Maize Genomics and Genetics 2024, Vol.15, No.1, 36-48 http://cropscipublisher.com/index.php/mgg 40 genes, understanding gene expression patterns, and elucidating regulatory networks are essential for improving maize breeding and developing varieties with enhanced agronomic traits. Figure 1 Characterization of eQTL and eQTL-regulated genes (Adopted from Wang et al., 2017) Image caption: (A) Number of eQTL mapped for each gene. The x axis and y axis represent the number of eQTL mapped for each gene and the number of genes in each group, respectively; (B) The expression variation explained by local and distant eQTL. Local eQTL explains more expression variation than distant eQTL; (C) The distribution of genes regulated by local and/or distant eQTL; (D) Functional enrichment analysis for local eQTL-regulated genes. Each bubble stands for one functional class and the size of bubble indicates the number of enriched genes in each class. The y axis shows the Pvalue of hypergeometric test with Benjamini and Hochberg multiple test correction (Adopted from Wang et al., 2017) One notable finding is the presence of co-regulated gene clusters in both maize and teosinte. These clusters often consist of genes with related functions and shared chromatin modifications, indicating a coordinated regulation of gene expression. For instance, genes involved in flavonoid biosynthesis and glycolysis are regulated by specific transcription factors such as the bHLH transcription factor R1 and hexokinase HEX9, respectively. These regulatory networks are crucial for the plant's metabolic processes and stress responses (Wang et al., 2017). Domestication and subsequent breeding have significantly impacted the gene expression patterns in maize. Many genes targeted by selection during domestication exhibit coordinated cis-regulatory divergence. For example, the Bx genes involved in benzoxazinoid biosynthesis have undergone significant cis-regulatory changes, which are associated with maize's adaptation to temperate environments and its distinct herbivore community (Wang et al., 2017). 5 Agricultural Impact 5.1 Yield and productivity improvements The domestication and subsequent breeding of maize from its wild ancestor teosinte have resulted in significant yield and productivity improvements. Modern maize exhibits a compact plant structure with a single dominant stalk and large, easily accessible ears, traits that have been heavily selected to maximize yield. One of the key loci involved in these changes is the teosinte branched1 (tb1) gene, which controls plant architecture by suppressing the growth of axillary branches, thus allowing the plant to focus resources on the main stalk and ear development (Doebley et al., 1995).
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