant (Hermes and TMP1919) and sensitive (Lira and Orshanskiy) to Al, which were exposed to control conditions and aluminum treatment for 4, 12, and 24 h. In total, 44.9–63.3 million paired-end 100-nucleotide reads were generated for each sequencing library. Based on the obtained high-throughput sequencing data, genes with differential expression under aluminum exposure were revealed in flax. The majority of the top 50 up-regulated genes were involved in transmembrane transport and transporter activity in both the Al-resistant and Al-sensitive cultivars. However, genes encoding proteins with glutathione transferase and UDP-glycosyltransferase activity were in the top 50 up-regulated genes only in the flax cultivars resistant to aluminum. For qPCR analysis in extended sampling, two UDP-glycosyltransferases (UGTs), and three glutathione S-transferases (GSTs) were selected. The general trend of alterations in the expression of the examined genes was the up-regulation under Al stress, especially after 4 h of Al exposure. Moreover, in the flax cultivars resistant to aluminum, the increase in expression was more pronounced than that in the sensitive cultivars. We speculate that the defense against the Al toxicity via GST antioxidant activity is the probable mechanism of the response of flax plants to aluminum stress. We also suggest that UGTs could be involved in cell wall modification and protection from reactive oxygen species (ROS) in response to Al stress in L. usitatissimum. Thus, GSTs and UGTs, probably, play an important role in the response of flax to Al via detoxification of ROS and cell wall modification.

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“…Library normalization was performed with total number of reads. The comparison of mRNA levels in N, P, and NPK libraries was carried out using fold change (normalized read count in NPK or P/normalized read count in N) and p-value ( χ 2 test) parameters [17]. …”

Section: Methodsmentioning

confidence: 99%

Gene expression profiling of flax (Linum usitatissimum L.) under edaphic stress

et al. 2016

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BackgroundCultivated flax (Linum usitatissimum L.) is widely used for production of textile, food, chemical and pharmaceutical products. However, various stresses decrease flax production. Search for genes, which are involved in stress response, is necessary for breeding of adaptive cultivars. Imbalanced concentration of nutrient elements in soil decrease flax yields and also results in heritable changes in some flax lines. The appearance of Linum Insertion Sequence 1 (LIS-1) is the most studied modification. However, LIS-1 function is still unclear.ResultsHigh-throughput sequencing of transcriptome of flax plants grown under normal (N), phosphate deficient (P), and nutrient excess (NPK) conditions was carried out using Illumina platform. The assembly of transcriptome was performed, and a total of 34924, 33797, and 33698 unique transcripts for N, P, and NPK sequencing libraries were identified, respectively. We have not revealed any LIS-1 derived mRNA in our sequencing data. The analysis of high-throughput sequencing data allowed us to identify genes with potentially differential expression under imbalanced nutrition. For further investigation with qPCR, 15 genes were chosen and their expression levels were evaluated in the extended sampling of 31 flax plants. Significant expression alterations were revealed for genes encoding WRKY and JAZ protein families under P and NPK conditions. Moreover, the alterations of WRKY family genes differed depending on LIS-1 presence in flax plant genome. Besides, we revealed slight and LIS-1 independent mRNA level changes of KRP2 and ING1 genes, which are adjacent to LIS-1, under nutrition stress.ConclusionsDifferentially expressed genes were identified in flax plants, which were grown under phosphate deficiency and excess nutrition, on the basis of high-throughput sequencing and qPCR data. We showed that WRKY and JAS gene families participate in flax response to imbalanced nutrient content in soil. Besides, we have not identified any mRNA, which could be derived from LIS-1, in our transcriptome sequencing data. Expression of LIS-1 flanking genes, ING1 and KRP2, was suggested not to be nutrient stress-induced. Obtained results provide new insights into edaphic stress response in flax and the role of LIS-1 in these process.Electronic supplementary materialThe online version of this article (doi:10.1186/s12870-016-0927-9) contains supplementary material, which is available to authorized users.

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Excess fertilizer responsive miRNAs revealed in Linum usitatissimum L

Cited by 34 publications

References 38 publications

Application of the RAPD and miRNA markers in the genotyping of Silybum marianum (L.) Gaertn.

Application of the RAPD and miRNA markers in the genotyping of Silybum marianum (L.) Gaertn.

Glutathione S-transferases and UDP-glycosyltransferases Are Involved in Response to Aluminum Stress in Flax

Gene expression profiling of flax (Linum usitatissimum L.) under edaphic stress

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