Maize Genomics and Genetics 2024, Vol.15, No.4, 160-170 http://cropscipublisher.com/index.php/mgg 164 The study of the chloroplast genome and other genomic features in maize has provided valuable insights into its domestication, genetic diversity, population structure, and adaptation. These findings not only enhance understanding of maize evolution but also have implications for crop improvement and agricultural practices. 5 Case Studies and Applications 5.1 Tracing lineage and ancestry Chloroplast genome studies have proven invaluable in tracing the lineage and ancestry of maize (Zea mays). For instance, the analysis of plastome sequences in South American maize landraces has revealed significant haplotype diversity, which aligns with the geographic structuring of nuclear gene pools. López et al. (2021) used next-generation sequencing technology to analyze the complete chloroplast genomes of 30 South American maize landraces and 3 wild maize species, identifying 124 polymorphic loci. These polymorphic loci were mainly concentrated in regions such as psbE-rps18, petN-rpoB, trnL_UAG-ndhF, and rpoC2-atpI. The study results showed significant differences in haplotype distribution between Andean and South American lowland maize landraces, reflecting the gene pool structure inferred from nuclear markers (Figure 2) (López et al., 2021). These insights are crucial for understanding the domestication and evolutionary history of maize, providing a framework for understanding evolutionary processes at low taxonomic levels and becoming increasingly important for future plant barcoding efforts. Figure 2 (A) Median-joining network of complete Z. mays plastomes. Circle size is proportional to haplotype frequencies Colours denote category (inbred line, teosinte, ancient sample) or previous group assignment of landraces based on nuclear markers according to Bracco et al. (2016) (Andean, NEA Flours, NEA Popcorns, Tropical Lowland, Highland Mexico and USA). Markers on the lines joining haplotypes represent one mutational step and black circles indicate missing vectors. Edge lengths are not to scale; (B) Morphological diversity in South American landraces carrying H1 and H2 haplotypes (Adopted from López et al., 2021) Image caption: The figure shows that haplotype H1 is most common in NEA Flours maize and also appears in five other groups, but is absent in Andean landraces. Haplotype H2 is predominant in Andean samples and absent in lowland groups. These network relationships reveal the distribution and interrelationships of haplotypes in maize and wild maize species across different groups (Adapted from López et al., 2021)
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