Table 2.
Global transcriptomic analysis revealing gene expression profiles in response to major abiotic and biotic stresses in flax.
| Trait/tissue | Platform/tool | DEGs/DEUs | Key points | References |
|---|---|---|---|---|
| Flax seed responses to salt stress | Illumina HiSeq 2000 | 7,736, 1,566, and 452 in alkaline salt stress, neutral salt stress and alkaline stress, respectively | Wax biosynthesis, pathogen-related proteins, and photosynthesis related genes | Yu et al., 2014 |
| Illumina high throughput sequencing | 33,774 Upregulated-18,040 Downregulated-15,734 |
Provide high resolution gene expression profile | Wu et al., 2019a | |
| Flax leaf responses of drought sensitive and tolerant varieties | PacBio Iso-Seq RSEM |
In cv. Z141 (drought tolerant) Upregulated-3,245 Downregulated-4,167; In cv. NY-17 (drought sensitive) Upregulated-2,381 Downregulated-3,515 |
Proline biosynthesis and DNA repair from ROS damage | Wang et al., 2021 |
| Flax (seed, root, and shoot) under drought stress | CombiMatrix 90 K Array | 183 Upregulated-72 Downregulated-111 |
Maintain growth and homeostasis | Dash et al., 2014 |
| Flax seeds under normal and PEG induced osmotic stress | Illumina platform | 3,922 Upregulated-1,487 Downregulated-2,432 |
Biochemical and signal transduction pathway | Wu et al., 2018 |
| Flax seedlings (root) under high soil acidity and aluminum stress | Illumina platform | Compartmentalization of Ca2+ in vacuoles and intracellular regulation | Zyablitsin et al., 2018 | |
| Flax rust (leaf tissue) under pathogenic stress (Melampsora lini) | Illumina genome analyzer II | 16,271 | Hydrolysis and uptake of nutrients and plant pathogenicity related gene encoding | Nemri et al., 2014 |
| Illumina HiSeq 2,500 | 58 | Avirulence and effector genes and genes encoding secreted proteins | Wu et al., 2019b | |
| Response to Fusarium wilt (Fusarium oxysporum) | Illumina HiSeq 2000 | 100 | Reception and transduction of pathogen signals | Galindo-Gonzalez and Deyholos, 2016 |
| 47 | Defense response, defense signaling, stress response, and primary and secondary metabolism regulation | Kostyn et al., 2012 | ||
| NextSeq 500 high-throughput sequencer (Illumina) | pathogenesis-related protein encoding, ROS production, and cell wall biogenesis | Dmitriev et al., 2017 |
DEGs, differentially expressed genes; DEUs, differentially expressed unigenes; qRT-PCR, quantitative real time-polymerase chain reaction; RNA, Ribonucleic acid; PEG, polyethylene glycol; ROS, reactive oxygen species; and RSEM, RNA-seq by expectation–maximization.