Mapping Quantitative Trait Loci (QTLs) for Reproductive Stage Salinity Tolerance in Rice
Abstract
1. Introduction
2. Material and Methods
2.1. Plant Material and Experimental Conditions
2.2. Phenotypic Data Collection and Phenotypic Correlation Analysis
2.3. DNA Extraction and Genotyping
2.4. Genetic Linkage Map Construction and QTL Analysis
3. Results
3.1. Phenotypic Variation/Evaluation
3.2. Trait Correlation and Linkage Map
3.3. QTL Mapping of Salt Tolerance-Related Traits (Plant Height, Panicle Number, Panicle Length, Biomass, and Yield)
3.4. QTL Mapping of Salt Tolerance-Related Biochemical Traits (Na+ Concentration, Na+/K+ Ratio, and Salinity Tolerance)
3.5. QTL Clusters
4. Discussion
4.1. QTLs Associated with Salinity Tolerance in Rice
4.2. QTLs for Component Traits of Salinity Tolerance on Chromosome 2
4.3. QTLs for Component Traits of Salinity Tolerance on Chromosome 11
4.4. QTLs for Component Traits of Salinity Tolerance on Chromosome 12
5. Conclusions
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Parental Lines | Recombinant Inbred Lines | |||||||||||||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Jarava | RPBio226 | Mean | Range | Skewness | Kurtosis | |||||||||||||
C | FS | PS | C | FS | PS | C | FS | PS | C | FS | PS | C | FS | PS | C | FS | PS | |
PH | 109 | 98.5 | 68.37 | 95.8 | 78.6 | 40 | 96.47 ± 6.95 | 72.7 ± 7.61 | 61.16 ± 8.59 | 76.6–121 | 65.2–104.4 | 37.5–80.5 | −0.34 | −0.01 | −0.32 | 0.19 | 0.31 | −0.01 |
PN | 10.2 | 6.8 | 5.62 | 6.7 | 5.6 | 1 | 7.89 ± 1.39 | 2.79 ± 1.27 | 5.37 ± 2.79 | 4.1–11.8 | 4.2–9.6 | 1–14 | 0.05 | 0.96 | 0.96 | 0.27 | −0.6 | 0.64 |
PL | 22.4 | 20 | 19.34 | 21.1 | 16.5 | 9 | 20.79 ± 1.74 | 14.37 ± 3.65 | 17.06 ± 3.41 | 16.5–25.3 | 15.8–22.4 | 8–31.75 | 0.04 | −0.16 | 0.27 | −0.09 | 1.47 | 2.45 |
BM | 42.2 | 33.5 | 18 | 35 | 26.3 | 5 | 35.74 ± 7.64 | 18.83 ± 7.21 | 17.10 ± 7.40 | 19.7–57 | 19.5–46.9 | 2–37.5 | 0.23 | 0.66 | 0.62 | −0.49 | 0.51 | 0.06 |
YL | 19.2 | 13.1 | 8.18 | 15.1 | 7.4 | 1.5 | 13.33 ± 3.4 | 11.44 ± 2.79 | 5.32 ± 3.14 | 7.9–22.5 | 4.3–20.3 | 1–16 | 0.31 | 0.31 | 1.02 | −0.15 | 0.29 | 1 |
Na+ | 183.5 | 286.6 | 185.17 ± 43.28 | 97.4–296.9 | 0.53 | −0.21 | ||||||||||||
K+ | 64.5 | 37.03 | 47.81 ± 19.34 | 17.1–119 | 1.24 | 2.01 | ||||||||||||
Na+/K+ | 2.89 | 7.81 | 4.74 ± 2.33 | 1.1–12.9 | 0.99 | 1.27 | ||||||||||||
Score | 4.5 | 8.25 | 5.37 ± 2.27 | 1–9 | 0.08 | −0.81 |
Traits | Parental Lines | Recombinant Inbred Lines | ||||
---|---|---|---|---|---|---|
Jarava | RPBio226 | Mean | Range | Skewness | Kurtosis | |
SSI Plant height | 0.1 | 0.18 | 0.99 ± 0.58 | −0.57–2.25 | −0.26 | −0.19 |
SSI Tiller number | 0.33 | 0.16 | 0.83 ± 1.37 | −5.90–4.06 | −0.94 | 3.03 |
SSI Panicle number | 0.32 | 0.24 | 0.83 ± 1.38 | −6.33–4.05 | −1.02 | 3.71 |
SSI Panicle length | −0.03 | 0.08 | 0.96 ± 0.58 | −0.79–2.53 | −0.18 | −0.02 |
SSI Biomass | 0.21 | 0.25 | 0.75 ± 1.64 | −5.50–4.75 | −0.5 | 1.14 |
SSI Yield | 0.24 | 0.55 | 0.73 ± 1.85 | −5.33–4.61 | −0.81 | 0.16 |
Trait | Stress | PH | TN | PN | PL | BM | YL | Na+ Conc | K+ Conc | Na+/K+ Conc | Score |
---|---|---|---|---|---|---|---|---|---|---|---|
TN | Control | ||||||||||
FS | −0.03 | ||||||||||
PS | 0.28 ** | ||||||||||
PN | Control | 0.05 | |||||||||
FS | −0.03 | 0.99 | |||||||||
PS | 0.26 ** | 0.68 ** | |||||||||
PL | Control | 0.35 ** | 0.1 ** | ||||||||
FS | 0.68 ** | −0.12 | −0.11 | ||||||||
PS | 0.45 ** | 0.00 | 0.15 | ||||||||
BM | Control | 0.4 ** | 0.5 ** | 0.21 ** | |||||||
FS | 0.2 ** | 0.25 ** | 0.26 ** | 0.12 | |||||||
PS | 0.2 * | 0.32 ** | 0.16 | 0.26 ** | |||||||
YL | Control | 0.29 ** | 0.41 ** | 0.14 | 0.74 ** | ||||||
FS | 0.2 ** | 0.1 | 0.1 | 0.12 | 0.67 ** | ||||||
PS | 0.2 * | 0.36 ** | 0.24 * | 0.30 ** | 0.87 ** | ||||||
Na+ conc | PS | −0.16 | −0.19 * | −0.09 | 0.05 | −0.35 ** | −0.38 ** | ||||
K+ conc | PS | 0.05 | 0.31 ** | 0.21 * | −0.01 | 0.35 ** | 0.41 ** | −0.34 | |||
Na++/K+ conc | PS | −0.09 | −0.33 ** | −0.33 | −0.02 | −0.50 ** | −0.57 ** | 0.54 | −0.67 | ||
Score | PS | −0.13 | −0.27 ** | 0.19 * | −0.23 * | −0.61 ** | −0.71 ** | 0.36 | −0.44 ** | 0.68 ** | 1 |
Trait | QTL | Chr | LOD Score | Marker Interval | Additive Effect | PVE% |
---|---|---|---|---|---|---|
PH | qPHSt-2 | 2 | 5.2 | RM262-RM263 | 42.45 | 28.12 |
qPHSt-6.1 | 6 | 2.62 | RM589-RM586 | −2.64 | 5.93 | |
qPHSt-6.2 | 6 | 3.41 | RM204-RM276 | −2.64 | 10.32 | |
PN | qPNSt-1 | 1 | 2.66 | RM10115-RM3426 | 0.31 | 7.56 |
qPNSt-11 | 11 | 2.71 | RM224-RM207 | −0.53 | 10.44 | |
PL | qPLSt-6 | 6 | 3.16 | RM589-RM586 | −0.49 | 6.89 |
BM | qBMSt-2 | 2 | 2.69 | RM262-RM263 | 1.81 | 9.03 |
qBMSt-10 | 10 | 3.93 | RM24893-RM25846 | −4.49 | 10.78 | |
qBMSt-11 | 11 | 2.94 | RM224-RM207 | −1.76 | 9.33 | |
qBMSt-12 | 12 | 3.02 | RM27971-RM7102 | −1.99 | 9.97 | |
SPYL | qYLSt-12 | 12 | 2.81 | RM27940-RM27971 | −0.78 | 6.41% |
Trait | QTL | Chr | LOD Score | Marker Interval | Additive Effect | PVE% |
---|---|---|---|---|---|---|
PH | qPHSt-12.2 | 12 | 2.5 | RM27940-RM27971 | −9.07 | 8.07 |
PN | qTNSt-10 | 10 | 2.73 | RM24893-RM25846 | −0.5 | 6.1 |
PL | qPLSt-1.1 | 1 | 3.93 | RM3426-RM5638 | −1.05 | 13.25 |
qPLSt-1.2 | 1 | 2.97 | RM11504-RM3482 | −0.86 | 10.9 | |
qPLSt-2 | 2 | 2.5 | RM3294-RM12849 | −0.77 | 6.97 | |
ST | qSTR-2 | 2 | 2.6 | RM110-RM423 | 0.6 | 8.9 |
qSTR-11 | 11 | 2.23 | RM3717-RM286 | 0.69 | 8.9 | |
NC | qSN-11 | 11 | 2.92 | RM26622-RM21 | 24.77 | 6.49 |
qSN-12 | 12 | 2.8 | RM17-RM28587 | 26.86 | 7.51 | |
NK | qSNK-12.1 | 12 | 3.53 | RM17-RM28587 | 1.27 | 15.65 |
qSNK-12.2 | 12 | 2.77 | RM28587-RM28882 | 1.06 | 11.19 | |
qYLSt-2 | 2 | 2.05 | RM13863-RM3316 | 0.72 | 5.8 |
RILs | Score | Yield (g) | Na+ Conc. | K+ Conc. | Na+/K+ | QTL | % Inc. Over SP | % Inc. Over RP |
---|---|---|---|---|---|---|---|---|
RP 5899-RIL-52 | 1 | 11.5 | 164.6 | 84.7 | 1.94 | qSN-12 + qSNK-12.1 + qYLSt-12 | 86.96 | 28.87 |
RP 5899-RIL-57 | 1 | 11 | 154.3 | 46.7 | 3.30 | qSN-11 | 86.36 | 25.64 |
RP 5899-RIL-60 | 1 | 15 | 148.2 | 48.3 | 3.07 | qSTR-2 + qSN-12 + qSNK-12.1 + qSNK-12.2 + qYLSt-12 | 90.00 | 45.47 |
RP 5899-RIL-114 | 1 | 5.5 | 131.7 | 33.2 | 3.97 | qSN-12 + qSNK-12.1 + qSNK-12.2 | 72.73 | −48.73 |
RP 5899-RIL-141 | 1 | 9 | 168 | 88.1 | 1.91 | qSN-11 + qSN-12 + qSNK-12.1 | 83.33 | 9.11 |
RP 5899-RIL-142 | 1 | 11 | 132.7 | 119 | 1.12 | qSTR-2 + qSN-12 + qSNK-12.1 | 86.36 | 25.64 |
Jarava | 4.5 | 8.18 | 183.5 | 64.5 | 2.89 | |||
RP Bio226 | 8.25 | 1.5 | 286.6 | 37.03 | 7.81 |
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Sugasi, Y.D.; Srivastava, A.; Badri, J.; Pandey, M.; Parmar, B.; Singh, A.K.; Kishor, P.B.K.; Tilatoo, R. Mapping Quantitative Trait Loci (QTLs) for Reproductive Stage Salinity Tolerance in Rice. Crops 2024, 4, 684-700. https://doi.org/10.3390/crops4040047
Sugasi YD, Srivastava A, Badri J, Pandey M, Parmar B, Singh AK, Kishor PBK, Tilatoo R. Mapping Quantitative Trait Loci (QTLs) for Reproductive Stage Salinity Tolerance in Rice. Crops. 2024; 4(4):684-700. https://doi.org/10.3390/crops4040047
Chicago/Turabian StyleSugasi, Yamini Deepthi, Akanksha Srivastava, Jyothi Badri, Manish Pandey, Brajendra Parmar, Arun Kumar Singh, Polavarapu Bilhan Kavi Kishor, and Ram Tilatoo. 2024. "Mapping Quantitative Trait Loci (QTLs) for Reproductive Stage Salinity Tolerance in Rice" Crops 4, no. 4: 684-700. https://doi.org/10.3390/crops4040047
APA StyleSugasi, Y. D., Srivastava, A., Badri, J., Pandey, M., Parmar, B., Singh, A. K., Kishor, P. B. K., & Tilatoo, R. (2024). Mapping Quantitative Trait Loci (QTLs) for Reproductive Stage Salinity Tolerance in Rice. Crops, 4(4), 684-700. https://doi.org/10.3390/crops4040047