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. When comparing the chloroplast genome of Zea with those of other plant species, several similarities and differences can be observed. The overall structure, including the presence of LSC, SSC, and IR regions, is highly conserved across different species, such as those in the Zingiberaceae family (Li et al., 2019a; 2020b; Yang et al., 2022). Studies have found that the chloroplast genes of maize, rice, and wheat evolve at similar rates among grass species, with photosynthesis genes undergoing strong purifying selection (Matsuoka et al., 2002). However, variations in the size of these regions and the presence or absence of certain genes can occur. For instance, the absence of the rps19 gene in some Zingiberaceae species due to the expansion of the LSC region highlights the dynamic nature of chloroplast genome evolution (Yang et al., 2022). Additionally, the identification of highly divergent regions and single nucleotide polymorphisms (SNPs) in various species provides valuable markers for phylogenetic studies and species identification (Li et al., 2020a; Li et al., 2020b; Yang et al., 2022). The chloroplast genome of Zea is structurally and functionally similar to those of other plant species, with specific variations that contribute to its unique evolutionary path. These insights into the chloroplast genome of Zea enhance understanding of maize domestication and its adaptation to different 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).
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