Maize Genomics and Genetics 2024, Vol.15, No.5, 218-227 http://cropscipublisher.com/index.php/mgg 222 the rapid diversification of lineages within Zea, as evidenced by the consistent estimates of divergence times from various markers (Ross-Ibarra et al., 2009). Case examples of gene flow between Zea species and its consequences can be seen in the study of pea aphid host races, where genomic hotspots of differentiation have been identified in regions associated with reproductive isolation and host-plant specialization (Nouhaud et al., 2018). These findings suggest that hybridization and gene flow can lead to the emergence of new adaptive traits and contribute to the evolutionary dynamics of Zea species. 5 Implications for Crop Improvement 5.1 Contributions to maize breeding programs The application of phylogenomic insights has significantly enhanced maize breeding programs by providing a deeper understanding of the genetic basis of important traits. For instance, the comprehensive assessment of maize evolution through genome-wide resequencing has identified numerous genes with strong signals of selection, which are crucial for major morphological changes in maize (Figure 2) (Hufford et al., 2012b). This information is invaluable for breeders aiming to develop new varieties with improved traits. Figure 2 Neighbor-joining tree and changing morphology of domesticated maize and its wild relatives (Adopted from Hufford et al., 2012b) Image caption: Taxa in the neighbor-joining tree (right) are represented by different colors: parviglumis (green), landraces (red), improved lines (blue), mexicana (yellow), and Tripsacum (brown). Morphological changes (left) are shown for female inflorescences and plant architecture during domestication and improvement (Adopted from Hufford et al., 2012b) Moreover, the integration of genomic prediction methods, such as GBLUP and BayesB, has facilitated more accurate predictions of hybrid performance, thereby optimizing the selection process in breeding programs (Technow et al., 2014). This approach allows breeders to focus on the performance of experimental hybrids rather than solely on parental lines, enhancing the efficiency of breeding strategies. Additionally, the identification of specific genetic loci associated with ear traits through GWAS and QTL mapping has provided targets for improving maize yield (Dong et al., 2023). By leveraging these genetic insights, breeders
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