Transcriptomic and Physiological Analysis Reveals Genes Associated with Drought Stress Responses in Populus alba × Populus glandulosa
Abstract
:1. Introduction
2. Results
2.1. Growth and Physiological Response to Drought Stress in Poplar
2.2. Effect of Drought Stress on Soluble Sugars, Lipid Peroxidation, Proline, H2O2, and Antioxidant Activities
2.3. RNA Sequencing, Assembly, and Annotation
2.4. Analysis of Differentially Expressed Genes in the Response to Drought Stress
2.5. Functional Enrichment of DEGs in the Response to Drought Stress
2.6. DEGs Involved in Proline, Antioxidants, and ABA
2.7. Validation of RNA-Seq Results by qPCR
3. Discussion
4. Materials and Methods
4.1. Plant Materials and Drought Stress Treatment
4.2. Measurement of Chlorophyll, Soluble Sugars, Starch, Proline, MDA, H2O2, Soluble Proteins, ABA and Antioxidant Enzymes
4.3. RNA Extraction, cDNA Library Construction, Sequencing
4.4. Assembly Normalization and Quality Assessment
4.5. Differentially Expressed Genes (DEGs) Analysis
4.6. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) Pathway Analysis
4.7. Quantitative PCR (qPCR) Validation of RNA-Seq Data
4.8. Statistical Analysis
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Clone | Treatment | mg/g FW | Chl a/b | Chl/Car | |||
---|---|---|---|---|---|---|---|
Chl a | Chl b | Total Chl | Carotenoids | ||||
72-30 | Control | 1.76 ± 0.09 ab | 0.73 ± 0.04 a | 2.49 ± 0.31 a | 0.53 ± 0.02 a | 2.42 ± 0.07 b | 4.70 ± 0.11 n.s |
Drought | 1.92 ± 0.07 a | 0.72 ± 0.04 ab | 2.68 ± 0.20 a | 0.55 ± 0.02 a | 2.68 ± 0.16 a | 4.84 ± 0.01 n.s | |
72-31 | Control | 1.51 ± 0.10 b | 0.64 ± 0.05 b | 2.14 ± 0.15 b | 0.45 ± 0.02 b | 2.38 ± 0.06 b | 4.81 ± 0.11 n.s |
Drought | 1.91 ± 0.15 a | 0.76 ± 0.05 a | 2.68 ± 0.20 a | 0.57 ± 0.05 a | 2.51 ± 0.07 ab | 4.68 ± 0.13 n.s |
Clone | Treatment | mg/g FW | |||
---|---|---|---|---|---|
Glucose | Fructose | Sucrose | Starch | ||
72-30 | Control | 1.18 ± 0.10 d | 1.00 ± 0.11 c | 54.70 ± 1.20 b | 0.28 ± 0.11 ab |
Drought | 2.46 ± 0.25 b | 2.69 ± 0.04 a | 82.38 ± 2.45 a | 0.28 ± 0.08 ab | |
72-31 | Control | 2.10 ± 0.13 c | 2.03 ± 0.25 b | 51.51 ± 3.97 b | 0.37 ± 0.12 a |
Drought | 2.92 ± 0.22 a | 3.01 ± 0.42 a | 49.83 ± 5.30 b | 0.19 ± 0.05 b |
Sample | Raw Reads | Clean Reads | Mapped (%) | Q30 (%) | GC (%) |
---|---|---|---|---|---|
72-30_d1_1 | 21,322,525 | 19,423,209 | 91.94% | 95 | 47 |
72-30_d1_2 | 25,534,053 | 23,613,885 | 92.22% | 95 | 48 |
72-30_d1_3 | 27,750,144 | 24,773,305 | 84.14% | 95 | 49 |
72-30_d12_1 | 29,270,661 | 26,337,948 | 90.26% | 95 | 47 |
72-30_d12_2 | 29,362,659 | 26,669,548 | 89.28% | 95 | 48 |
72-30_d12_3 | 32,321,191 | 29,446,757 | 88.63% | 95 | 46 |
72-31_d1_1 | 28,614,343 | 26,106,663 | 86.77% | 95 | 47 |
72-31_d1_2 | 32,949,652 | 29,442,606 | 89.40% | 95 | 46 |
72-31_d1_3 | 32,479,330 | 30,465,003 | 88.08% | 95 | 48 |
72-31_d12_1 | 30,944,699 | 29,702,711 | 85.40% | 95 | 48 |
72-31_d12_2 | 29,104,362 | 27,656,786 | 81.95% | 95 | 49 |
72-31_d12_3 | 27,334,799 | 26,081,336 | 80.33% | 95 | 50 |
Sum | 346,988,418 | 319,719,757 | |||
Mean | 28,915,701.5 | 26,643,313.08 | 87.37% | 95 | 47.7 |
Gene ID | Gene Description | Log2 FC | p-Value | TAIR ID | Gene Symbol | Regulation |
---|---|---|---|---|---|---|
LogFC > 0 | ||||||
LOC118043229 | galactinol synthase 2-like | 12.27314 | 1.13 × 10−13 | AT2G47180 | GolS1 | Up |
LOC118043085 | bidirectional sugar transporter SWEET15-like | 11.40774 | 2.21 × 10−21 | AT5G13170 | SAG29 | Up |
LOC118053155 | zeatin O-xylosyltransferase-like | 10.90792 | 2.54 × 10−18 | AT2G15490 | UGT73B4 | Up |
LOC118057602 | uncharacterized protein | 10.08275 | 5.60 × 10−11 | AT5G50360 | Up | |
LOC118033421 | embryonic protein DC-8 | 9.94831 | 1.14 × 10−14 | AT2G36640 | ECP63 | Up |
LOC118062093 | dehydration-responsive element-binding protein 2D-like | 9.40484 | 5.60 × 10−13 | AT1G75490 | Up | |
LOC118052105 | umecyanin-like | 9.22683 | 2.11 × 10−11 | AT2G25060 | ENODL14 | Up |
LOC118061594 | non-specific lipid-transfer protein-like protein | 9.08816 | 6.39 × 10−6 | AT3G22600 | Up | |
LOC118034863 | late embryogenesis abundant protein D-7 | 9.00364 | 2.88 × 10−13 | AT3G15670 | Up | |
LOC118055598 | glucose and ribitol dehydrogenase-like | 8.91445 | 9.97 × 10−28 | AT1G54870 | Up | |
LogFC < 0 | ||||||
LOC118040537 | auxin-induced protein 15A-like | −5.69993 | 0.0013 | AT4G34770 | Down | |
LOC118059218 | uncharacterized protein | −5.49169 | 0.0040 | AT4G04745 | Down | |
LOC118047630 | acetyl-CoA-benzylalcohol acetyltransferase-like | −5.44358 | 0.0007 | AT3G26040 | Down | |
LOC118039754 | protein RADIALIS-like 2 | −5.42122 | 0.0039 | AT1G75250 | RL6 | Down |
LOC118044774 | uncharacterized protein | −5.39230 | 0.0065 | AT4G12690 | Down | |
LOC118043148 | protein HEADING DATE 3A-like | −5.24861 | 0.0306 | AT1G65480 | FT | Down |
LOC118063338 | syntaxin-112-like | −5.18643 | 0.0395 | AT2G18260 | SYP112 | Down |
LOC118053660 | uncharacterized protein | −5.17855 | 0.0099 | AT3G01410 | Down | |
LOC118042489 | cyclin-U4-1-like | −5.16138 | 0.0385 | AT2G44740 | CYCP4;1 | Down |
LOC118058270 | RNA exonuclease 4-like | −5.13317 | 8.59 × 10−5 | AT3G27970 | Down |
Gene ID | Gene Description | Log 2FC | p-Value | TAIR ID | Gene Symbol | Regulation |
---|---|---|---|---|---|---|
LogFC > 0 | ||||||
LOC118057602 | uncharacterized protein | 8.97992 | 7.9 × 10−19 | AT5G50360 | Up | |
LOC118056377 | probable protein phosphatase 2C 75 isoform X1 | 7.09109 | 4.6 × 10−6 | AT5G51760 | AHG1 | Up |
LOC118028052 | WUSCHEL-related homeobox 2-like | 6.87533 | 2.2 × 10−5 | AT5G59340 | WOX2 | Up |
LOC118043229 | galactinol synthase 2-like | 6.48803 | 3.5 × 10−61 | AT2G47180 | GolS1 | Up |
LOC118047047 | uncharacterized protein | 6.37664 | 4.0 × 10−9 | AT1G07985 | Up | |
LOC118044732 | uncharacterized protein | 6.14501 | 5.2 × 10−31 | AT5G50360 | Up | |
LOC118032224 | uncharacterized protein | 6.08772 | 6.9 × 10−4 | AT4G33467 | Up | |
LOC118046914 | translocator protein homolog | 6.07722 | 6.3 × 10−6 | AT2G47770 | TSPO | Up |
LOC118053986 | putative disease resistance RPP13-like protein 1 | 5.97234 | 9.5 × 10−4 | AT3G14470 | Up | |
LOC118029876 | heavy metal-associated isoprenylated plant protein 27 | 5.91057 | 4.6 × 10−3 | AT5G66110 | HIPP27 | Up |
LogFC < 0 | ||||||
LOC118058995 | auxin-responsive protein SAUR24-like | −6.84085 | 2.3 × 10−6 | AT5G18020 | SAUR20 | Down |
LOC118061976 | ornithine decarboxylase-like | −6.12173 | 1.2 × 10−4 | AT5G11880 | Down | |
LOC118056925 | uncharacterized protein | −5.77476 | 8.6 × 10−4 | AT3G15115 | Down | |
LOC118045856 | major allergen Pru ar 1-like | −5.69965 | 1.3 × 10−3 | AT1G24020 | MLP423 | Down |
LOC118039754 | protein RADIALIS-like 2 | −5.61201 | 1.1 × 10−3 | AT1G75250 | RL6 | Down |
LOC118044774 | uncharacterized protein | −5.61180 | 1.1 × 10−4 | AT4G12690 | Down | |
LOC118035984 | axial regulator YABBY 1-like | −5.56260 | 1.4 × 10−3 | AT2G45190 | AFO | Down |
LOC118051349 | probable serine/threonine-protein kinase PBL7 | −5.48302 | 4.1 × 10−4 | AT1G54820 | Down | |
LOC118028545 | leucoanthocyanidin dioxygenase-like | −5.46618 | 2.9 × 10−5 | AT4G22880 | LDOX | Down |
LOC118055368 | terpene synthase 10-like | −5.45600 | 3.3 × 10−2 | AT3G25830 | TPS-CIN | Down |
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Kim, T.-L.; Lim, H.; Denison, M.I.J.; Oh, C. Transcriptomic and Physiological Analysis Reveals Genes Associated with Drought Stress Responses in Populus alba × Populus glandulosa. Plants 2023, 12, 3238. https://doi.org/10.3390/plants12183238
Kim T-L, Lim H, Denison MIJ, Oh C. Transcriptomic and Physiological Analysis Reveals Genes Associated with Drought Stress Responses in Populus alba × Populus glandulosa. Plants. 2023; 12(18):3238. https://doi.org/10.3390/plants12183238
Chicago/Turabian StyleKim, Tae-Lim, Hyemin Lim, Michael Immanuel Jesse Denison, and Changyoung Oh. 2023. "Transcriptomic and Physiological Analysis Reveals Genes Associated with Drought Stress Responses in Populus alba × Populus glandulosa" Plants 12, no. 18: 3238. https://doi.org/10.3390/plants12183238