Maize Genomics and Genetics 2024, Vol.15, No.5, 239-246 http://cropscipublisher.com/index.php/mgg 239 Research Article Open Access Comparative Genomics of Maize: Insights into Evolution and Function Jin Zhou, Minli Xu Hainan Provincial Key Laboratory of Crop Molecular Breeding, Sanya, 572025, Hainan, China Corresponding author: limin.xu@hitar.org Maize Genomics and Genetics, 2024, Vol.15, No.5 doi: 10.5376/mgg.2024.15.0023 Received: 03 Aug., 2024 Accepted: 17 Sep., 2024 Published: 08 Oct., 2024 Copyright © 2024 Zhou and Xu, This is an open access article published under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. Preferred citation for this article: Zhou J., and Xu M.L., 2024, Comparative genomics of maize: insights into evolution and function, Maize Genomics and Genetics, 15(5): 239-246 (doi: 10.5376/mgg.2024.15.0023) Abstract Comparative genomics of maize (Zea mays) has provided transformative insights into the evolutionary processes and functional mechanisms that have shaped this important crop. Through the analysis of whole-genome sequences, gene family expansions, and structural variations, researchers have deepened their understanding of maize's domestication, adaptation, and diversification. Key findings include the identification of conserved regulatory elements that play critical roles in gene expression, the impact of gene duplication events that have led to functional diversification, and the discovery of genomic regions linked to traits such as yield, stress tolerance, and disease resistance. These studies have also revealed the evolutionary relationships between maize and other members of the grass family (Poaceae), contributing to a broader understanding of plant evolution. The application of these findings extends to maize breeding and biotechnology, where genomic data is being used to develop more resilient and higher-yielding maize varieties. As genomic technologies such as CRISPR, pan-genomics, and multi-omics integration continue to advance, the field of maize comparative genomics is poised to play a critical role in addressing future challenges in agriculture and food security. Keywords Comparative genomics; Maize evolution; Gene duplication; Domestication; Maize breeding 1 Introduction Maize (Zeamays), one of the most significant crops globally, plays a dual role as both a staple food source and a model organism for plant genetics. Its economic importance is underscored by its use in food, feed, and biofuel production, making it essential for agricultural sustainability. Beyond agriculture, maize has been a powerful tool in genomics research due to its genetic diversity and complex genome structure. The domestication of maize began approximately 9 000 years ago in the Balsas River region of southern Mexico, where it was derived from its wild ancestor teosinte. Over millennia, selective breeding and adaptation to diverse environments have enhanced its genetic complexity, making it an excellent model for studying genome evolution and gene function in plants (Hufford et al., 2021). Comparative genomics is a crucial approach in plant biology that examines the similarities and differences between the genomes of different species. This method helps identify conserved and divergent genomic regions, enabling researchers to uncover evolutionary processes and functional elements that define species-specific traits (Huang and Hong, 2024). In maize, comparative genomics has revealed significant insights into genome architecture, such as gene duplications, deletions, and chromatin rearrangements, which contribute to the plant's phenotypic diversity and adaptability. Studies comparing maize to closely related species, like sorghum and rice, have highlighted important evolutionary trends, including genome fractionation and recombination, that have shaped maize’s genomic landscape. These findings are essential for understanding maize's unique evolutionary history and its potential for agricultural improvement (Lozano et al., 2021; Tian et al., 2021). This study utilizes comparative genomics to deepen the understanding of maize evolution and functional genomics. By analyzing structural variations, gene expression, and methylation patterns across different maize lines, it aims to identify genetic elements critical for traits such as stress tolerance and pathogen resistance. The research also provides new insights into maize adaptability, offering guidance for strategies to enhance crop
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