Developing Novel Rice Genotypes Harboring Specific QTL Alleles Associated with High Grain Yield under Water Shortage Stress
Abstract
:1. Introduction
2. Results
2.1. The Response of the Newly Developed Lines to Water Shortage Stress
2.2. High Heritability in the Broad Sense under Water-Shortage Stress
2.3. Marker Selection Based on Parents’ Genotyping
2.4. Marker-Trait Association for GY under Water Stress and Normal Conditions
2.5. Consistent Allele Effect across the Different Water Regimes
3. Discussion
3.1. Phenotypic Response and Lines Performance under Well-Watered and Stress Conditions
3.2. GY Heritability under Water Shortage Stress Condition
3.3. Genotypic Evaluation of the Parents with the Markers Linked to GY QTLs
3.4. Marker GY Association Analysis and Common Parent Allele Effect
3.5. Consistent QTL Effect under Both Stress and Well-Watered Conditions
3.6. The Newly Developed Lines Harboring High Effect QTLs
4. Materials and Methods
4.1. Plant Material Development
4.2. Climate and Soil Properties
4.3. Field Evaluation Procedures
4.4. Phenotypic Data Statistical Analysis
4.5. Molecular Analysis
4.6. Genetic Analysis and Single Marker Analysis (SMA)
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Characters | Days to Heading | Plant Height (cm) | Panicle Weight (g) | Panicle Length (cm) | Yield (kg/m2) | Seed Set (%) | 1000-Grain Weight (g) | Drought Susceptibility Index | Reduction % | |||||||
---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
Genotypes (Fn) | N | S | N | S | N | S | N | S | N | S | N | S | N | S | ||
M.J5460S/GIZA177-3 | 88.73 | 95.26 | 90.36 | 75.33 | 5.83 | 3.39 | 20.85 | 18.06 | 1.38 | 0.59 | 94.51 | 69.28 | 30.31 | 24.13 | 0.572 | 57.195 |
M.J5460S/GIZA177-12 | 92.06 | 96.26 | 101.67 | 80.33 | 5.43 | 2.73 | 21.30 | 20.42 | 1.20 | 0.54 | 95.65 | 67.18 | 29.42 | 23.40 | 0.548 | 54.849 |
M.J5460S/GIZA177-18 | 91.22 | 96.38 | 99.70 | 95.33 | 4.07 | 2.76 | 23.55 | 17.22 | 1.08 | 0.46 | 94.58 | 63.14 | 28.59 | 23.10 | 0.570 | 56.957 |
M.J5460S/GIZA177-22 | 93.40 | 100.93 | 120.16 | 76.33 | 5.21 | 1.19 | 23.22 | 16.62 | 1.05 | 0.17 | 92.76 | 29.60 | 30.13 | 22.17 | 0.842 | 84.244 |
M.J5460S/GIZA177-28 | 92.09 | 93.93 | 113.38 | 96.67 | 5.22 | 1.34 | 26.57 | 22.13 | 1.13 | 0.20 | 91.76 | 38.07 | 27.39 | 23.13 | 0.828 | 82.764 |
M.J5460S/SAKHA105-6 | 90.53 | 97.93 | 97.13 | 85.33 | 5.72 | 2.38 | 25.51 | 21.71 | 1.19 | 0.38 | 95.29 | 56.77 | 31.42 | 23.40 | 0.679 | 67.896 |
M.J5460S/SAKHA105-15 | 92.22 | 103.60 | 99.09 | 75.33 | 5.48 | 2.32 | 20.84 | 15.44 | 1.12 | 0.43 | 95.38 | 55.49 | 32.45 | 21.47 | 0.614 | 61.358 |
M.J5460S/SAKHA105-20 | 95.15 | 99.93 | 98.11 | 79.67 | 5.64 | 1.21 | 19.00 | 16.18 | 1.06 | 0.20 | 92.68 | 27.63 | 34.22 | 21.03 | 0.808 | 80.784 |
M.J5460S/SAKHA106-1 | 90.07 | 95.93 | 98.42 | 79.67 | 5.63 | 1.22 | 21.83 | 18.16 | 1.22 | 0.19 | 93.41 | 24.15 | 32.48 | 22.33 | 0.842 | 84.242 |
M.J5460S/SAKHA106-5 | 95.46 | 103.60 | 112.74 | 90.11 | 5.54 | 1.40 | 22.90 | 21.00 | 1.34 | 0.24 | 93.55 | 32.39 | 28.22 | 23.25 | 0.819 | 81.882 |
M.J5460S/SAKHA106-6 | 88.58 | 102.60 | 86.58 | 75.33 | 5.79 | 1.36 | 23.09 | 16.59 | 1.28 | 0.18 | 94.41 | 21.67 | 30.13 | 21.42 | 0.857 | 85.725 |
M.J5460S/SAKHA106-12 | 98.87 | 105.15 | 112.50 | 73.56 | 5.59 | 1.72 | 22.96 | 17.12 | 1.28 | 0.24 | 91.61 | 35.01 | 29.38 | 21.77 | 0.816 | 81.612 |
M.J5460S/SAKHA106-15 | 90.41 | 110.04 | 114.76 | 60.44 | 5.27 | 2.30 | 23.93 | 16.64 | 1.24 | 0.38 | 91.65 | 54.08 | 30.51 | 23.28 | 0.692 | 69.208 |
M.J5460S/SAKHA106-18 | 91.73 | 98.93 | 87.71 | 80.11 | 3.53 | 1.51 | 20.30 | 17.22 | 1.00 | 0.20 | 92.12 | 18.39 | 28.36 | 22.33 | 0.798 | 79.821 |
M.J5460S/SAKHA106-25 | 95.47 | 111.93 | 90.64 | 75.78 | 4.65 | 2.92 | 18.27 | 15.40 | 1.07 | 0.40 | 94.49 | 50.68 | 26.29 | 21.20 | 0.625 | 62.496 |
M.J5460S/GZ.7768-4 | 94.57 | 102.93 | 85.73 | 75.44 | 5.58 | 2.28 | 22.31 | 19.06 | 1.18 | 0.36 | 92.34 | 56.60 | 31.56 | 22.20 | 0.693 | 69.318 |
M.J5460S/GZ.7768-7 | 97.07 | 114.93 | 92.39 | 75.67 | 5.64 | 1.34 | 24.30 | 20.06 | 1.23 | 0.19 | 93.73 | 28.70 | 26.79 | 23.00 | 0.843 | 84.328 |
M.J5460S/GZ.7768-10 | 95.47 | 100.93 | 106.20 | 80.00 | 5.53 | 3.08 | 20.44 | 16.36 | 1.28 | 0.47 | 92.07 | 67.09 | 28.44 | 23.20 | 0.634 | 63.396 |
M.J5460S/GZ.7768-30 | 92.80 | 102.93 | 90.84 | 77.33 | 5.59 | 2.69 | 22.22 | 19.66 | 1.38 | 0.38 | 93.41 | 56.12 | 30.07 | 24.20 | 0.724 | 72.368 |
M.J5460S | 84.00 | 89.93 | 95.67 | 82.33 | 5.75 | 3.48 | 21.86 | 18.31 | 1.20 | 0.60 | 93.14 | 72.25 | 29.05 | 24.17 | 0.498 | 49.847 |
Giza177 | 85.71 | 95.93 | 102.59 | 65.33 | 3.45 | 1.10 | 23.54 | 16.07 | 0.96 | 0.33 | 95.11 | 61.17 | 28.71 | 23.10 | 0.659 | 65.892 |
Sakha105 | 87.51 | 94.93 | 99.94 | 60.44 | 3.56 | 1.24 | 23.97 | 16.60 | 0.98 | 0.20 | 93.88 | 33.07 | 29.44 | 23.15 | 0.795 | 79.477 |
Sakha106 | 88.94 | 94.93 | 104.41 | 73.11 | 3.48 | 1.68 | 24.13 | 17.11 | 1.10 | 0.20 | 93.25 | 45.31 | 26.76 | 23.87 | 0.816 | 81.620 |
GZ7768 | 87.86 | 116.93 | 105.64 | 70.44 | 3.64 | 1.09 | 21.07 | 17.47 | 1.06 | 0.19 | 95.77 | 31.38 | 26.98 | 22.17 | 0.817 | 81.681 |
Azucena | 101.64 | 108.93 | 158.53 | 122.56 | 4.05 | 3.02 | 26.06 | 23.27 | 0.91 | 0.62 | 90.90 | 74.19 | 31.86 | 24.50 | 0.318 | 31.783 |
IRAT 170 | 86.83 | 94.93 | 128.00 | 110.56 | 4.89 | 3.13 | 27.84 | 22.48 | 0.92 | 0.65 | 90.49 | 72.76 | 31.85 | 24.27 | 0.294 | 29.433 |
Mean | 91.86 | 101.18 | 103.57 | 80.48 | 4.99 | 2.07 | 22.76 | 18.32 | 1.15 | 0.35 | 93.38 | 47.78 | 29.65 | 22.89 | 0.69 | 69.24 |
LSD | 1.98 | 1.44 | 1.99 | 1.67 | 0.65 | 0.53 | 1.09 | 0.83 | 0.06 | 0.01 | 0.82 | 0.55 | 0.73 | 0.44 | - | - |
Characters | Replications (df = 2) | Genotypes (df = 25) | Coefficient of Variation | |||
---|---|---|---|---|---|---|
N | S | N | S | N | S | |
Days to heading | 1.637 ns | 0.073 ns | 51.49 ** | 141.35 ** | 0.844 | 0.406 |
Plant height (cm) | 1.187 ns | 0.639 ns | 718.86 ** | 563.00 ** | 0.756 | 0.684 |
Panicle weight (g) | 0.123 ns | 0.002 ns | 2.22 ** | 1.976 ** | 1.677 | 2.704 |
Panicle length (cm) | 0.263 ns | 0.184 ns | 15.33 ** | 15.939 ** | 1.033 | 0.739 |
Yield M-2 (kg/m2) | 0.001 ns | 0.001 ns | 0.055 ** | 0.076 ** | 0.067 | 0.004 |
Seed set (%) | 0.057 ns | 0.012 ns | 6.66 ** | 968.72 ** | 0.142 | 0.125 |
1000-grain weight (g) | 0.101 ns | 0.041 ns | 12.33 ** | 3.044 ** | 0.359 | 0.165 |
Characters | Mean | Range | GCV (%) | ECV (%) | PCV (%) | H2 (%) | |
---|---|---|---|---|---|---|---|
Min | Max | ||||||
Well-watered condition | |||||||
Days to heading | 91.861 | 84.00 | 101.64 | 4.48 | 1.69 | 4.78 | 87.510 |
Plant height (cm) | 103.573 | 85.73 | 158.53 | 14.94 | 1.35 | 15.00 | 99.184 |
Panicle weight (g) | 4.991 | 3.45 | 5.83 | 16.93 | 9.10 | 19.22 | 77.564 |
Panicle length (cm) | 22.765 | 18.27 | 27.84 | 9.85 | 3.10 | 10.33 | 90.989 |
Yield M-2 (kg/m2) | 1.149 | 0.91 | 1.38 | 11.73 | 2.89 | 12.09 | 94.269 |
Seed set (%) | 93.383 | 90.49 | 95.77 | 1.58 | 0.47 | 1.65 | 92.015 |
1000-grain weight (g) | 29.648 | 26.29 | 34.22 | 6.81 | 1.54 | 6.98 | 95.147 |
Water-stress condition | |||||||
Days to heading | 101.178 | 89.93 | 116.93 | 6.77 | 0.69 | 6.81 | 98.980 |
Plant height (cm) | 80.483 | 60.44 | 122.56 | 17.01 | 1.36 | 17.07 | 99.370 |
Panicle weight (g) | 2.072 | 1.09 | 3.48 | 38.62 | 11.61 | 40.33 | 91.709 |
Panicle length (cm) | 18.321 | 15.40 | 23.27 | 12.53 | 3.08 | 12.90 | 94.287 |
Yield M-2 (kg/m2) | 0.347 | 0.17 | 0.65 | 45.81 | 2.53 | 45.88 | 99.695 |
Seed set (%) | 47.776 | 18.39 | 74.19 | 37.61 | 0.56 | 37.62 | 99.978 |
1000-grain weight (g) | 22.891 | 21.03 | 24.50 | 4.37 | 1.22 | 4.54 | 92.729 |
Marker Allele | QTL | Water Stress Condition | Well Irrigation Condition | ||
---|---|---|---|---|---|
R2 | Allele Effect (kg/m2) | R2 | Allele Effect (kg/m2) | ||
RM555_240 | 2.2 | 17.8 * | 0.12 | 1.1 ns | 0.03 |
RM525_144 | 2.2 | 6.2 ns | 0.08 | 0.1 ns | 0.01 |
RM14551_620 | 3.1 | 25.3 ** | 0.17 | 34.7 ** | 0.17 |
RM3199_186 | 3.2 | 15.9 * | 0.11 | 0.0 ns | 0.00 |
RM410_195 | 9.1 | 27.8 ** | 0.17 | 22.5 ** | 0.13 |
RM257_166 | 9.1 | 31.6 ** | 0.16 | 11.8 ns | 0.08 |
RM242_208 | 9.1 | 60.3 ** | 0.21 | 2.60 ns | 0.04 |
No | Entries | Parents | Origin | Water-Stress Response |
---|---|---|---|---|
1 | M.J5460S | rT60-6 MS | China | Tolerant |
2 | Giza177 | [Giza171] Ymji Ni.1//PiNo.4 | Egypt | Sensitive |
3 | Sakha105 | GZ5581/GZ4316 | Egypt | Sensitive |
4 | Sakha106 | Giza177/Hexi30 | Egypt | Sensitive |
5 | GZ7768 | GZ5320/Taninung70 | Egypt | Sensitive |
6 | Azucena | Landrace | Philippines | Tolerant |
7 | IRAT170 | IRAT13/Palawan | Ivory Cost | Tolerant |
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Abdelrahman, M.; Selim, M.E.; ElSayed, M.A.; Ammar, M.H.; Hussein, F.A.; ElKholy, N.K.; ElShamey, E.A.; Khan, N.; Attia, K.A. Developing Novel Rice Genotypes Harboring Specific QTL Alleles Associated with High Grain Yield under Water Shortage Stress. Plants 2021, 10, 2219. https://doi.org/10.3390/plants10102219
Abdelrahman M, Selim ME, ElSayed MA, Ammar MH, Hussein FA, ElKholy NK, ElShamey EA, Khan N, Attia KA. Developing Novel Rice Genotypes Harboring Specific QTL Alleles Associated with High Grain Yield under Water Shortage Stress. Plants. 2021; 10(10):2219. https://doi.org/10.3390/plants10102219
Chicago/Turabian StyleAbdelrahman, Mohamed, Mahmoud E. Selim, Mahmoud A. ElSayed, Megahed H. Ammar, Fatma A. Hussein, Neama K. ElKholy, Essam A. ElShamey, Naeem Khan, and Kotb A. Attia. 2021. "Developing Novel Rice Genotypes Harboring Specific QTL Alleles Associated with High Grain Yield under Water Shortage Stress" Plants 10, no. 10: 2219. https://doi.org/10.3390/plants10102219