Maize Genomics and Genetics 2024, Vol.15, No.1, 36-48 http://cropscipublisher.com/index.php/mgg 38 environmental conditions through changes in metabolic pathways. These adaptations include the evolution of specific metabolites that enhance the plant's growth and resistance to pests and diseases (Xu et al., 2019). The domestication of maize from teosinte involved significant genetic and morphological changes driven by human selection. These changes enhanced the plant's suitability for cultivation, consumption, and adaptation to diverse environments, transforming it into one of the world's most important staple crops. 3 Genomic Comparisons 3.1 Genome structure and organization The genome structure and organization of maize and teosinte exhibit both similarities and significant differences, reflecting the evolutionary changes brought about by domestication. Teosinte (Zea mays ssp. parviglumis) and maize (Zeamays ssp. mays) share the same basic chromosome number (2n=20) and largely similar chromosomal structures, which allows for interbreeding and the production of fertile hybrids (Doebley and Stec, 1991). However, structural variations such as copy number variations (CNVs) and presence-absence variations (PAVs) are prominent in their genomes, contributing to their phenotypic diversity (Swanson-Wagner et al., 2010). Genomic analyses have identified significant gene content variation among different maize inbreds and teosinte genotypes. For instance, teosinte possesses a higher number of genes with copy number variations compared to maize. These CNVs and PAVs are often found in multiple genotypes, indicating that they predate domestication and have been maintained despite selection pressures (Li et al., 2021). 3.2 Key genetic differences between teosinte and maize The key genetic differences between teosinte and maize are primarily associated with loci that control traits relevant to domestication and agriculture. One of the most notable genetic loci is teosinte branched1 (tb1), which plays a critical role in the plant's architecture. In teosinte, the tb1 gene promotes the development of long lateral branches, while in maize, a mutation in tb1 results in reduced branching and a more compact plant structure suitable for cultivation (Doebley et al., 1995). Another significant locus is teosinte glume architecture1 (tga1), which affects the hardness and coverage of the kernels. In teosinte, the kernels are encased in a hard fruitcase, whereas in maize, a mutation in tga1 disrupts this structure, exposing the kernels and making them accessible for consumption (Dorweiler and Doebley, 1997). There are genes associated with metabolic processes that differ significantly between maize and teosinte. For example, genes involved in the synthesis of secondary metabolites such as alkaloids, terpenoids, and benzoxazinoids exhibit divergence between these two subspecies. This metabolic divergence reflects the adaptation of maize to different environmental conditions and human agricultural practices (Xu et al., 2019). 3.3 Genomic regions associated with domestication traits Genomic regions associated with domestication traits in maize have been identified through quantitative trait loci (QTL) mapping and other genetic analyses. These regions typically contain genes that have undergone strong selection during the domestication process. One such region is the locus on chromosome 1 that includes tb1, which significantly affects plant architecture and branching patterns (Doebley et al., 1995). Another critical region is the one containing the tga1 gene on chromosome 4, which controls the hardness and protection of the kernels. The domestication of maize involved selecting for mutations in this region that led to the development of softer, exposed kernels, which are easier to harvest and consume (Dorweiler and Doebley, 1997). Recent studies have also highlighted the role of other genomic regions and genes in the domestication and improvement of maize. For instance, the presence-absence variations (PAVs) and CNVs in certain genes contribute to phenotypic diversity and adaptation to different environments. These structural variations are often found in genes involved in stress responses, growth regulation, and metabolic processes (Li et al., 2021). Moreover, comparative transcriptomic studies have revealed that around 75% of genes are highly conserved between maize and teosinte, while the remaining genes exhibit divergence due to selection pressures during
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