Maize Genomics and Genetics 2024, Vol.15, No.4, 191-203 http://cropscipublisher.com/index.php/mgg 196 that govern plastid genome evolution in the genus Zea. The studies cited here contribute to a comprehensive understanding of these changes and their implications for plant biology and evolution (Walbot and Coe, 1979; Orton et al., 2017; Sun et al., 2018; Ping et al., 2022; Tripathi et al., 2022). 5 Case Study: Comparative Analysis of the Plastid Genome in Maize and Its Wild Relatives 5.1 Comparative analysis of the plastid genomes of maize (Zeamays) and teosinte The comparative analysis of the plastid genomes of maize (Zeamays) and its wild progenitor, teosinte (Zeamays ssp. parviglumis), reveals significant insights into the evolutionary processes that have shaped modern maize. Teosinte, which grows naturally in Southern Mexico, maintains a high level of genetic diversity that is crucial for the diversification and domestication of maize (Adhikari et al., 2021). Single-molecule long-read sequencing has been employed to analyze the teosinte genome, identifying 70 044 nonredundant transcript isoforms and constructing a draft genome with 16 633 high-quality contigs (Li et al., 2021). This analysis showed that genes from families that expanded from teosinte to maize were significantly enriched in the RNA modification pathway and had more transcript isoforms in teosinte than in maize (Li et al., 2021). Furthermore, cellular studies have shown that many cellular traits observed in developing maize caryopses are also present in teosinte, suggesting that these traits evolved independently of domestication and predate human selection pressure (Dermastia et al., 2009). This includes early programmed cell death in the maternal placento-chalazal layer, accumulation of phenolics and flavonoids, and the formation of wall ingrowths in the basal endosperm transfer layer (Dermastia et al., 2009). These findings indicate a high degree of conservation in the cellular processes between maize and teosinte, providing a deeper understanding of the evolutionary history of maize. 5.2 Impact of microstructural changes on maize domestication and cultivation The domestication of maize from teosinte involved significant microstructural changes in the genome, driven by artificial selection. Analysis of single-nucleotide polymorphisms (SNPs) in 774 genes indicates that 2 to 4% of these genes experienced artificial selection, while the remaining genes show evidence of a population bottleneck associated with domestication (Wright et al., 2005). This artificial selection has led to the clustering of candidate selected genes near quantitative trait loci (QTL) that contribute to phenotypic differences between maize and teosinte (Wright et al., 2005). One notable example is the ZEA CENTRORADIALIS 8 (ZCN8) gene, which plays a central role in mediating flowering time in maize. A SNP in the ZCN8 promoter was identified as being strongly associated with flowering time and was a target of selection during early domestication. This SNP co-segregated with a major QTL for flowering time in maize-teosinte mapping populations, highlighting the impact of microstructural changes on the adaptation of maize to different environments (Figure 2) (Guo et al., 2018). Additionally, the introgression of chromosome segments from teosinte into maize has been shown to enhance traits such as flooding tolerance. For instance, a flooding-tolerant genotype containing a chromosome segment from Zea nicaraguensis was identified, suggesting the presence of a major QTL for flooding tolerance in that region (Mano and Omori, 2013). This demonstrates how microstructural changes and introgression from wild relatives can be utilized to improve maize cultivation under various environmental conditions. 5.3 Application of genome comparison in maize improvement The comparative analysis of the plastid genomes of maize and its wild relatives has significant implications for maize improvement. The genetic diversity present in teosinte can be harnessed to develop maize lines with enhanced traits such as stress tolerance and yield. For example, the introgression of alleles from teosinte into maize has been shown to produce lines with unique features such as protogynous behavior, short anthesis-silking intervals, and multiple ears per plant (Adhikari et al., 2021). These traits are valuable for breeding programs aimed at improving maize resilience and productivity.
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