Nitrogen Uptake and Distribution in Different Chinese Cabbage Genotypes under Low Nitrogen Stress
Abstract
:1. Introduction
2. Results
2.1. Response to LN of Different Chinese Cabbage Varieties
2.1.1. Field Experiment of Chinese Cabbage under Different N Supplying Levels
2.1.2. Hydroponic Experiments of Chinese Cabbage under CK and LN Conditions
2.2. N-RELATED Physiological Indexes under LN Condition in Different Chinese Cabbage Varieties
2.3. Transcriptome Analysis of the Effects of LN Stress on Chinese Cabbage
2.4. Gene Ontology (GO) and Pathway Analysis for Differentially Expressed Genes under LN Stress
2.5. DEGs Analysis Involved in the N Responsive Process
2.6. Expression Analysis of Essential Genes in N Metabolism Pathway in Response to LN Stress
3. Discussion
4. Materials and Methods
4.1. Test Materials
4.2. Experimental Design
4.2.1. Field Experiment
4.2.2. Solution Culture Experiment
4.3. Sampling and Measurement Methods
4.3.1. Investigation of Agronomic Traits
4.3.2. Root Morphology Analysis
4.3.3. Determination of Related Indexes of Nitrogen Metabolism
4.4. RNAseq Materials and Methods
4.4.1. RNA Isolation
4.4.2. cDNA Library Construction, Sequencing, and Data Processing
4.4.3. Analysis of Gene Expression Profile of Chinese Cabbage in Response to LN Stress
4.4.4. Quantitative RT-PCR Analysis
4.4.5. Data Processing and Analysis
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Conflicts of Interest
References
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Part | Trait | L14 | L40 | ||
---|---|---|---|---|---|
LN | CK | LN | CK | ||
Shoot | SFW(g plant−1) | 0.75 ± 0.08 b | 0.93 ± 0.39 a | 0.72 ± 0.07 b | 0.74 ± 0.09 b |
SDW(g plant−1) | 0.027 ± 0.001 a | 0.034 ± 0.007 a | 0.027 ± 0.001 a | 0.026 ± 0.005 a | |
Root | RFW(g plant−1) | 0.097 ± 0.009 a | 0.064 ± 0.007 b | 0.103 ± 0.009 a | 0.087 ± 0.009 ab |
RDW(g plant−1) | 0.0063 ± 0.0002 a | 0.0044 ± 0.0004 b | 0.0054 ± 0.0006 ab | 0.0047 ± 0.0005 b | |
TRL(cm plant−1) | 19.23 ± 1.58 a | 18.67 ± 2.08 ab | 14.87 ± 0.91 b | 11.27 ± 2.61 c | |
LRL(cm plant−1) | 363.41 ± 12.47 a | 169.1 ± 6.77 c | 279.78 ± 12.06 b | 188.41 ± 8.95 c | |
RSA(cm2 plant−1) | 18.42 ± 1.86 a | 10.41 ± 1.36 b | 17.26 ± 0.97 a | 12.15 ± 1.62 b |
Sample | Total Raw Reads | Total Clean Reads | Q20 Percentage | Total Map | Unique Map | Total Genes | Novel Transcript |
---|---|---|---|---|---|---|---|
CK14S | 46,383,112 | 45,027,680 | 98.45 | 92.21% | 89.81% | 29,776 | 5324 |
CK14R | 47,421,702 | 45,802,951 | 98.31 | 90.15% | 88.41% | 29,771 | 5319 |
LN14S | 46,323,061 | 45,363,247 | 98.39 | 91.91% | 89.92% | 29,585 | 5133 |
LN14R | 49,639,339 | 48,482,294 | 98.31 | 90.25% | 88.27% | 30,335 | 5883 |
CK40S | 47,193,171 | 46,107,124 | 98.43 | 91.90% | 89.03% | 29,167 | 4786 |
CK40R | 46,282,418 | 45,051,759 | 98.30 | 90.51% | 88.68% | 29,308 | 4927 |
LN40S | 46,018,595 | 44,930,999 | 98.39 | 91.08% | 89.79% | 29,951 | 5570 |
LN40R | 45,126,988 | 44,067,133 | 98.28 | 90.53% | 88.68% | 30,000 | 5619 |
KEGGID | Description | LN14L vs. CK14L | LN14R vs. CK14R | LN40L vs. CK40L | LN40R vs. CK40R | ||||
---|---|---|---|---|---|---|---|---|---|
p-Value | GeneRatio | p-Value | GeneRatio | p-Value | GeneRatio | p-Value | GeneRatio | ||
ath00053 | Ascorbate and aldarate metabolism | 0.006 | 4/62 | 0 | 0 | 0 | |||
ath00195 | Photosynthesis | 0.000 | 10/62 | 0 | 0 | 0 | |||
ath00196 | Photosynthesis—antenna proteins | 0.000 | 9/62 | 0.034 | 5/191 | 0.000 | 10/642 | 0 | |
ath00220 | Arginine biosynthesis | 0 | 0.012 | 3/191 | 0 | 0 | |||
ath00250 | Alanine, aspartate and glutamate metabolism | 0 | 0.000 | 9/191 | 0 | 0 | |||
ath00280 | Valine, leucine and isoleucine degradation | 0 | 0.006 | 7/191 | 0 | 0 | |||
ath00350 | Tyrosine metabolism | 0 | 0.030 | 5/191 | 0 | 0 | |||
ath00380 | Tryptophan metabolism | 0 | 0 | 0.004 | 14/642 | 0 | |||
ath00400 | Phenylalanine, tyrosine and tryptophan biosynthesis | 0 | 0.028 | 6/191 | 0 | 0.042 | 4/111 | ||
ath00460 | Cyanoamino acid metabolism | 0 | 0.046 | 5/191 | 0 | 0.036 | 4/111 | ||
ath00640 | Propanoate metabolism | 0 | 0.044 | 4/191 | 0 | 0 | |||
ath00730 | Thiamine metabolism | 0.038 | 2/62 | 0 | 0 | 0 | |||
ath00860 | Porphyrin and chlorophyll metabolism | 0.035 | 3/62 | 0 | 0 | 0 | |||
ath00904 | Diterpenoid biosynthesis | 0 | 0 | 0 | 0.005 | 3/111 | |||
ath00906 | Carotenoid biosynthesis | 0 | 0 | 0 | 0.007 | 4/111 | |||
ath00908 | Zeatin biosynthesis | 0 | 0.013 | 4/191 | 0 | 0 | |||
ath00910 | Nitrogen metabolism | 0 | 0.000 | 10/191 | 0 | 0 | |||
ath00920 | Sulfur metabolism | 0 | 0.006 | 6/191 | 0.008 | 11/642 | 0 | ||
ath00940 | Phenylpropanoid biosynthesis | 0 | 0.000 | 21/191 | 0 | 0.000 | 13/111 | ||
ath00960 | Tropane, piperidine and pyridine alkaloid biosynthesis | 0 | 0.012 | 5/191 | 0 | 0 | |||
ath00966 | Glucosinolate biosynthesis | 0 | 0.001 | 5/191 | 0.026 | 6/642 | 0 | ||
ath04016 | MAPK signaling pathway—plant | 0 | 0 | 0.000 | 32/642 | 0.000 | 12/111 | ||
ath04075 | Plant hormone signal transduction | 0 | 0 | 0 | 0.002 | 15/111 | |||
ath04130 | SNARE interactions in vesicular transport | 0 | 0 | 0.008 | 11/642 | 0 | |||
ath04626 | Plant-pathogen interaction | 0 | 0.018 | 13/191 | 0.034 | 31/642 | 0.000 | 14/111 | |
ath04712 | Circadian rhythm—plant | 0.001 | 4/62 | 0 | 0 | 0 |
Function | Gene Name | Gene ID | Chr. | Start | End | log2 Ratio (LN/CK) | |||
---|---|---|---|---|---|---|---|---|---|
Root | Shoot | ||||||||
L14 | L40 | L14 | L40 | ||||||
Nitrate transport | NRT1 | BraA06g009460.3C | A06 | 5,163,603 | 5,163,896 | 2.43 | 1.78 | 1.32 | |
NRT1 | BraA06g009470.3C | A06 | 5,167,089 | 5,168,324 | 1.42 | 1.94 | 1.73 | ||
NRT1 | BraA08g031180.3C | A08 | 20,956,829 | 20,960,518 | 1.13 | 1.55 | |||
NRT1 | BraA09g060970.3C | A09 | 42,614,336 | 42,618,089 | 1.31 | ||||
NRT2.1 | BraA06g005350.3C | A06 | 3,179,020 | 3,180,823 | 8.16 | 3.34 | |||
NRT2.5 | BraA08g030690.3C | A08 | 20,761,898 | 20,763,666 | 8.37 | ||||
NRT2.7 | BraA02g005540.3C | A02 | 2,623,331 | 2,624,856 | −2.01 | ||||
Nitrate assimilation | GDH2 | BraA03g002960.3C | A03 | 1,321,750 | 1,323,677 | −2.11 | −1.15 | −1.03 | |
GLU1 | BraA10g032170.3C | A10 | 19,964,582 | 19,972,116 | 1.02 | ||||
GS2 | BraA08g009150.3C | A08 | 8,134,274 | 8,136,484 | 1.62 | ||||
GSR1 | BraA04g010460.3C | A04 | 8,265,796 | 8,268,190 | 1.03 | 1.48 | |||
Photosynthesis | ACA3 | BraA10g032140.3C | A10 | 19,954,817 | 19,956,218 | −2.45 | |||
BCA3 | BraA07g014010.3C | A07 | 12,918,461 | 12,920,370 | 4.14 | −1.34 | 3.42 | ||
BCA4 | BraA02g019760.3C | A02 | 11,362,629 | 11,365,101 | 1.21 | ||||
CA1 | BraA01g044810.3C | A01 | 29,518,958 | 29,521,894 | −1.41 | ||||
CA2 | BraA02g005650.3C | A02 | 2,674,642 | 2,677,016 | 4.37 | −3.24 | |||
Auxin synthesis | NIT2 | BraA02g006840.3C | A02 | 3,245,216 | 3,246,972 | 1.28 |
Chemical Element | Nutrient Solution | Treat | |
---|---|---|---|
CK(6.0 mM) | LN(0.2 mM) | ||
ME | KNO3 | 3 mM | 0.1 mM |
KCl | 0.0 mM | 3 mM | |
KH2PO4 | 1.5 mM | 1.5 mM | |
K2HPO4 | 1.5 mM | 1.5 mM | |
(NH4)SO4 | 0.75 mM | 25 µM | |
MgCl2 | 1 mM | 1 mM | |
K2SO4 | 2 mM | 2 mM | |
Ca(NO3)2 | 0.75 mM | 0.75mM | |
CaCl2 | 3.25 mM | 3.25 mM | |
Fe | Na2Fe-EDTA | 40 µM | 40 µM |
TE | H3BO3 | 60 µM | 60 µM |
MnSO4 | 14 µM | 14 µM | |
ZnSO4 | 1 µM | 1 µM | |
CuSO4 | 0.6 µM | 0.6 µM | |
NiCl2 | 0.4 µM | 0.4 µM | |
H2MoO4 | 0.3 µM | 0.3 µM | |
CoCl2 | 20 nM | 20 nM |
Genes | Forward Primer | Reverse Primer |
---|---|---|
BraA08g033360.3C (Bra-Action) | ATACCAGGCTTGAGCATACCG | GCCAAAGAGGCCATCAGACAA |
BraA06g009460.3C | ATTGAGCACATTGGCGTTAGGA | ACCACTTGGAGAAAACGAGGAAA |
BraA06g009470.3C | CTTCCTGAAACAAAATCTCAAACCC | AAGCCACCGAGGAGACAGAGC |
BraA08g031180.3C | TTATTGCGGCGGAAGGCG | CATCGGTTAGTGTTGAAAGTGTCCA |
BraA09g032690.3C | ATTTCCTCCTGGCTGCCTTGA | TGGGTCGCTCCTCGTAGTCGT |
BraA02g006840.3C | CGGTGCTGCTATTTGCTG | CTTCGTGTTGCTCTGGGT |
BraA03g002960.3C | TGAAACACAAAGAGGCAA | ATGGAGCAACAGTTCGTC |
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Zhang, Y.; Li, J.; Zhou, D.; Song, J.; Gao, J. Nitrogen Uptake and Distribution in Different Chinese Cabbage Genotypes under Low Nitrogen Stress. Int. J. Mol. Sci. 2022, 23, 1573. https://doi.org/10.3390/ijms23031573
Zhang Y, Li J, Zhou D, Song J, Gao J. Nitrogen Uptake and Distribution in Different Chinese Cabbage Genotypes under Low Nitrogen Stress. International Journal of Molecular Sciences. 2022; 23(3):1573. https://doi.org/10.3390/ijms23031573
Chicago/Turabian StyleZhang, Yihui, Jingjuan Li, Dandan Zhou, Jie Song, and Jianwei Gao. 2022. "Nitrogen Uptake and Distribution in Different Chinese Cabbage Genotypes under Low Nitrogen Stress" International Journal of Molecular Sciences 23, no. 3: 1573. https://doi.org/10.3390/ijms23031573
APA StyleZhang, Y., Li, J., Zhou, D., Song, J., & Gao, J. (2022). Nitrogen Uptake and Distribution in Different Chinese Cabbage Genotypes under Low Nitrogen Stress. International Journal of Molecular Sciences, 23(3), 1573. https://doi.org/10.3390/ijms23031573