Genetic Dissection of Panicle Morphology Traits in Super High-Yield Hybrid Rice Chaoyou 1000
Abstract
:1. Introduction
2. Result
2.1. Phenotypic Analysis of Parents and Populations
2.2. Correlation Analysis of Panicle-Related Traits
2.3. Construction of Genetic Map
2.4. Main-QTL Analysis
2.5. Digenic Epistatic QTL Pairs (E-QTL) Underlying Panicle Morphology Traits
2.6. Q × E Interaction Analysis in F2 and F2:3 Populations
3. Discussion
4. Materials and Methods
4.1. Plant Material
4.2. Field Experiment
4.3. Traits Investigation and Data Analysis
4.4. DNA Extraction and Marker Analysis
4.5. Genetic Map Construction and QTL Detection
5. Conclusions
Supplementary Materials
Author Contributions
Funding
Data Availability Statement
Conflicts of Interest
References
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Chr. | Physical Distance (Mb) | Mean Physical Distance (Mb) | Genetic Distance (cM) | Mean Genetic Distance (cM) | The Number of Marker |
---|---|---|---|---|---|
1 | 43.20 | 3.32 | 288.52 | 22.19 | 13 |
2 | 36.00 | 3.00 | 293.95 | 24.50 | 12 |
3 | 37.85 | 4.73 | 260.65 | 32.58 | 8 |
4 | 34.1 | 2.44 | 212.8 | 15.20 | 14 |
5 | 29.79 | 2.98 | 151.17 | 15.12 | 10 |
6 | 30.96 | 3.10 | 229.03 | 22.90 | 10 |
7 | 28.87 | 3.21 | 160.66 | 17.85 | 9 |
8 | 28.56 | 3.17 | 129.42 | 14.38 | 9 |
9 | 23.61 | 2.62 | 149.86 | 16.65 | 9 |
10 | 24.39 | 2.71 | 125.43 | 13.94 | 9 |
11 | 30.3 | 2.75 | 146.68 | 13.33 | 11 |
12 | 25.37 | 2.82 | 114.32 | 12.70 | 9 |
Total | 373 | 3.07 | 2262.48 | 18.45 | 123 |
Trait Name | Environment | QTL | Chr. | Marker Interval | LOD | R2 (%) |
---|---|---|---|---|---|---|
PN | HZ | qPN-7F | 7 | RM1132-RM3555 | 2.83 | 10.60 |
PBN | HN | qPBN-4L | 4 | CM4-27-RM349 | 12.08 | 46.09 |
PBN | HZ | qPBN-4F | 4 | CM4-27-RM349 | 4.49 | 17.52 |
SBN | HN | qSBN-4.1L | 4 | RM349-RM1113 | 2.59 | 9.26 |
SBN | HZ | qSBN-4.2F | 4 | CM4-25-CM4-27 | 2.64 | 9.71 |
SBN | HN | qSBN-7L | 7 | CM7-6-RM11 | 4.25 | 11.80 |
SBN | HN | qSBN-9L | 9 | CM9-15-CM9-14 | 4.57 | 16.75 |
SBN | HN | qSBN-12L | 12 | RM1337-RM101 | 2.78 | 7.26 |
PL | HZ | qPL-1F | 1 | RM8097-CM1-10 | 2.56 | 11.97 |
PL | HZ | qPL-5F | 5 | CM5-5-CM5-4 | 2.65 | 10.28 |
PL | HN | qPL-7L | 7 | CM7-6-RM11 | 6.79 | 21.33 |
PL | HZ | qPL-7F | 7 | CM7-6-RM11 | 2.65 | 8.67 |
PL | HN | qPL-8L | 8 | RM5556-CM8-6 | 2.69 | 7.21 |
GN | HZ | qGN-2F | 2 | CM2-12-CM2-13 | 2.80 | 15.79 |
GN | HN | qGN-3L | 3 | CM3-8-CM3-23 | 3.28 | 26.64 |
GN | HN | qGN-4.1L | 4 | CM4-27-RM349 | 2.73 | 15.91 |
GN | HZ | qGN-4.2F | 4 | CM4-25-CM4-27 | 2.80 | 10.75 |
GN | HN | qGN-7L | 7 | CM7-6-RM11 | 2.54 | 9.22 |
FGN | HN | qFGN-3L | 3 | CM3-8-CM3-23 | 2.63 | 20.36 |
FGN | HN | qFGN-4L | 4 | RM349-RM1113 | 2.74 | 12.02 |
FGN | HN | qFGN-7L | 7 | RM3755-CM7-6 | 2.65 | 9.65 |
EGN | HN | qEGN-1L | 1 | STS-CM1-31 | 4.65 | 28.89 |
EGN | HN | qEGN-2L | 2 | CM2-15-CM2-5 | 4.85 | 28.24 |
EGN | HN | qEGN-2.2L | 2 | CM2-2-CM2-35 | 6.29 | 29.98 |
EGN | HZ | qEGN-2.3F | 2 | RM3316-CM2-6 | 3.03 | 9.25 |
SSR | HN | qSSR-1L | 1 | STS-CM1-31 | 3.23 | 24.54 |
SSR | HN | qSSR-2.1L | 2 | CM2-5-CM2-15 | 5.30 | 27.55 |
SSR | HN | qSSR-2.2L | 2 | CM2-2-CM2-35 | 2.84 | 22.01 |
SSR | HN | qSSR-5L | 5 | RM3616-CM5-17 | 2.89 | 4.96 |
SSR | HN | qSSR-6L | 6 | CM6-14-CM6-18 | 4.12 | 30.86 |
SSR | HN | qSSR-10L | 10 | CM10-14-RM1375 | 3.02 | 26.66 |
PSD | HN | qPSD-4.1L | 4 | CM4-27-RM349 | 2.73 | 13.82 |
PSD | HZ | qPSD-4.2F | 4 | RM3839-CM4-25 | 3.98 | 15.28 |
Population | Trait | Region1 | Region2 | |||||||
---|---|---|---|---|---|---|---|---|---|---|
Chr. | Marker Interval | M-QTL | Chr. | Marker Interval | M-QTL | LOD | AA | R2 | ||
F2 | PN | 2 | CM2-15-CM2-5 | 8 | CM8-15-CM8-23 | 5.90 | −0.77 | 20.16 | ||
PN | 3 | CM3-13-CM3-11 | 8 | CM8-15-CM8-23 | 7.16 | 0.16 | 23.24 | |||
PL | 8 | RM5556-CM8-6 | 12 | CM12-15-SSR | 5.51 | 0.43 | 10.47 | |||
PBN | 4 | RM349-RM1113 | 11 | CM11-21-CM11-41 | 6.80 | −0.99 | 8.60 | |||
PBN | 2 | CM2-2-CM2-35 | 4 | RM349-RM1113 | 6.51 | 0.86 | 8.97 | |||
PBN | 4 | CM4-27-RM349 | 8 | CM8-13-CM8-21 | 5.73 | 0.32 | 9.35 | |||
SBN | 4 | RM3839-CM4-25 | 9 | CM9-13-CM9-15 | qSBN-9L | 5.65 | 0.53 | 14.89 | ||
GN | 4 | CM4-27-RM349 | 8 | CM8-13-CM8-21 | 6.87 | −6.83 | 17.09 | |||
GN | 2 | CM2-2-CM2-35 | 7 | RM11-RM1132 | 6.29 | 1.78 | 20.90 | |||
FGN | 2 | CM2-5-CM2-3 | 4 | RM349-RM1113 | qFGN-4L | 6.13 | 37.80 | 13.52 | ||
FGN | 2 | CM2-5-CM2-3 | 11 | CM11-29-CM11-21 | 5.87 | 2.02 | 19.40 | |||
EGN | 2 | CM2-15-CM2-5 | qEGN-2L | 2 | CM2-15-CM2-5 | qEGN-2L | 11.68 | −9.71 | 22.18 | |
EGN | 1 | STS-CM1-31 | qEGN-1L | 2 | CM2-3-CM2-1 | 12.88 | 14.70 | 18.29 | ||
EGN | 1 | STS-CM1-31 | qEGN-1L | 3 | CM3-13-CM3-11 | 13.80 | −2.45 | 21.78 | ||
EGN | 2 | CM2-15-CM2-5 | qEGN-2L | 3 | CM3-23-CM3-35 | 11.98 | −9.40 | 22.85 | ||
EGN | 2 | CM2-15-CM2-5 | qEGN-2L | 4 | CM4-25-CM4-27 | 9.74 | −8.90 | 17.66 | ||
EGN | 1 | STS-CM1-31 | qEGN-1L | 5 | CM5-4-CM5-1 | 11.37 | -8.82 | 21.78 | ||
EGN | 2 | CM2-15-CM2-5 | qEGN-2L | 5 | CM5-4-CM5-1 | 10.15 | 6.75 | 16.95 | ||
EGN | 2 | CM2-15-CM2-5 | qEGN-2L | 6 | CM6-18-CM5-20 | 12.55 | −4.77 | 21.59 | ||
EGN | 2 | CM2-15-CM2-5 | qEGN-2L | 7 | CM6-28-STS | 12.12 | −7.90 | 21.75 | ||
SSR | 1 | CM6-28-STS | 2 | CM2-15-CM2-5 | qSSR-2.1L | 8.68 | 0.03 | 18.39 | ||
SSR | 2 | CM2-15-CM2-5 | qSSR-2.1L | 5 | RM3616-CM5-17 | 8.49 | −0.05 | 17.83 | ||
SSR | 2 | CM2-15-CM2-5 | qSSR-2.1L | 6 | CM6-14-CM6-18 | qSSR-6L | 9.52 | −0.03 | 18.77 | |
SSR | 6 | CM6-14-CM6-18 | qSSR-6L | 6 | CM6-14-CM6-18 | qSSR-6L | 10.56 | 0.03 | 18.84 | |
SSR | 1 | STS-CM1-31 | qSSR-1L | 7 | STS-CM7-2 | 9.57 | −0.09 | 19.60 | ||
SSR | 1 | STS-CM1-31 | qSSR-1L | 10 | CM10-14-RM1375 | 8.54 | -0.02 | 17.91 | ||
SSR | 2 | CM2-15-CM2-5 | qSSR-2.1L | 10 | CM10-14-RM1375 | 9.98 | −0.04 | 18.62 | ||
SSR | 2 | CM2-15-CM2-5 | qSSR-2.1L | 11 | STS-CM11-5 | 7.37 | −0.01 | 18.44 | ||
PSD | 2 | CM2-3-CM2-1 | 4 | CM4-27-RM349 | qPSD-4.1L | 5.08 | 2.01 | 11.82 | ||
PSD | 3 | CM3-18-CM3-13 | 4 | CM4-27-RM349 | qPSD-4.1L | 5.72 | 2.49 | 14.00 | ||
PSD | 4 | CM4-27-RM349 | qPSD-4.1L | 7 | RM11-RM1132 | 5.04 | 0.12 | 11.19 | ||
PSD | 4 | CM4-27-RM349 | qPSD-4.1L | 8 | CM8-13-CM8-21 | 7.51 | −0.44 | 11.53 | ||
F2:3 | PN | 2 | CM2-15-CM2-5 | 11 | CM11-5-CM11-37 | 5.90 | −0.25 | 30.52 | ||
PN | 4 | CM4-19-CM4-21 | 12 | SSR-CM12-27 | 5.75 | −1.06 | 13.17 | |||
PN | 4 | RM349-RM1113 | 7 | RM11-RM1132 | qPN-7F | 7.68 | -2.18 | 23.22 | ||
PN | 7 | RM11-RM1132 | qPN-7F | 9 | CM9-7-CM9-10 | 6.54 | −0.93 | 24.74 | ||
PN | 10 | CM10-14-RM1375 | 10 | RM5689-CM10-10 | 6.09 | 0.44 | 19.83 | |||
PL | 9 | CM8-17-STS | 10 | CM10-9-CM10-7 | 5.72 | −1.31 | 8.76 | |||
PL | 4 | CM4-25-CM4-27 | 7 | CM6-28-STS | 5.67 | −0.90 | 15.36 | |||
PBN | 1 | STS-CM1-31 | 8 | RM5556-CM8-6 | 5.58 | −0.43 | 23.29 | |||
PBN | 4 | CM4-19-CM4-21 | 7 | CM6-28-STS | 5.91 | 0.82 | 16.80 | |||
PBN | 6 | CM6-14-CM6-18 | 8 | CM8-11-CM8-13 | 5.70 | 1.33 | 21.43 | |||
SBN | 4 | CM4-27-RM349 | 8 | CM8-15-CM8-23 | 6.73 | −3.22 | 20.34 | |||
SBN | 4 | CM4-15-CM4-34 | 9 | CM9-13-CM9-15 | 5.82 | 13.56 | 15.50 | |||
GN | 2 | CM2-15-CM2-5 | 9 | CM9-9-CM9-7 | 5.96 | 1.26 | 28.02 | |||
GN | 4 | RM3839-CM4-25 | qGFN-4.2F | 8 | CM8-15-CM8-23 | 5.56 | −0.82 | 21.04 | ||
SSR | 2 | CM2-15-CM2-5 | 2 | CM2-5-CM2-3 | 5.90 | 0.12 | 21.43 | |||
SSR | 2 | CM2-15-CM2-5 | 5 | CM5-19-RM3616 | 5.36 | 0.06 | 16.30 | |||
SSR | 4 | CM4-25-CM4-27 | 5 | CM5-19-RM3616 | 5.30 | 0.07 | 10.67 | |||
SSR | 2 | CM2-15-CM2-5 | 6 | CM6-14-CM6-18 | 7.59 | 0.13 | 30.75 | |||
PSD | 2 | CM2-15-CM2-5 | 3 | CM3-8-CM3-23 | 5.12 | −0.63 | 25.82 | |||
PSD | 1 | STS-CM1-31 | 4 | CM4-25-CM4-27 | qPSD-4.2F | 5.60 | −0.03 | 22.70 | ||
PSD | 4 | CM4-25-CM4-27 | qPSD-4.2F | 9 | CM9-13-CM9-15 | 6.45 | −0.63 | 16.18 |
QTLs | Traits | Chr. | Marker Interval | R2 (%) | R2byA (%) | R2byE (%) | AbyE01 | AbyE02 |
---|---|---|---|---|---|---|---|---|
qPN-7F | PN | 7 | RM1132-RM3555 | 5.88 | 1.63 | 4.25 | 0.23 | −0.23 |
qPL-5F | PL | 5 | CM5-5-CM5-4 | 5.45 | 1.24 | 4.21 | 0.15 | −0.15 |
qPL-7F | PL | 7 | CM7-6-RM11 | 12.24 | 12.04 | 0.20 | −0.10 | 0.10 |
qPL-8L | PL | 8 | RM5556-CM8-6 | 3.21 | 2.52 | 0.69 | −0.17 | 0.17 |
qPBN-4F | PBN | 4 | CM4-27-RM349 | 22.16 | 20.91 | 1.25 | −0.20 | 0.20 |
qSBN-4.2F | SBN | 4 | CM4-25-CM4-27 | 6.25 | 5.46 | 0.79 | 0.62 | −0.62 |
qSBN-7L | SBN | 7 | CM7-6-RM11 | 6.01 | 5.27 | 0.74 | −1.33 | 1.33 |
qSBN-9L | SBN | 9 | CM9-15-CM9-14 | 4.03 | 2.23 | 1.80 | −2.11 | 2.11 |
qSBN-12L | SBN | 12 | RM1337-RM101 | 5.20 | 4.90 | 0.30 | −0.42 | 0.42 |
qGN-4L | GN | 4 | CM4-27-RM349 | 7.47 | 6.98 | 0.49 | −0.05 | 0.05 |
qGN-7L | GN | 7 | CM7-6-RM11 | 5.56 | 5.41 | 0.15 | −2.09 | 2.09 |
qFGN-7L | FGN | 7 | RM3755-CM7-6 | 3.41 | 1.45 | 1.95 | −10.03 | 10.03 |
qSSR-5L | SSR | 5 | RM3616-CM5-17 | 2.25 | 1.14 | 1.12 | 0.00 | 0.00 |
qPSD-4.2F | PSD | 4 | M45-M46 | 7.89 | 7.32 | 0.57 | 0.09 | −0.09 |
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Jiang, J.; Wang, L.; Fan, G.; Long, Y.; Lu, X.; Wang, R.; Liu, H.; Qiu, X.; Zeng, D.; Li, Z. Genetic Dissection of Panicle Morphology Traits in Super High-Yield Hybrid Rice Chaoyou 1000. Plants 2024, 13, 179. https://doi.org/10.3390/plants13020179
Jiang J, Wang L, Fan G, Long Y, Lu X, Wang R, Liu H, Qiu X, Zeng D, Li Z. Genetic Dissection of Panicle Morphology Traits in Super High-Yield Hybrid Rice Chaoyou 1000. Plants. 2024; 13(2):179. https://doi.org/10.3390/plants13020179
Chicago/Turabian StyleJiang, Jing, Li Wang, Gucheng Fan, Yu Long, Xueli Lu, Run Wang, Haiyang Liu, Xianjin Qiu, Dali Zeng, and Zhixin Li. 2024. "Genetic Dissection of Panicle Morphology Traits in Super High-Yield Hybrid Rice Chaoyou 1000" Plants 13, no. 2: 179. https://doi.org/10.3390/plants13020179
APA StyleJiang, J., Wang, L., Fan, G., Long, Y., Lu, X., Wang, R., Liu, H., Qiu, X., Zeng, D., & Li, Z. (2024). Genetic Dissection of Panicle Morphology Traits in Super High-Yield Hybrid Rice Chaoyou 1000. Plants, 13(2), 179. https://doi.org/10.3390/plants13020179