Maize Genomics and Genetics 2024, Vol.15, No.4, 182-190 http://cropscipublisher.com/index.php/mgg 183 2 Background on Maize Evolution 2.1 Origin and domestication of maize Maize (Zea mays ssp. mays) is one of the most important crops globally, with its domestication tracing back approximately 9 000 years to the Balsas Basin in southwestern Mexico. The domestication process involved the transformation of the wild grass teosinte (Zea mays ssp. parviglumis) into the cultivated maize we know today. Recent genomic studies have suggested that the domestication of maize may have involved multiple events and significant gene flow from other teosinte subspecies, such as Zea mays ssp. mexicana, challenging the earlier consensus of a single domestication event (Kistler et al., 2020; Moreno-Letelier et al., 2020). Additionally, archaeological evidence indicates that maize was dispersed to South America as a partial domesticate, where it underwent further domestication and improvement before being reintroduced to Central America (Kistler et al., 2020). 2.2 Genetic diversity in wild and cultivated maize The genetic diversity of maize is vast, encompassing a wide range of landraces and modern varieties. This diversity results from both ancient and contemporary gene flow events between wild relatives and cultivated maize. Studies have shown that the maize genome contains over 103 000 pan-genes, with significant variation in gene content, genome structure, and DNA methylation patterns across different maize lines (Hufford et al., 2020; Xu et al., 2020). Figure 1A and 1C illustrate these variations in the gene models categorized by different phylostrata and the distribution of core, near-core, dispensable, and private genes, demonstrating the genetic diversity and structural complexity of the maize genome. The genetic architecture of maize has been shaped by both natural selection and human-mediated breeding, leading to the development of traits beneficial for various environments and agricultural practices (Chen et al., 2020; Hu et al., 2022). The introgression of genes from teosinte has played a crucial role in maize's adaptation to diverse ecological niches, including highland regions (Calfee et al., 2021; Hu et al., 2022), as supported by the expression profiles in different tissues shown in Figure 1D of the diagram (Figure 1). This substantiates the significant genetic diversity present in maize, which is crucial for its adaptation and resilience across various environments. 2.3 Historical perspectives on gene flow in maize Gene flow has been a significant factor in the evolutionary history of maize. Hybridization between maize and its wild relatives, such as teosinte, has introduced genetic variation that has facilitated maize's adaptation to new environments and contributed to its global spread. For instance, introgression from the highland teosinte Zea mays ssp. mexicana has been crucial for maize's adaptation to high-altitude regions in Mexico (Calfee et al., 2021). Additionally, the backflow of genetic material from South American maize varieties to Central America has been hypothesized to enhance the genetic diversity and productivity of maize in these regions (Kistler et al., 2020). The selective sorting of ancestral introgression along environmental gradients further highlights the complex interplay between gene flow and local adaptation in maize evolution (Calfee et al., 2021). 3 Methodologies in Gene Flow Studies 3.1 Genetic markers and molecular tools Genetic markers and molecular tools are fundamental in studying gene flow in maize. Techniques such as next-generation sequencing (NGS) have revolutionized the field by enabling rapid and comprehensive sequencing of plant genomes. For instance, the use of Illumina sequencing to analyze nearly complete genomes of Maize dwarf mosaic virus (MDMV) isolates has provided insights into genetic diversity and evolutionary relationships (Wijayasekara et al., 2021). Additionally, genotyping by target sequencing (GBTS) technology has been employed to develop low-density genotyping platforms, such as the 5.5 K SNP markers panel, which are crucial for genetic and molecular breeding studies (Ma et al., 2022). These tools facilitate the identification of genetic variations and the mapping of quantitative traits, thereby enhancing the understanding of gene flow dynamics in maize. 3.2 Population genomics Population genomics involves the study of genetic variations within and between populations of maize. High-quality genomic sequences from diverse maize lines have been produced to map important traits and demonstrate the genetic diversity of maize (Hufford et al., 2021). This approach has revealed significant variation
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