Modeling of Flowering Time in Vigna radiata with Approximate Bayesian Computation
Abstract
:1. Introduction
2. Materials and Methods
2.1. The Overview
2.2. Plant Material
2.3. Climate Data
- a day length D,
- a minimal temperature ,
- a maximal temperature ,
- a precipitation R,
- for field experiments were taken from a publicly available website https://rp5.ru/Weather_in_the_world (accessed on 26 January 2020) that provides historical weather archives for 172,500 locations, reported by weather stations. The data on solar radiation S were obtained from the NASA Langley Research Center (LaRC) POWER Project funded through the NASA Earth Science/Applied Science Program [47].
2.4. Prediction of Time to Flowering with a Pool of Models
2.5. Approximate Bayesian Computation
2.6. Construction of the Pool of Models
2.7. Estimation of Impacts of Climatic Factors and Genotype Information to the Model
2.8. Simulation of Climate Warming
3. Results
3.1. A Pool of Models for Time to Flowering
3.2. The Best Model in the Pool
3.3. Impacts of Climatic Factors and SNPs to the Model
3.4. Simulation of Climate Warming
4. Discussion
5. Conclusions
Author Contributions
Funding
Institutional Review Board Statement
Informed Consent Statement
Data Availability Statement
Acknowledgments
Conflicts of Interest
References
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Date of Sowing | Date of Harvest | Geographical Coordinates |
---|---|---|
28/08/1984 | 24/10/1984 | N 23650 E 1201755 |
17/09/1985 | 03/10/1985 | N 23650 E 1201755 |
16/06/2016 | 22/08 to mid-September | N 173028 E 781610 |
21/09/2018 | from 24–28 December 2018 | N 23650 E 1201755 |
03/05/2018 | from mid-July | N 4518 E 4052 |
12/05/2018 | from mid-July | N 4614 E 4801 |
Num | Chr | Pos | Major | Minor |
---|---|---|---|---|
0 | NC_028351.1 | 10609109 | T | C |
1 | NC_028352.1 | 1756685 | A | T |
2 | NC_028353.1 | 4083774 | A | T |
3 | NC_028353.1 | 7715763 | T | C |
4 | NC_028354.1 | 19007443 | T | C |
5 | NC_028354.1 | 19193706 | A | T |
6 | NC_028356.1 | 5599756 | C | A |
7 | NC_028356.1 | 18228698 | C | T |
8 | NC_028357.1 | 36154036 | G | T |
9 | NC_028357.1 | 51548743 | T | C |
10 | NC_028358.1 | 42385899 | G | T |
11 | NC_028358.1 | 43289540 | T | C |
12 | NC_028358.1 | 43289553 | G | A |
13 | NC_028361.1 | 10688905 | A | C |
14 | NW_014541837.1 | 1074368 | C | T |
CR PCC | CR MED | CR RMS | TE PCC | TE MED | TE RMS | |
---|---|---|---|---|---|---|
0 | 0.97 | 7 | 11.91 | 0.98 | 8 | 12.19 |
1 | 0.97 | 6 | 11.55 | 0.98 | 7 | 11.75 |
2 | 0.97 | 7 | 12.09 | 0.98 | 7 | 12.71 |
3 | 0.97 | 8 | 12.60 | 0.97 | 8 | 12.20 |
4 | 0.97 | 6 | 12.26 | 0.97 | 7 | 12.44 |
5 | 0.97 | 7 | 12.65 | 0.97 | 7 | 13.90 |
6 | 0.97 | 7 | 12.73 | 0.97 | 8 | 13.46 |
7 | 0.97 | 6 | 12.32 | 0.94 | 7 | 19.19 |
8 | 0.97 | 6 | 12.00 | 0.98 | 7 | 12.14 |
9 | 0.97 | 6 | 11.23 | 0.98 | 7 | 11.64 |
10 | 0.97 | 7 | 12.67 | 0.98 | 7 | 13.54 |
11 | 0.97 | 8 | 12.93 | 0.96 | 9 | 14.62 |
12 | 0.97 | 7 | 12.30 | 0.98 | 7 | 11.84 |
13 | 0.97 | 8 | 12.48 | 0.97 | 9 | 12.96 |
14 | 0.97 | 8 | 12.77 | 0.97 | 8 | 12.78 |
15 | 0.97 | 8 | 13.13 | 0.97 | 9 | 13.06 |
16 | 0.96 | 6 | 13.60 | 0.96 | 7 | 15.79 |
17 | 0.97 | 10 | 13.11 | 0.96 | 10 | 14.66 |
18 | 0.97 | 8 | 13.35 | 0.97 | 9 | 13.62 |
19 | 0.97 | 10 | 13.19 | 0.97 | 10 | 12.66 |
20 | 0.97 | 7 | 13.47 | 0.98 | 7 | 12.74 |
21 | 0.96 | 11 | 14.51 | 0.97 | 11 | 14.33 |
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Ageev, A.; Lee, C.-R.; Ting, C.-T.; Schafleitner, R.; Bishop-von Wettberg, E.; Nuzhdin, S.V.; Samsonova, M.; Kozlov, K. Modeling of Flowering Time in Vigna radiata with Approximate Bayesian Computation. Agronomy 2021, 11, 2317. https://doi.org/10.3390/agronomy11112317
Ageev A, Lee C-R, Ting C-T, Schafleitner R, Bishop-von Wettberg E, Nuzhdin SV, Samsonova M, Kozlov K. Modeling of Flowering Time in Vigna radiata with Approximate Bayesian Computation. Agronomy. 2021; 11(11):2317. https://doi.org/10.3390/agronomy11112317
Chicago/Turabian StyleAgeev, Andrey, Cheng-Ruei Lee, Chau-Ti Ting, Roland Schafleitner, Eric Bishop-von Wettberg, Sergey V. Nuzhdin, Maria Samsonova, and Konstantin Kozlov. 2021. "Modeling of Flowering Time in Vigna radiata with Approximate Bayesian Computation" Agronomy 11, no. 11: 2317. https://doi.org/10.3390/agronomy11112317
APA StyleAgeev, A., Lee, C.-R., Ting, C.-T., Schafleitner, R., Bishop-von Wettberg, E., Nuzhdin, S. V., Samsonova, M., & Kozlov, K. (2021). Modeling of Flowering Time in Vigna radiata with Approximate Bayesian Computation. Agronomy, 11(11), 2317. https://doi.org/10.3390/agronomy11112317