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

Abstract

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.

Upregulation of NETO2 gene in colorectal cancer

“…The expression levels of target genes were normalized to those of the reference genes. Finally, relative (T/N) expression level of target genes was calculated using the ΔΔCt method [ 24 ]. Since the relative inner variability between the calculated mRNA levels of the reference genes was found to be less than two-fold, a variation in the expression of the target genes of two-fold or greater was considered to be significant.…”

Untitled

“…[19] qPCR data were analyzed using the relative quantification (ΔΔCt) method. [20,21] Relative mRNA level of the genes was calculated using ATG program compatible with relative quantification software (Thermo Fisher Scientific, USA). [22] At least 2-fold mRNA level changes were considered as significant.…”

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

“…Expression analysis allows scientists to identify genes that are expressed in particular flax tissues (Day et al, 2005; Venglat et al, 2011; Zhang and Deyholos, 2016). Moreover, the responses of flax to drought (Dash et al, 2014), salinity, and alkalinity stresses (Yu et al, 2016), nutrient imbalance (Dmitriev et al, 2016), and Fusarium oxysporum infection (Wojtasik et al, 2015, 2016) have been studied and stress-responsive genes identified.…”