PAID ACCESS | Published on : 24-Mar-2026 | Pages: 30-45 | Doi : 10.37446/edibook152024/30-45
The increased demand for food necessitates the development of improved crop varieties at a rapid pace, which is hardly possible with conventional tools and techniques of crop breeding. Molecular breeding addresses this challenge by integration of advanced molecular tools with traditional breeding methods to accelerate breeding cycles, improve selection accuracy, and effectively target complex traits. Molecular breeding encompasses various components including marker-assisted selection, quantitative trait loci (QTL), genome-wide association studies (GWAS), gene discovery and deployment through marker-assisted backcross breeding (MABB), and gene pyramiding. These advancements have fundamentally transformed crop breeding ecosystems across various crops. Cutting-edge technologies, such as genomic selection and gene editing, have strengthened the breeder’s toolkit enabling precise genome modifications for the development of improved traits. Thus, molecular breeding has played a transformative role in genetic crop improvement and the development of resilient, high-yielding, and climate-smart crop varieties. Ultimately, the integration of molecular breeding strategies is pivotal in addressing the urgent challenges posed by a growing global population, climate change, and finite resources. Through these methods, agriculture is better equipped to deliver sustainable solutions for future food security.
Marker assisted selection, GWAS, Genomic Selection, Gene editing, Gene pyramiding, Susceptibility gene
Botstein, D., White, R. L., Skolnick, M., & Davis, R. W. (1980). Construction of a genetic linkage map in man using restriction fragment length polymorphisms. American Journal of Human Genetics, 32(3), 314–331.
Cobb, J. N., Jumaa, S. H., Khan, A., & Lee, W. (2019). The application of machine learning in plant breeding and genetics. Frontiers in Plant Science, 10, 1515. https://doi.org/10.3389/fpls.2019.01515
Collard, B. C. Y., & Mackill, D. J. (2008). Marker-assisted selection: An approach for precision plant breeding in the twenty-first century. Philosophical Transactions of the Royal Society B: Biological Sciences, 363(1495), 557–572. https://doi.org/10.1098/rstb.2007.2170
Doudna, J. A., & Charpentier, E. (2014). The new frontier of genome engineering with CRISPR-Cas9. Science, 346(6213), 1258096. https://doi.org/10.1126/science.1258096
Elshire, R. J., Glaubitz, J. C., Sun, Q., Poland, J. A., Kawamoto, K., Buckler, E. S., & Mitchell, S. E. (2011). A robust, simple, and cost-effective method for genome-wide genotyping. PLOS ONE, 6(5), e19379. https://doi.org/10.1371/journal.pone.0019379
Falk, D. E., & Ghesquiere, M. (1990). Strategies for the effective deployment of resistance genes in cultivars. Annual Review of Phytopathology, 28(1), 329–354. https://doi.org/10.1146/annurev.py.28.090190.001553
Fernie, A. R., & Yan, J. (2019). De novo domestication: An opportunity to rapidly improve plant nutrition and yield. Nature Food, 1(3), 154–156. https://doi.org/10.1038/s43016-019-0007-1
Furbank, R. T., & Tester, M. (2011). Phenomics-Technologies to relieve the phenotyping bottleneck. Trends in Plant Science, 16(11), 635–644. https://doi.org/10.1016/j.tplants.2011.09.005
Gaudelli, N. M., Komor, A. C., Rees, H. A., Packer, J. S., Liu, P., Liu, Y., & Liu, D. R. (2017). Programmable base editing of A.T to G.C in genomic DNA without double-stranded DNA cleavage. Nature, 551(7683), 464–471. https://doi.org/10.1038/nature24644
Godfray, H. C. J., Beddington, J. R., Crute, I. R., Haddad, L., Lawrence, D., Muir, J. F., & Toulmin, C. (2010). Food security: The challenge of feeding 9 billion people. Science, 327(5967), 812–818. https://doi.org/10.1126/science.1185383
Heslot, N., Jannink, J. L., & Sorrells, M. E. (2012). Perspectives for genomic selection in plant breeding. Euphytica, 186(2), 295–308. https://doi.org/10.1007/s10681-011-0587-1
International Rice Genome Sequencing Project. (2005). The map-based sequence of the rice genome. Nature, 436(7052), 793–800. https://doi.org/10.1038/nature03895
Jannink, J. L., Lorenz, A. J., & Iwata, H. (2010). Genomic selection in plant breeding: From theory to practice. Briefings in Functional Genomics, 9(3), 166–177. https://doi.org/10.1093/bfgp/elq001
Jiang, Y., Li, C., Zhang, X., & Song, J. (2022). Deep learning for plant phenotyping: Applications and future challenges. Plant Phenomics, 2022, 9864275. https://doi.org/10.34133/2022/9864275
Jinek, M., Chylinski, K., Fonfara, I., Hauer, M., Doudna, J. A., & Charpentier, E. (2012). A programmable dual-RNA-guided DNA endonuclease in adaptive bacterial immunity. Science, 337(6096), 816–821. https://doi.org/10.1126/science.1225829
Kruger, N. J., Liboriussen, P. T., & Miller, A. J. (2021). Systems biology approaches for crop improvement. Current Opinion in Plant Biology, 60, 101991. https://doi.org/10.1016/j.pbi.2020.101991
Lander, E. S., & Botstein, D. (1989). Mapping Mendelian factors underlying quantitative traits using RFLP linkage maps. Genetics, 121(1), 185–199.
Li, M., Yang, Z., & Chang, C. (2022). Susceptibility is new resistance: Wheat susceptibility genes and exploitation in resistance breeding. Agriculture, 12(9), 1419. https://doi.org/10.3390/agriculture12091419
Maranna, S., Verma, K., Talukdar, A., Lal, S. K., Kumar, A., & Mukherjee, K. (2016). Introgression of null allele of Kunitz trypsin inhibitor through marker-assisted backcross breeding in soybean (Glycine max L. Merr.). BMC Genetics, 17, 1–9. https://doi.org/10.1186/s12863-016-0413-2
McCouch, S. R., Zhao, K., Wright, M., Kresovich, S., Houseman, A., & Brien, E. (2011). Development of an 8K SNP chip for rice. Rice Genomics and Genetics Conference Presentation.
Meuwissen, T. H. E., Hayes, B. J., & Goddard, M. E. (2001). Prediction of total genetic value using genome-wide dense marker maps. Genetics, 157(4), 1819–1829.
Pang, S., Lu, Z., Cheng, H., Zhang, J., & Yang, S. (2021). CRISPR/Cas9-mediated gene editing: A promising approach for engineering durable disease resistance in crops. Molecular Plant Pathology, 22(12), 1667–1679. https://doi.org/10.1111/mpp.13104
Phuong, N. D., Cunnac, S., Gioi, D. H., Xuan, T. D., Quyen, C. L., & Xuan, H. N. (2025). Identification of a susceptibility gene for Xanthomonas oryzae pv. oryzae in Vietnamese elite rice (Oryza sativa L.) cultivar Bacthom 7. Plant Breeding. https://doi.org/10.1111/pbr.13283
Schnable, P. S., Ware, D., Fulton, R. S., Stein, L. D., Wei, F., Pasternak, S., & Wilson, R. K. (2009). The B73 maize genome: Complexity, diversity, and dynamics. Science, 326(5956), 1112–1115. https://doi.org/10.1126/science.1178534
Singh, S., Sidhu, J. S., Huang, N., Vikal, Y., Li, Z., Brar, D. S., Dhaliwal, H. S., & Khush, G. S. (2001). Pyramiding three bacterial blight resistance genes (xa5, xa13, and Xa21) using marker-assisted selection into indica rice cultivar PR106. Theoretical and Applied Genetics, 102, 1011–1015. https://doi.org/10.1007/s001220000495
Singh, U. M., Dixit, S., Alam, S., Yadav, S., Prasanth, V. V., Singh, A. K., Kumar, A. (2021). Marker-assisted forward breeding to develop a drought, bacterial leaf blight, and blast resistant rice cultivar. The Plant Genome, 15, e20170. https://doi.org/10.1002/tpg2.20170
Smith, S. C., Smith, W. D., & Jones, A. B. (1990). The integration of molecular biology into modern plant breeding programs. Journal of Agricultural Science, 105(2), 112–120.
Tautz, D. (1989). Hypervariability of simple sequences as a general source for polymorphic DNA markers. Nucleic Acids Research, 17(16), 6463–6471. https://doi.org/10.1093/nar/17.16.6463
United Nations, Department of Economic and Social Affairs, Population Division. (2013). World population prospects: The 2012 revision-Highlights and advance tables. United Nations.
Varshney, R. K., Mahendar, T., & Saxena, R. K. (2014). Genomics for plant breeding: Recent advances and prospects. The Plant Journal, 79(4), 623–635. https://doi.org/10.1111/tpj.12594
Waltz, E. (2016). Gene-edited CRISPR mushroom escapes US regulation. Nature, 532(7600), 293. https://doi.org/10.1038/nature.2016.19754
Wang, W., Mauleon, R., Hu, Z., Chebotarov, D., Suzuki, E., Zhao, K., Ware, D. (2018). Genomic variation in 3,010 diverse accessions of Asian cultivated rice. Nature, 557(7703), 43–49. https://doi.org/10.1038/s41586-018-0063-9
Wang, X., Guo, X., Ma, X., Luo, L., Fang, Y., Zhao, N., Li, R. (2021). Development of new rice (Oryza sativa L.) breeding lines through marker-assisted introgression and pyramiding of brown planthopper, blast, bacterial leaf blight resistance, and aroma genes. Agronomy, 11(12), 2525. https://doi.org/10.3390/agronomy11122525
Yu, J., & Buckler, E. S. (2006). Genetic association mapping and genomic selection for complex traits in crop plants. Plant Physiology, 141(1), 1–13. https://doi.org/10.1104/pp.105.076497
Zhang, Y., Pribil, M., He, P., & Sze, H. (2017). Targeting the rice OsHKT1;5 transporter gene with CRISPR/Cas9 for enhanced salt tolerance. Scientific Reports, 7, 11776. https://doi.org/10.1038/s41598-017-11977-9
Zhu, H., Zhou, Y., He, H., Wang, W., & Zhang, H. (2020). CRISPR/Cas9-mediated editing of the OsRGL gene enhances drought tolerance and water-use efficiency in rice. Plant Biotechnology Journal, 18(11), 2259–2268. https://doi.org/10.1111/pbi.13372.