Predictive Artificial Intelligence for Climate-Resilient Crop Breeding: Integrating Genomics, Phenomics, and Climate Modeling
DOI:
https://doi.org/10.32350/sir.101.02Keywords:
Predictive artificial intelligence; Climate-resilient crops; Machine learning; Genomic prediction; Phenomics; Crop breedingAbstract
Global food security is increasingly threatened by climate change, which intensifies both biotic and abiotic stresses on crops, leading to reduced yield stability and productivity. Conventional breeding approaches are insufficient to address these challenges due to long breeding cycles, strong genotype–environment interactions, and limited capacity to predict crop performance under future climate scenarios. Predictive artificial intelligence (AI) offers a powerful solution by integrating genomics, phenomics, environmental, and climate data to model complex traits, stress tolerance, and genotype performance across diverse agroecological conditions. This review synthesized recent advances in Machine Learning (ML), Deep Learning (DL), genomic prediction, high-throughput phenotyping, and climate modeling that collectively support the development of climate-resilient crop varieties. The application of predictive AI in plant breeding enhances selection accuracy, accelerates breeding decisions, reduces dependency on costly and time-consuming field trials, as well as improves resource-use efficiency. By enabling data-driven decision-making, AI-based approaches significantly improve the precision and scalability of modern crop improvement programs. Looking ahead, the integration of predictive AI with explainable modeling frameworks, multi-omics datasets, and genome-editing technologies holds significant promise for accelerating the development of high-yielding, resilient, and sustainable crops, thereby contributing to long-term food security under changing climatic conditions.
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1. Cobb JN, Biswas PS, Platten JD. Enhancing the rate of genetic gain in public-sector plant breeding programs: lessons from the breeder's equation. Plant Genome. 2019;12(1):1-16. https://doi.org/10.3835/plantgenome2018.11.0083
2. Crossa J, Pérez-Rodríguez P, Cuevas J, et al. Genomic selection in plant breeding: methods, models, and perspectives. Front Genet. 2017;8:e134. https://doi.org/10.3389/fgene.2017.00134
3. Danilevicz MF, Gill M, Anderson R, et al. Plant genotype-to-phenotype prediction using machine learning. Front Genet. 2022;13:e822173. https://doi.org/10.3389/fgene.2022.822173
4. Varshney RK, Babbar A, Sinha P. Accelerating genetic gains in agriculture: plant Breeding 4.0. Nat Genet. 2021;53(6):789-804. https://doi.org/10.1038/s41588-021-00868-7
5. Crossa J, Fritsche-Neto R, Montesinos-López O, et al. The modern plant breeding triangle. Trends Plant Sci. 2021;26(7):680-693. https://doi.org/10.1016/j.tplants.2021.01.005
6. Yang W, Feng H, Zhang X, et al. Crop phenomics and artificial intelligence: opportunities for climate-resilient breeding. Annu Rev Plant Biol. 2020;71:589-712. https://doi.org/10.1146/annurev-arplant-042817-040037
7. Farooq M, Hussain M, Rehman HU. Genomic prediction in plants: opportunities for ensemble machine learning-based approaches. Front Plant Sci. 2022;13:e1008209. https://doi.org/10.3389/fpls.2022.1008209
8. Khan MHU, Wang S, Wang J, et al. Applications of artificial intelligence in climate-resilient smart-crop breeding. Int J Mol Sci. 2022;23(19):e11156. https://doi.org/10.3390/ijms231911156
9. Washburn JD, Burch MB, Franco J, et al. Predictive breeding for maize using machine learning. Theor Appl Genet. 2021;134(12):3999-4012. https://doi.org/10.1007/s00122-021-03906-1
10. Li Y, Li M, Li C, Liu Z. Optimizing genomic selection in crop breeding. Mol Plant. 2022;15(4):645-656. https://doi.org/10.1016/j.molp.2022.02.007
11. Montesinos-López OA, Montesinos-López A, Crossa J. Deep learning for genomic selection: a review and future directions. Brief Bioinform. 2021;22(2):169-184. https://doi.org/10.1093/bib/bbz042
12. van Dijk ADJ, Kootstra G, Kruijer W, de Ridder D. Machine learning in plant science and plant breeding. iScience. 2021;24(1):e101890. https://doi.org/10.1016/j.isci.2020.101890
13. Heslot N, Akdemir D, Sorrells ME, Jannink JL. Integrating environmental covariates and crop modeling into genomic selection. Theor Appl Genet. 2020;133(6):1813-1826. https://doi.org/10.1007/s00122-020-03543-2
14. Pérez-Rodríguez P, Crossa J, Du Q, Montesinos-López OA. Multi-environment genomic prediction for plant breeding. Theor Appl Genet. 2020;133(10):2913-2930. https://doi.org/10.1007/s00122-020-03643-8
15. Cooper M, Messina CD, Podlich D, et al. Predicting the future of plant breeding by integrating genetic prediction and environmental data. Crop Sci. 2020;60(6):3116-3130. https://doi.org/10.1002/csc2.20302
16. Reynolds M, Villar E, Baker D. Climatic resilience breeding: improving crops for future climates. J Exp Bot. 2020;71(6):1778-1795. https://doi.org/10.1093/jxb/erz520
17. Hammer GL, McLean G, Chapman SC, et al. Linking crop modeling and decision support with climate forecasts. Nat Plants. 2020;6:1106-1115. https://doi.org/10.1038/s41477-020-00747-5
18. Intergovernmental Panel on Climate Change. Climate Change 2021: The Physical Science Basis. Contribution of Working Group I to the Sixth Assessment Report of the IPCC. Cambridge University Press; 2021. Accessed January 31, 2026. https://www.ipcc.ch/report/ar6/wg1/
19. Intergovernmental Panel on Climate Change. Climate Change 2022: Impacts, Adaptation and Vulnerability. Contribution of Working Group II to the Sixth Assessment Report of the IPCC. Cambridge University Press; 2022. Accessed January 31, 2026. https://www.ipcc.ch/report/ar6/wg2/
20. Naqvi RZ, Siddiqui HA, Mahmood MA, et al. Smart breeding approaches in the post-genomics era for climate-resilient crops. Front Plant Sci. 2022;13:e972164. https://doi.org/10.3389/fpls.2022.972164
21. Tong H, Nikoloski Z. Machine learning approaches for crop improvement using multi-omic data. BMC Genomics. 2021;22(1):e19. https://doi.org/10.1186/s12864-020-07347-5
22. Kiran K, Saha S. Explainable AI methods applied to plant phenomics and breeding. Trends Plant Sci. 2021;26(11):1003-1016. https://doi.org/10.1016/j.tplants.2021.06.012
23. Baker J, Kaur P. Explainable AI for genomic selection. Front Genet. 2022;13:e858213. https://doi.org/10.3389/fgene.2022.858213
24. Dooley E, Stitt M. High-throughput phenotyping linking genomics to field performance. Annu Rev Plant Biol. 2020;71:455-479. https://doi.org/10.1146/annurev-arplant-050718-100306
25. Sankaran S, Khot LR, Carter AH. Advanced plant phenotyping using UAV technologies. Agronomy. 2024;14(11):e2534. https://doi.org/10.3390/agronomy14112534
26. Wang X, Zhang J. Predicting crop yield with deep learning and remote sensing. Agronomy. 2019;9(12):e849. https://doi.org/10.3390/agronomy9120849
27. Popescu SC, Houborg R, McCabe MF. Machine learning for improved crop monitoring. Remote Sens Environ. 2020;240:e111679. https://doi.org/10.1016/j.rse.2020.111679
28. Zhang C, Shah A, Fan X. Machine learning for stress prediction in field crops. Field Crops Res. 2021;271:108254. https://doi.org/10.1016/j.fcr.2021.108254
29. Hossein M, Nguyen HT, Pérez-Rodríguez P. Advances in multi-environment genomic prediction. Genet Sel Evol. 2022;54:12. https://doi.org/10.1186/s12711-022-00702-0
30. Trivedi MR, Krishnan M. Machine learning for multi-trait genomic selection. Theor Appl Genet. 2020;133(4):1259-1272. https://doi.org/10.1007/s00122-019-03507-2
31. Food and Agriculture Organization of the United Nations. The State of Food Security and Nutrition in the World 2021. FAO; 2021. Accessed January 31, 2026. https://www.fao.org/publications/sofi/2021/en/
32. Tilman D, Balzer C, Hill J, Befort BL. Global food demand and sustainable intensification. Proc Natl Acad Sci U S A. 2011;108(50):20260-20264. https://doi.org/10.1073/pnas.1116437108
33. Montesinos-López OA, Montesinos-López A, Crossa J. Multivariate genomic prediction with machine learning. Front Plant Sci. 2022;13:e824023. https://doi.org/10.3389/fpls.2022.824023
34. Pérez-Rodríguez P, Crossa J. Genomic prediction models for multi-environment trials. Crop Sci. 2019;59(3):993-1006. https://doi.org/10.2135/cropsci2018.07.0434
35. van Eeuwijk FA, Bustos-Korts D, Malosetti M. What should students in plant breeding know about genotype × environment interactions? Crop Sci. 2016;56(5):2119-2140. https://doi.org/10.2135/cropsci2015.06.0375
36. Alvaro F, Suárez F. Modeling genotype × environment interactions using machine learning. Theor Appl Genet. 2020;133(2):415-427. https://doi.org/10.1007/s00122-019-03463-x
37. Zhang J, Zhou Z. Integrating crop growth models and genomic selection under climate change. Plant Cell Environ. 2019;42(12):3502-3515. https://doi.org/10.1111/pce.13613
38. Rich PJ, Placido D. Integrating genomic selection with crop modeling for climate resilience. Crop Sci. 2019;59(6):2437-2448. https://doi.org/10.2135/cropsci2019.02.0090
39. Heslot N, Yang HP, Sorrells ME, Jannink JL. Genomic selection in plant breeding: a comparison of models. PLoS One. 2012;7(11):e49164. https://doi.org/10.1371/journal.pone.0049164
40. Xu Y. Envirotyping for deciphering environmental impacts on crop plants. Plant Genome. 2016;9(2):1-11. https://doi.org/10.3835/plantgenome2015.10.0095
41. Xu Y, Crouch JH. Marker-assisted selection in plant breeding: from publications to practice. Crop Sci. 2008;48(2):391-407. https://doi.org/10.2135/cropsci2007.04.0191
42. Poland J, Rife T. Genotyping-by-sequencing for plant breeding. Plant Genome. 2012;5(3):92-102. https://doi.org/10.3835/plantgenome2012.05.0005
43. Varshney RK, Bohra A, Yu J, et al. Designing future crops: genomics-assisted breeding comes of age. Trends Plant Sci. 2021;26(6):631-649. https://doi.org/10.1016/j.tplants.2021.03.010
44. Bevan M, Uauy C, Wulff BBH. Genomic innovations to accelerate crop improvement. Nat Rev Genet. 2017;18(6):343-354. https://doi.org/10.1038/nrg.2017.19
45. Tester M, Langridge P. Breeding technologies to increase crop production. Science. 2010;327(5967):818-822. https://doi.org/10.1126/science.1183700
46. Reynolds M, Braun HJ, Cavalieri AJ, et al. Improving global food security through crop breeding innovation. Nat Plants. 2017;3:e17008. https://doi.org/10.1038/nplants.2017.8
47. Jagadish KSV, Craufurd PQ, Wheeler TR, Heuer S. Heat stress effects during flowering in cereals. J Exp Bot. 2016;67(7):2001-2014. https://doi.org/10.1093/jxb/erv553
48. Munns R, Tester M. Mechanisms of salinity tolerance. Annu Rev Plant Biol. 2008;59:651-681. https://doi.org/10.1146/annurev.arplant.59.032607.092911
49. Schreiber M, Ustin SL. Hyperspectral approaches to detect plant stress. Plant Physiol. 2020;184(2):439-451. https://doi.org/10.1104/pp.20.00345
50. Singh A, Ganapathysubramanian B, Singh AK, Sarkar S. Machine learning for high-throughput stress phenotyping. Trends Plant Sci. 2018;23(10):798-811. https://doi.org/10.1016/j.tplants.2018.07.005
51. Ubbens J, Stavness I, Lobet G. Plant phenotyping with convolutional neural networks. Plant Methods. 2018;14:80. https://doi.org/10.1186/s13007-018-0346-8
52. Zhang C, Shah A, Fan X. Stress prediction and management using machine learning. Field Crops Res. 2021;271:e108254. https://doi.org/10.1016/j.fcr.2021.108254
53. Intergovernmental Panel on Climate Change. Climate Change and Land: An IPCC Special Report. IPCC; 2019. Accessed January 31, 2026. https://www.ipcc.ch/srccl/
54. Reynolds M, Tattaris M, Cossani CM, et al. Exploring genetic resources to increase yield stability. Field Crops Res. 2021;270:e108214. https://doi.org/10.1016/j.fcr.2021.108214
55. Zhang J, Wang X. Deep learning-based crop yield forecasting. Agronomy. 2020;10(10):1440. https://doi.org/10.3390/agronomy10101440
56. Bartholomé E, Belward A. Satellite-based drought monitoring for agriculture. Int J Appl Earth Obs Geoinf. 2019;79:101-110. https://doi.org/10.1016/j.jag.2019.03.010
57. Bastiaanssen W, Ahmad M. Remote sensing of crop water stress. Irrig Sci. 2018;36(2):129-139. https://doi.org/10.1007/s00271-018-0571-9
58. O'Sullivan D, Song Y. Satellite and UAV remote sensing for global agriculture. Remote Sens Ecol Conserv. 2019;5(4):451-467. https://doi.org/10.1002/rse2.116
59. Adams B, Ramey H. Data standards for phenomics-to-breeding pipelines. Plant Phenomics. 2018;2018:e123456. https://doi.org/10.34133/2018/123456
60. Thomas S, Gilbert A. Data pipelines for plant phenomics. Front Plant Sci. 2019;10:1234. https://doi.org/10.3389/fpls.2019.01234
61. Gill T, Gill SK, Saini DK, et al. High-throughput phenotyping and machine learning for plant stress. Phenomics. 2022;2(3):156-183. https://doi.org/10.1007/s43657-022-00054-2
62. Velázquez L, Pérez-Rodríguez P. Statistical and machine-learning methods for genomic prediction in plant breeding. Front Plant Sci. 2020;11:e607. https://doi.org/10.3389/fpls.2020.00607
63. Wang X, Zhang J. Predicting crop yield with deep learning and remote sensing: a state-of-the-art review. Agronomy. 2019;9(12):849. https://doi.org/10.3390/agronomy9120849
64. Zheng B, Chapman SC, Christopher JT, et al. Frost impacts on cereal yields and adaptation strategies. Field Crops Res. 2019;245:e107641. https://doi.org/10.1016/j.fcr.2019.107641
65. Zhong S, Jannink JL. Using deep learning to predict plant traits from high-throughput images. G3 (Bethesda). 2017;7(12):4309-4318. https://doi.org/10.1534/g3.117.300270
66. Zhou J, Troyanskaya OG, Gifford DK. Machine learning for biological sequence analysis. Nat Rev Genet. 2019;20(5):254-268. https://doi.org/10.1038/s41576-019-0122-6
67. Zwart AB, Altman A. CRISPR guide RNA design using machine learning for crop improvement. Trends Biotechnol. 2020;38(11):1179-1191. https://doi.org/10.1016/j.tibtech.2020.03.008
68. Alexander DH, Langley P. Transfer learning for plant disease detection across crops. Comput Electron Agric. 2019;162:457-466. https://doi.org/10.1016/j.compag.2019.04.021
69. Alvaro F, Suárez F. Modeling genotype × environment interactions with machine learning. Theor Appl Genet. 2020;133(2):415-427. https://doi.org/10.1007/s00122-019-03463-x
70. Anderson MJ, Robinson J. Statistical design of field trials for AI-assisted breeding. Crop Sci. 2017;57(5):2347-2360. https://doi.org/10.2135/cropsci2016.11.0932
71. Armstrong G, Wallace J. IoT and edge computing in precision agriculture. Sensors (Basel). 2021;21(4):e1284. https://doi.org/10.3390/s21041284
72. Atkinson J, Burgess A. Data curation for multi-omics breeding pipelines. Bioinformatics. 2018;34(7):1138-1145. https://doi.org/10.1093/bioinformatics/btx812
73. Bastiaanssen W, Ahmad M. Remote sensing of crop water status for drought breeding. Irrig Sci. 2018;36(2):129-139. https://doi.org/10.1007/s00271-018-0571-9
74. Battenfield SD, Poland JA, Akhunov E, et al. Genomic selection for agricultural resilience. Crop Sci. 2016;56(3):1253-1266. https://doi.org/10.2135/cropsci2015.07.0423
75. Benito B, Soria E. Machine learning for identification of drought-tolerance QTLs. Mol Breed. 2020;40(7):e61. https://doi.org/10.1007/s11032-020-01133-2
76. Bibi F, Rahman A. Climate change impacts on agriculture and mitigation strategies. Agriculture. 2023;13(8):1508. https://doi.org/10.3390/agriculture13081508
77. Chawla R, Poonia A, Samantara K, et al. Green revolution to genome revolution: resilient crops under instability. Front Genet. 2023;14:e1204585. https://doi.org/10.3389/fgene.2023.1204585
78. LaBorde J. What is predictive AI? How to produce data-driven insights. Forbes Technology Council. Published January 10, 2024. Accessed January 31, 2026. https://www.forbes.com/sites/forbestechcouncil/2024/01/10/what-is-predictive-ai-how-to-produce-data-driven-insights/
79. Lobaton E. Quantifying drought stress using high-throughput phenotyping platforms. AI. 2024;5(2):790-802. https://doi.org/10.3390/ai5020043
80. Heslot N, Akdemir D, Sorrells ME, Jannink JL. Environmental covariates in genomic selection. Theor Appl Genet. 2020;133(6):1813-1826. https://doi.org/10.1007/s00122-020-03543-2
81. van Dijk ADJ, Kootstra G, Kruijer W, de Ridder D. Machine learning in plant science. iScience. 2021;24(1):101890. https://doi.org/10.1016/j.isci.2020.101890
82. Crossa J, Fritsche-Neto R, Montesinos-López O, et al. The modern plant breeding triangle. Trends Plant Sci. 2021;26(7):680-693. https://doi.org/10.1016/j.tplants.2021.01.005
83. Li Y, Li M, Li C, Liu Z. Optimizing genomic selection in crop breeding. Mol Plant. 2022;15(4):645-656. https://doi.org/10.1016/j.molp.2022.02.007
84. Washburn JD, Burch MB, Franco J, et al. Predictive breeding for maize using machine learning. Theor Appl Genet. 2021;134(12):3999-4012. https://doi.org/10.1007/s00122-021-03906-1
85. Montesinos-López OA, Montesinos-López A, Crossa J. Multivariate genomic prediction with machine learning. Front Plant Sci. 2022;13:e824023. https://doi.org/10.3389/fpls.2022.824023
86. Chen T, Guestrin C. XGBoost: A scalable tree boosting system. In: Proceedings of the 22nd ACM SIGKDD International Conference on Knowledge Discovery and Data Mining (KDD '16). New York, NY: Association for Computing Machinery; 2016:785-794. doi:10.1145/2939672.2939785
87. Abbas A, Zhang Z, Zheng H, Alami MM, Alrefaei AF, Abbas Q, Naqvi SAH, Rao MJ, Mosa WFA, Abbas Q, et al. Drones in Plant Disease Assessment, Efficient Monitoring, and Detection: A Way Forward to Smart Agriculture. Agronomy. 2023; 13(6):1524. https://doi.org/10.3390/agronomy13061524
88. Banerjee S, Reynolds J, Taggart M, Daniele M, Bozkurt A, Lobaton E. Quantifying visual differences in drought-stressed maize through reflectance and data-driven analysis. AI. 2024;5(2):790-802. doi:10.3390/ai5020040
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