Table 3.
List of studies for transcriptomics approaches on salinity stress tolerance in rice, wheat and maize.
| Genotype | Tissue | Experimental conditions | Technique | Comments | Reference |
|---|---|---|---|---|---|
| Rice | |||||
| Oryza coarctata | Leaves and roots | Control, 450 mM NaCl, 700 mM NaCl, fully submerged plant in RO water, fully submerged plant in 450 mM NaCl | Deep transcriptome sequencing | 15,158 genes are differentially expressed under salinity mostly belonging to MYB, bHLH, AP2-EREBP, WRKY, bZIPand NAC classes of TFs | Garg et al. (2014) |
|
Pokkali (tolerant) IR64 (sensitive) |
Leaves and roots | 200 mM NaCl treatment (14-day-old seedlings | Whole-genome transcriptomics (WGT) | 507 differentially expressed genes, mostly bHLH and C2H2 TF families; terpenoid and wax metabolism genes upregulated in tolerant line | Shankar et al. (2016) |
| Dongxiang wild rice (Oryza rufipogon Griff.) | Leaves and roots | 200 mM NaCl treatment on 14-day-old seedlings for 12 days | WGT | 6867 DEGs in leaves and 4988 DEGs in roots. Most belonging to zinc finger proteins, NAC, bZIP, AP2/ERF & MYB TFs family genes; potassium transporters OsHKT1 and OsHKT7 were downregulated | Zhou et al. (2016) |
| Chilbo | Leaves | 250 mM NaCl treatment on 14-day-old seedlings for 12 days | WGT | 962 upregulated genes identified, mostly belonging to MYB family and ZF family of genes regulating sugar metabolism and amino-acid synthesis | Chandran et al. (2019) |
|
Dongdao-4 Jigeng-88 |
Leaves | 0 mM Na+ (10 mM Na2CO3 and 20 mM NaCl) for 1 day and then 60 mM Na+ (10 mM Na2CO3 and 40 mM NaCl) | RNA-seq | 3523 and 4066 DEGs responding to several gene families, involved in functions related to jasmonic acid, organic acid metabolism, iron homeostasis, phenylpropanoid and gibberellic acid synthesis | Li et al. (2020) |
| Wheat | |||||
| SR3 (tolerant) and JN177 | Root | Half-strength Hoagland solution with 340 mM NaCl at 3-leaf stage | Microarray, semi-quantitative RT-PCR (sqRT-PCR, qRT-PCR) | Upregulated: GST (ta_07226) and diacylglycerol kinase (ta_07191) encoding gene, | Liu et al. (2019) |
| SR3 (tolerant) | Shoots and roots | Hydroponic, 200 mM NaCl for 0-24 h at 3-leaf stage | Microarray, RT-PCR | TaMYB73 upregulated in roots and downregulated in leaves | He et al. (2012) |
| SN6306 | Leaves | MS agar medium with 0.4% NaCl for 2 days | qRT-PCR | Overexpression of TaRUB1 in transgenic Arabidopsis improved stress tolerance | Zhang et al. (2013) |
| Berkut, Krichauff, Gladius and Drysdale | Leaf sheath | First 0 and 75 mM NaCl, and second 1-100 mM NaCl (3-day stress) | Microarray analysis, qRT-PCR | Upregulated 39 genes associated with cellular and metabolic processes, cell organization and biogenesis; at 100 mM, 47 and 96 genes upregulated in Drysdale and Krichauff, respectively | Takahashi et al. (2015) |
| Bezostaja (sensitive) and Seri‐82 (tolerant) | Roots | Controlled condition, liquid Murashige and Skoog (MS) with 200 mM NaCl for 48 h | microRNA‐microarray, stem-loop reverse transcription,qRT‐PCR | 16 novel salt-stress associated miRNAs in roots, upregulated: hvu‐miR5049a, ppt‐miR1074, and osa‐miR444b.2 in sensitive line | Eren et al. (2015) |
| Altay2000 and UZ-11CWA-8 (tolerant) and Bobur (sensitive) | Third leaves | Hydroponics system with an increment of 50 mM NaCl for 3 days, and 150 mM continued upto 24 days | GWAS, RT-qPCR | Upregulated: TraesCS6A01G336500.1, TraesCS4B01G254300.1, TaABCF3 transporter genes | Oyiga et al. (2016, 2019) |
| Arg (tolerant) and Moghan3 (sensitive) | Roots of 3weekold seedlings | Green house; half-strength Hoagland solution with 150 mM NaCl for 12 h | RNA-seq, qRT-PCR,MapMan | Upregulated: ABC transporter gene Ta. ABAC15, 29 NAC genes, and 48 MYB TFs; Ta.ANN4, Ta.ACA7 and Ta.NCL2 genes control cytosolic calcium level increased under salt stress | Amirbakhtiar et al. (2019) |
| Qingmai 6 (tolerant) | Shoots and roots (two-weeks old seedlings) | 150 mM NaCl, and combination with 100 μM ethylene precursor ACC, and with 150 μM ethylene signaling inhibitor 1-MCP for 3, 6, 12, and 24 h | RNA-seq | Upregulated: TaCYP450 under stress; six genes played a role in ethylene dependent salt stress | Ma et al. (2020) |
| Chinese Spring (Triticum aestivum) | Mature leaves, roots, seedlings (30 days) | Half-strength Hoagland solution with 100 mM NaCl from germination to 30 days | RNA-seq,qRT-PCR | Upregulated: LEA, dehydrin and potassium transporter genes in roots, and sodium/cation exchanger and aquaporin genes in shoot | Bhanbhro et al. (2020) |
| Zentos (tolerant) and Syn86 (sensitive) | Leaves | Hydroponics system with 100 mM NaCl; salt stress started 3 days after transplanting | RNA-seq, RT-qPCR | Strongest salt-responsive gene TraesCS2A02G395 000. Few genes related to ABC transport, Na+/ Ca2+ exchange might play a role to exclude Na+ | Duarte-Delgado et al. (2020) |
| Kharchia Local | Roots of 6-day-seedling | Growth chamber, hyroponics, 15 dS/m for 3 days with 5 dS/m salinity daily increment, combination NaCl: CaCl2: Na2SO4 (2:1:1) for salinity treatment | RNA-seq, qRT-PCR | Upregulated genes encoding expansin, xyloglucan endotransglucosylase/hydrolase, dehydrins, peroxidases, and a few TFs WRKY, MYB, NAC, bHLH, AP2/ERF | Mahajan et al. (2020) |
| Luyuan502 | 2-weeks-old seedlings | Field with 0.3–0.7% salt; 150 mM NaCl for 2 weeks | RNA-seq, qRT-PCR | Upregulated ETHYLENE RESPONSE FACTORs (ERFs) (TaERF1, 2, 3, 4, and 6) decreased response of ethylene | Ma et al. (2021) |
| Jimai22 (tolerant) and Yangmai20 (sensitive) | Fourth leaves | Greenhouse; 100 mM NaCl for a week | RNA-seq, qRT-PCR | Upregulated genes encoding flavonoid 3′-mnooxygenase, HSP, cytochrome P450, zinc finger proteins, NAC, and WRKY. Co-expression of glutathione S-transferase (GSTU6) under salinity and drought stress | Dugasa et al. (2021) |
| Maize | |||||
| G.S. 46 | Leaf number 4 of 14-day-old plants | 2 mM KCl and1mM CaCl2 for 6 h and 15 mM Ca (NO3) for 2 h. (7 days after salination) | Real-time PCR | ROS scavenging more pronounced in young cells and comparatively reduced in older cells under salt stress. Ascorbate peroxidase and superoxide dismutase significantly higher in NaCl treatment. | Kravchik and Bernstein (2013) |
| B73 maize seedling | Leaf (2 h after NaCl treatment) | 200 mM NaCl | RNA-seq,qRT-PCR | Upregulated genes encode oxidoreductase, peroxidase, antioxidant, transcription regulator activities, ERFs, MYBs, b-carotene hydroxylase, and 9-cis- epoxy carotenoid dioxygenase undersalt stress | Li et al. (2017) |
| 242 maize inbred lines | Leaf (7 days after 220 mM NaCl treatment) | 220 mM NaCl treated | RNA-seq, qRT-PCR assay | L87, a salt-tolerant maize inbred line had higher ROS-related enzyme activities of superoxide dismutase, peroxidase, ascorbate peroxidase, catalase, SnRK2 (ABA), and WRKY than salt-sensitive line | Wang et al. (2019) |
| P138 (sensitive) and 8723 (tolerant) | Seedling (10 days after stress) | 180 mM NaCl (3 leaf stage) | qRT-PCR | Exogenous application of glycine betaine alleviates damaging effect of salt stress through the upregulation of ion balance, reactive oxygen scavenging mechanism, signal transduction activation and MYB and NAC TF families. | Chen et al. (2020) |
| L2010-3 (tolerant) BML1234 (sensitive) | Seedlings (3-daytreatment) | 150 mM NaCl | RNA-seq | Salt stress upregulated genes reported for Aux/IAA, SAUR, CBL-interacting kinase, ABA signal pathway, WRKY, bZIP, and MYB. | Zhang et al. (2021) |
| B73 | Endosperm and embryo tissue after 6 h of treatment | 200 mM NaCl-treated (germination) | Short-read RNA (srRNA) seq | Alternative splicing could be the more dominant regulatory mechanism in early salt-stress responses. The ABA biosynthesis gene, GRMZM2G127139 ABA1/LOS6/ZEP, was consistently repressed and one ABA-responsive gene, GRMZM2G162659 (EM1), was upregulated | Chen et al. (2021) |