title: Gene expression profiling of flax (Linum usitatissimum L.) under edaphic stress.
abstract: BACKGROUND
  Cultivated 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.
  
  
  RESULTS
  High-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.
  
  
  CONCLUSIONS
  Differentially 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.
authors.affiliation: Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
authors.forename: Alexey A
authors.initials: AA
authors.lastname: Dmitriev
authors.affiliation: Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
authors.forename: Anna V
authors.initials: AV
authors.lastname: Kudryavtseva
authors.affiliation: Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
authors.forename: George S
authors.initials: GS
authors.lastname: Krasnov
authors.affiliation: Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
authors.forename: Nadezhda V
authors.initials: NV
authors.lastname: Koroban
authors.affiliation: Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.|Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.
authors.forename: Anna S
authors.initials: AS
authors.lastname: Speranskaya
authors.affiliation: Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.
authors.forename: Anastasia A
authors.initials: AA
authors.lastname: Krinitsina
authors.affiliation: Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.|Faculty of Biology, Lomonosov Moscow State University, Moscow, Russia.
authors.forename: Maxim S
authors.initials: MS
authors.lastname: Belenikin
authors.affiliation: Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
authors.forename: Anastasiya V
authors.initials: AV
authors.lastname: Snezhkina
authors.affiliation: Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
authors.forename: Asiya F
authors.initials: AF
authors.lastname: Sadritdinova
authors.affiliation: All-Russian Research Institute for Flax, Torzhok, Russia.
authors.forename: Natalya V
authors.initials: NV
authors.lastname: Kishlyan
authors.affiliation: Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.|All-Russian Research Institute for Flax, Torzhok, Russia.
authors.forename: Tatiana A
authors.initials: TA
authors.lastname: Rozhmina
authors.affiliation: Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
authors.forename: Olga Yu
authors.initials: OY
authors.lastname: Yurkevich
authors.affiliation: Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
authors.forename: Olga V
authors.initials: OV
authors.lastname: Muravenko
authors.affiliation: Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia.
authors.forename: Nadezhda L
authors.initials: NL
authors.lastname: Bolsheva
authors.affiliation: Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, Russia. mnv-4529264@yandex.ru.
authors.forename: Nataliya V
authors.initials: NV
authors.lastname: Melnikova
mesh_terms: D019597:Flax / Q000235:genetics / Q000502:physiology*; D020869:Gene Expression Profiling; D018506:Gene Expression Regulation, Plant; D059014:High-Throughput Nucleotide Sequencing; D010940:Plant Proteins / Q000235:genetics* / Q000378:metabolism; D012333:RNA, Messenger / Q000235:genetics / Q000378:metabolism; D060888:Real-Time Polymerase Chain Reaction; D017422:Sequence Analysis, DNA; D012987:Soil / Q000737:chemistry*
chemical_list: D010940:Plant Proteins; D012333:RNA, Messenger; D012987:Soil
keywords: Edaphic stress; Excess nutrition; Flax; High-throughput sequencing; JAZ; LIS-1; Linum usitatissimum; Phosphate deficiency; WRKY; qPCR