Identification and characterization of miRNAs and targets in flax (Linum usitatissimum) under saline, alkaline, and saline-alkaline stresses

Yu, Ying; Wu, Guangwen; Yuan, Hongmei; Cheng, Lili; Zhao, Dongsheng; Huang, Wengong; Zhang, Shuquan; Zhang, Liguo; Chen, Hongyu; Zhang, Jian; Feng-zhi, Guan

doi:10.1186/s12870-016-0808-2

Cited by 61 publications

(40 citation statements)

References 56 publications

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“…However, overexpression of WRKY45 in Arabidopsis increased phosphate uptake [35]. For flax, the involvement of WRKY family genes only in saline-alkaline stress response was known [36, 37]. In the present work, we revealed significant expression decrease of WRKY33 , WRKY40 , and WRKY70 under NPK compared to P conditions for flax genotypes without LIS-1 (‘Stormont cirrus’ without LIS-1 and ‘Bethune’).…”

Section: Discussionsupporting

confidence: 49%

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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Section: Discussionsupporting

confidence: 49%

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

et al. 2016

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“…Compared to saline soils (NaCl/Na 2 SO 4 ), alkaline soils are composed primarily of NaHCO 3 /Na 2 CO 3 . An increasing number of researches have suggested that bicarbonate/carbonate alkaline stress imposes much severer repression on plant growth through the complex damages derived from excess Na + , HCO 3 − /CO 3 2− , high-pH (> 8.5) and poor soil structure [ 2 ]. Hence, improving the bicarbonate/carbonate alkaline tolerance is of profound importance to crop yields, and will greatly secure the food security.…”

Section: Introductionmentioning

confidence: 99%

A Glycine soja group S2 bZIP transcription factor GsbZIP67 conferred bicarbonate alkaline tolerance in Medicago sativa

Zhu

Jia

et al. 2018

BMC Plant Biol

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BackgroundEven though bicarbonate alkaline stress is a serious threat to crop growth and yields, it attracts much fewer researches than high salinity stress. The basic leucine zipper (bZIP) transcription factors have been well demonstrated to function in diverse abiotic stresses; however, their biological role in alkaline tolerance still remains elusive. In this study, we functionally characterized a bZIP gene from Glycine soja GsbZIP67 in bicarbonate alkaline stress responses.ResultsGsbZIP67 was initially identified as a putative bicarbonate responsive gene, on the basis of previous RNA-seq data of 50 mM NaHCO3-treated Glycine soja roots. GsbZIP67 protein possessed a conserved bZIP domain, and belonged to the group S2 bZIP, which is yet less well-studied. Our studies showed that GsbZIP67 targeted to nucleus in Arabidopsis protoplasts, and displayed transcriptional activation activity in yeast cells. The quantitative real-time PCR analyses unraveled the bicarbonate stress responsive expression and tissue specific expression of GsbZIP67 in wild soybean. Further phenotypic analysis illustrated that GsbZIP67 overexpression in alfalfa promoted plant growth under bicarbonate alkaline stress, as evidenced by longer roots and shoots. Furthermore, GsbZIP67 overexpression also modified the physiological indices of transgenic alfalfa under bicarbonate alkaline stress. In addition, the expression levels of several stress responsive genes were also augmented by GsbZIP67 overexpression.ConclusionsCollectively, in this study, we demonstrated that GsbZIP67 acted as a positive regulator of plant tolerance to bicarbonate alkaline stress. These results provide direct genetic evidence of group S2 bZIPs in bicarbonate alkaline stress, and will facilitate further studies concerning the cis-elements and/or downstream genes targeted by GsbZIP67 in stress responses.Electronic supplementary materialThe online version of this article (10.1186/s12870-018-1466-3) contains supplementary material, which is available to authorized users.

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“…Therefore, the molecular mechanisms underlying the responses of flax to unfavorable environments are intensively studied. In this regard, changes in the expression of stress-responsive genes and microRNAs have been detected in flax plants under abiotic stresses, such as drought [ 8 ], salinity and alkalinity [ 9 , 10 ], nutrient imbalance [ 11 ], and high concentrations of aluminum ions [ 12 , 13 ].…”

Section: Introductionmentioning

confidence: 99%

Differential gene expression in response to Fusarium oxysporum infection in resistant and susceptible genotypes of flax (Linum usitatissimum L.)

et al. 2017

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BackgroundFlax (Linum usitatissimum L.) is a crop plant used for fiber and oil production. Although potentially high-yielding flax varieties have been developed, environmental stresses markedly decrease flax production. Among biotic stresses, Fusarium oxysporum f. sp. lini is recognized as one of the most devastating flax pathogens. It causes wilt disease that is one of the major limiting factors for flax production worldwide. Breeding and cultivation of flax varieties resistant to F. oxysporum is the most effective method for controlling wilt disease. Although the mechanisms of flax response to Fusarium have been actively studied, data on the plant response to infection and resistance gene candidates are currently very limited.ResultsThe transcriptomes of two resistant and two susceptible flax cultivars with respect to Fusarium wilt, as well as two resistant BC2F5 populations, which were grown under control conditions or inoculated with F. oxysporum, were sequenced using the Illumina platform. Genes showing changes in expression under F. oxysporum infection were identified in both resistant and susceptible flax genotypes. We observed the predominant overexpression of numerous genes that are involved in defense response. This was more pronounced in resistant cultivars. In susceptible cultivars, significant downregulation of genes involved in cell wall organization or biogenesis was observed in response to F. oxysporum. In the resistant genotypes, upregulation of genes related to NAD(P)H oxidase activity was detected. Upregulation of a number of genes, including that encoding beta-1,3-glucanase, was significantly greater in the cultivars and BC2F5 populations resistant to Fusarium wilt than in susceptible cultivars in response to F. oxysporum infection.ConclusionsUsing high-throughput sequencing, we identified genes involved in the early defense response of L. usitatissimum against the fungus F. oxysporum. In response to F. oxysporum infection, we detected changes in the expression of pathogenesis-related protein-encoding genes and genes involved in ROS production or related to cell wall biogenesis. Furthermore, we identified genes that were upregulated specifically in flax genotypes resistant to Fusarium wilt. We suggest that the identified genes in resistant cultivars and BC2F5 populations showing induced expression in response to F. oxysporum infection are the most promising resistance gene candidates.Electronic supplementary materialThe online version of this article (10.1186/s12870-017-1192-2) contains supplementary material, which is available to authorized users.

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Identification and characterization of miRNAs and targets in flax (Linum usitatissimum) under saline, alkaline, and saline-alkaline stresses

Cited by 61 publications

References 56 publications

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

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

A Glycine soja group S2 bZIP transcription factor GsbZIP67 conferred bicarbonate alkaline tolerance in Medicago sativa

Differential gene expression in response to Fusarium oxysporum infection in resistant and susceptible genotypes of flax (Linum usitatissimum L.)

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