Transcriptomic Analysis Reveals Salt Tolerance Mechanisms Present in Date-Plum Persimmon Rootstock (Diospyros lotus L.)
Abstract
:1. Introduction
2. Materials and Methods
2.1. Plant Material and RNA Extraction
2.2. Plant Phenotyping
2.3. RNA Extraction
2.4. RNA Sequencing
2.5. Pre-Processing of RNA-Seq Data
2.6. Transcriptome de Novo Assembly and Annotation
2.7. Differential Expression Analyses
3. Results
3.1. Plant Physiological Responses Associated to Salt Stress Tolerance
3.2. Gene Expression Changes in Response to Salinity
4. Discussion
4.1. Ion Transport
4.2. Photosynthesis, Respiration Systems, and ROS Signaling
4.3. Root Architecture Involvement
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Conflicts of Interest
References
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Days | Variable | Tolerant | Sensitive | Control | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|
0 | Height (cm) | 14 | ± | 3 | ns | 14.3 | ± | 1.3 | ns | 11.8 | ± | 1.3 | ns |
0 | Nodes | 5.4 | ± | 0.9 | ns | 5.5 | ± | 0.5 | ns | 4.5 | ± | 0.6 | ns |
0 | Internode length (cm) | 2.6 | ± | 0.7 | ns | 2.6 | ± | 0.4 | ns | 2.6 | ± | 0.5 | ns |
30 | Height (cm) | 27 | ± | 6 | a | 25 | ± | 4 | a | 42 | ± | 6 | b |
30 | Nodes | 13 | ± | 2 | ns | 13.6 | ± | 1.0 | ns | 15.5 | ± | 0.6 | ns |
30 | Internode length (cm) | 2.0 | ± | 0.3 | ab | 1.8 | ± | 0.2 | a | 2.7 | ± | 0.3 | b |
30 | Symptoms | 1.4 | ± | 0.9 | ab | 2.4 | ± | 0.5 | b | 0.0 | ± | 0.0 | a |
30 | Defoliation (%) | 0.0 | ± | 0.0 | ns | 0.0 | ± | 0.0 | ns | 0.0 | ± | 0.0 | ns |
45 | Height (cm) | 33 | ± | 7 | a | 26 | ± | 4 | a | 60 | ± | 6 | b |
45 | Nodes | 19 | ± | 5 | ab | 17 | ± | 2 | a | 25.3 | ± | 1.9 | b |
45 | Internode length (cm) | 1.8 | ± | 0.1 | b | 1.6 | ± | 0.2 | b | 2.4 | ± | 0.1 | a |
45 | Symptoms | 2.0 | ± | 0.7 | b | 3.0 | ± | 0.0 | c | 0.0 | ± | 0.0 | a |
45 | Defoliation (%) | 0.1 | ± | 0.1 | ns | 0.1 | ± | 0.1 | ns | 0.0 | ± | 0.0 | ns |
60 | Height (cm) | 41 | ± | 7 | b | 28 | ± | 4 | a | 80 | ± | 20 | c |
60 | Nodes | 26 | ± | 4 | b | 19.8 | ± | 1.6 | a | 37 | ± | 6 | b |
60 | Internode length (cm) | 1.59 | ± | 0.12 | a | 1.40 | ± | 0.14 | a | 2.1 | ± | 0.4 | b |
60 | Symptoms | 1.8 | ± | 1.1 | a | 3.3 | ± | 0.5 | b | 0.0 | ± | 0.0 | a |
60 | Defoliation (%) | 0.19 | ± | 0.09 | ab | 0.4 | ± | 0.2 | b | 0.0 | ± | 0.0 | a |
30 | Relative height | 1.9 | ± | 0.4 | a | 1.7 | ± | 0.2 | a | 3.6 | ± | 0.2 | b |
45 | Relative height | 2.4 | ± | 0.6 | ab | 1.8 | ± | 0.2 | a | 5.1 | ± | 0.2 | b |
60 | Relative height | 3.1 | ± | 0.8 | b | 1.9 | ± | 0.2 | a | 6.7 | ± | 1.7 | c |
Variable | Tolerant | Sensitive | Control | |||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|
ψH (MPa) | −0.77 | ± | 0.17 | b | −0.35 | ± | 0.11 | a | −0.81 | ± | 0.13 | b |
ACO2 (µmol CO2/m2s) | 8 | ± | 2 | b | 1.2 | ± | 0.9 | a | 11 | ± | 3 | b |
gs (mmol H2O/m2s) | 180 | ± | 100 | b | 40 | ± | 30 | a | 200 | ± | 200 | b |
Ci (µmol CO2/mol) | 300 | ± | 20 | a | 350 | ± | 30 | b | 250 | ± | 50 | ab |
Cl− (mg/100 mg d.w.) | 4.3 | ± | 0.6 | b | 5.8 | ± | 0.4 | c | 0.50 | ± | 0.08 | a |
Ca2+ (mg/100 mg d.w.) | 0.40 | ± | 0.07 | ab | 0.34 | ± | 0.09 | a | 0.56 | ± | 0.14 | b |
K+ (mg/100 mg d.w.) | 1.3 | ± | 0.4 | ns | 1.0 | ± | 0.3 | ns | 1.4 | ± | 0.4 | ns |
Mg2+ (mg/100 mg d.w.) | 0.19 | ± | 0.04 | ns | 0.181 | ± | 0.019 | ns | 0.177 | ± | 0.012 | ns |
Na+ (mg/100 mg d.w.) | 4.7 | ± | 1.1 | b | 5.2 | ± | 0.5 | b | 0.21 | ± | 0.06 | a |
P (mg/100 mg d.w.) | 0.13 | ± | 0.03 | b | 0.108 | ± | 0.017 | b | 0.061 | ± | 0.014 | a |
S (mg/100 mg d.w.) | 0.065 | ± | 0.016 | a | 0.07 | ± | 0.03 | a | 0.11 | ± | 0.03 | b |
Na+/K+ | 3.8 | ± | 0.7 | b | 5.4 | ± | 1.6 | b | 0.15 | ± | 0.05 | a |
Na+/Ca2+ | 11.7 | ± | 1.2 | b | 15.9 | ± | 3.8 | b | 0.40 | ± | 0.16 | a |
Sequence Description | log2 FC | p-Value (adj) | Tissue |
---|---|---|---|
CALCIUM | |||
Mitochondrial calcium uptake protein 1-like | 0.93 | 1.1 × 10−8 | L |
Cation/calcium exchanger 3-like | 0.75 | 5.7 × 10−3 | |
Extracellular calcium sensing receptor-like | 0.85 | 1.0 × 10−4 | L |
Calcium-transporting ATPase-like 1 | 1.25 | 3.0 × 10−4 | |
Calcium-transporting ATPase-like 2 | 1.28 | 5.3 × 10−7 | |
Calcium-transporting ATPase-like 3 | 1.30 | 1.6 × 10−5 | |
Calcium uniporter protein-like | −1.50 | 1.2 × 10−3 | L |
SODIUM | |||
Sodium/hydrogen exchanger 2-like-1 | 0.60 | 1.5 × 10−5 | |
Sodium/hydrogen exchanger 2-like-2 | −0.74 | 3.6 × 10−16 | |
POTASSIUM | |||
Chloroplastic K+ efflux antiporter 3, -like | 0.95 | 2.1 × 10−3 | |
Potassium channel AKT2/3-like 1 | 1.83 | 1.3 × 10−14 | |
Potassium channel AKT2/3-like 2 | 1.90 | 3.5 × 10−11 | |
Probable potassium transporter-like | −2.21 | 2.2 × 10−14 | |
Potassium channel KAT3-like | 1.44 | 3.5 × 10−3 | |
Potassium channel SKOR-like 1 | 3.16 | 6.9 × 10−4 | L |
Potassium channel SKOR-like 2 | 4.13 | 5.3 × 10−4 | L |
CATIONS | |||
Mechanosensitive ion channel-like | 1.10 | 3.0 × 10−12 | |
Chloroplastic mechanosensitive ion channel 2-like | 0.70 | 2.0 × 10−4 | |
Cation/H(+) antiporter like-1 | 1.75 | 1.1 × 10−3 | |
Cation/H(+) antiporter 18-like | −1.07 | 7.2 × 10−3 | |
Cation/H(+) antiporter like-2 | −1.82 | 8.3 × 10−3 | |
Cation/H(+) antiporter 14-like | −1.64 | 4.4 × 10−3 | |
Vacuolar cation/proton exchanger-like | −2.98 | 2.5 × 10−4 | L |
Vacuolar cation/proton exchanger 3-like 1 | −2.83 | 7.6 × 10−4 | L |
Vacuolar cation/proton exchanger 3-like 2 | −2.71 | 2.6 × 10−3 | L |
ANIONS | |||
S-type anion channel SLAH1-like | −1.70 | 1.0 × 10−3 | |
Voltage-dependent anion-selective channel 2-like | 5.32 | 5.8 × 10−4 | L |
Chloride channel protein-like 1 | −0.88 | 3.4 × 10−9 | |
Chloride channel protein-like 2 | −0.64 | 5.5 × 10−3 | L |
Voltage dependent anion channel 1-like | 1.24 | 5.8 × 10−6 | L |
Aluminum-activated malate transporter-like | 3.58 | 2.3 × 10−10 | L |
OTHER NUTRIENTS | |||
Ammonium transporter-like | 1.91 | 2.3 × 10−9 | L |
Ammonium transporter 1 member 1-like | 1.94 | 8.9 × 10−4 | L |
Magnesium/proton exchanger-like | 1.12 | 2.8 × 10−8 | L |
Boron transporter 1-like | 1.56 | 5.3 × 10−4 | |
Zinc transporter-like | 2.79 | 1.8 × 10−5 | L |
Phosphate transporter PHO1-like | 3.82 | 1.1 × 10−18 | |
H+ ATPases | |||
Plasma membrane H+-ATPase-like | 0.85 | 1.5 × 10−3 | |
Plasmalemma H+-ATPase 1-like | 0.92 | 4.2 × 10−3 | |
Plasma membrane ATPase 4-like | 1.17 | 1.9 × 10−5 | |
V-type proton ATPase subunit G-like | 7.33 | 2.9 × 10−4 | L |
Sequence Description | log2 FC | p-Value (adj) | Tissue |
---|---|---|---|
PHOTOSYNTHESIS AND RESPIRATION | |||
PSI reaction center subunit N-like-1 | 2.32 | 2.5 × 10−7 | L |
PSI reaction center subunit N-like-2 | 2.13 | 1.5 × 10−8 | L |
PSI reaction center subunit III-like | 2.26 | 1.8 × 10−8 | L |
PSI reaction center subunit V-like | 1.86 | 3.2 × 10−6 | L |
PSII reaction center W-like | 1.66 | 1.2 × 10−6 | L |
PSII PsbY-like | 1.75 | 1.5 × 10−6 | L |
PSII repair protein PSB27-H1-like | 0.93 | 4.6 × 10−3 | L |
Cytochrome c oxidase subunit 5A-like | 6.86 | 5.4 × 10−3 | L |
Sequence Description | Log2 FC | p-Value (adj) | Tissue |
---|---|---|---|
ROS DETOXIFICATION | |||
Peroxiredoxin 1-like | 4.49 | 8.4 × 10−4 | L |
Type II Peroxiredoxin 2-like | 1.18 | 7.3 × 10−8 | L |
Peroxidase-like | −1.03 | 1.1 × 10−3 | L |
Peroxidase 12-like 1 | 3.89 | 4.0 × 10−18 | L |
Peroxidase 12-like 2 | 5.09 | 6.2 × 10−3 | L |
Spermidine synthase-like | 1.95 | 8.7 × 10−5 | L |
Thermospermine synthase ACAULIS5-like | 2.12 | 2.4 × 10−11 |
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Gil-Muñoz, F.; Delhomme, N.; Quiñones, A.; Naval, M.d.M.; Badenes, M.L.; García-Gil, M.R. Transcriptomic Analysis Reveals Salt Tolerance Mechanisms Present in Date-Plum Persimmon Rootstock (Diospyros lotus L.). Agronomy 2020, 10, 1703. https://doi.org/10.3390/agronomy10111703
Gil-Muñoz F, Delhomme N, Quiñones A, Naval MdM, Badenes ML, García-Gil MR. Transcriptomic Analysis Reveals Salt Tolerance Mechanisms Present in Date-Plum Persimmon Rootstock (Diospyros lotus L.). Agronomy. 2020; 10(11):1703. https://doi.org/10.3390/agronomy10111703
Chicago/Turabian StyleGil-Muñoz, Francisco, Nicolas Delhomme, Ana Quiñones, Maria del Mar Naval, Maria Luisa Badenes, and M. Rosario García-Gil. 2020. "Transcriptomic Analysis Reveals Salt Tolerance Mechanisms Present in Date-Plum Persimmon Rootstock (Diospyros lotus L.)" Agronomy 10, no. 11: 1703. https://doi.org/10.3390/agronomy10111703
APA StyleGil-Muñoz, F., Delhomme, N., Quiñones, A., Naval, M. d. M., Badenes, M. L., & García-Gil, M. R. (2020). Transcriptomic Analysis Reveals Salt Tolerance Mechanisms Present in Date-Plum Persimmon Rootstock (Diospyros lotus L.). Agronomy, 10(11), 1703. https://doi.org/10.3390/agronomy10111703