Maize Genomics and Genetics 2024, Vol.15, No.5, 239-246 http://cropscipublisher.com/index.php/mgg 244 The insights gained from comparative genomics are being directly applied to maize breeding and biotechnology. CRISPR and other genome-editing technologies are now commonly used to introduce targeted improvements in traits such as disease resistance, stress tolerance, and yield. By leveraging comparative genomics, breeders can better identify critical genes that contribute to these traits, and genomic prediction models are improving the efficiency of hybrid maize breeding programs. Furthermore, innovations in pan-genomics have highlighted the diversity within maize populations, revealing rare alleles that may have gone unnoticed in traditional breeding, thus expanding the toolbox for developing maize varieties better suited to specific environments (Liu et al., 2019). Continued research in maize comparative genomics will be crucial for addressing unresolved questions related to the plant's adaptation, domestication, and genetic diversity. Emerging technologies like long-read sequencing and single-molecule real-time sequencing are expected to further enhance our understanding of complex genomic regions, including repetitive elements and centromeres. The broader impact of maize genomics extends beyond maize, offering a model for other crops where similar approaches can be applied. Future research must focus on integrating multi-omics data to fully capture the complexity of maize biology and translate these findings into tangible improvements in crop performance under various environmental conditions. Acknowledgments The publisher sincerely thanks the anonymous peer reviewers for their thorough evaluation of this manuscript. Conflict of Interest Disclosure The authors affirm that this research was conducted without any commercial or financial relationships that could be construed as a potential conflict of interest. References Brandenburg J.T., Mary-Huard T., Rigaill G., Hearne S., Corti H., Joets J., Vitte C., Charcosset A., Nicolas S.D., and Tenaillon M.I,, 2017, Independent introductions and admixtures have contributed to adaptation of European maize and its American counterparts, PLoS Genetics, 13(6): e1006666. https://doi.org/10.1371/journal.pgen.1006666 PMID: 28301472 PMCID: PMC5373671 Chen J.F., Shrestha R., Ding J.Q., Zheng H.J., Mu C.H., Wu J.Y., and Mahuku G., 2016, Genome-wide association study and QTL mapping reveal genomic loci associated with Fusarium ear rot resistance in tropical maize germplasm, G3: Genes|Genomes|Genetics, 6(12): 3803-3815. https://doi.org/10.1534/g3.116.034561 PMID: 27742723 PMCID: PMC5144952 Georgescu C.H., Manson A.L., Griggs A.D., Desjardins C.A., Pironti A., Wapinski I., Abeel T., Haas B.J., and Earl A.M., 2018, SynerClust: a highly scalable, synteny-aware orthologue clustering tool, Microbial Genomics, 4(11): e000231. https://doi.org/10.1099/mgen.0.000231 PMID: 30418868 PMCID: PMC6321874 Huang D.D., 2024, CRISPR/Cas9 genome editing in legumes: opportunities for functional genomics and breeding, Legume Genomics and Genetics, 15(4): 199-209. https://doi.org/10.5376/lgg.2024.15.0020 Huang J., Zheng J.F., Yuan H., and McGinnis K., 2018, Distinct tissue-specific transcriptional regulation revealed by gene regulatory networks in maize, BMC Plant Biology, 18(1): 111. https://doi.org/10.1186/s12870-018-1329-y PMID: 29879919 PMCID: PMC6040155 Huang W.Z., and Hong Z.M., 2024, Marker-assisted selection in cassava: from theory to practice, Plant Gene and Trait, 15(1): 33-43. https://doi.org/10.5376/pgt.2024.15.0005 Hurst P., Schnable J.C., and Holding D.R., 2021, Tandem duplicate expression patterns are conserved between maize haplotypes of the α‐zein gene family, Plant Direct, 5(9): e346. https://doi.org/10.1002/pld3.346 Hufford M.B., Seetharam A.S., Woodhouse M.R., Chougule K., Ou S., Liu J., Ricci W.A., Guo T., Olson A.J., Qiu Y., Coletta R.D. Tittes S.B., Hudson A.I., Marand A.P., Wei S., Lu Z., Wang B., Tello-Ruiz M., Piri R.D., Wang N., Kim D.W., Zeng Y., O’Connor C.H., Li X., Gilbert A. M., Baggs E., Krasileva K., Portwood J.L., Cannon E.K.S., Andorf C.M., Manchanda N., Snodgrass S., Hufnagel D.E., Jiang Q., Pedersen S., Syring M.L., Kudrna D., Llaca V., Fengler K., Schmitz R., Ross-Ibarra J., Yu J., Gent J., Hirsch C., Ware D., and Dawe R.K., 2021, De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes, Science, 373: 655-662. https://doi.org/10.1126/science.abg5289
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