Maize Genomics and Genetics 2024, Vol.15, No.1, 36-48 http://cropscipublisher.com/index.php/mgg 39 domestication. This includes genes with strong selection signals that contribute to important agronomic traits such as yield, stress tolerance, and nutrient use efficiency (Huang et al., 2016). The genomic comparisons between teosinte and maize have provided valuable insights into the genetic changes associated with domestication. Key genetic loci such as tb1 and tga1 play crucial roles in defining the morphological and physiological traits that distinguish maize from its wild ancestor. Understanding these genetic differences and the associated genomic regions can aid in the development of improved maize varieties through the incorporation of beneficial alleles from teosinte. 4 Functional Genomics and Gene Expression 4.1 Identification of functional genes in teosinte and maize The identification of functional genes in teosinte and maize has provided crucial insights into the genetic basis of domestication and the adaptation of maize to diverse environments. Comparative genomic studies have revealed that approximately 75% of the genes are highly conserved between maize and teosinte. These genes are involved in essential biological processes and metabolic pathways, underscoring their fundamental roles in both species (Huang et al., 2016). The transcriptome analysis of teosinte has identified specific genes that show adaptive sequence divergence. For instance, around 1516 unigenes are uniquely expressed in teosinte, indicating their potential role in environmental adaptation and stress responses. Additionally, 99 unigenes with strong selection signals and 57 unigenes with high Ka/Ks ratios suggest that these genes have been under strong selection during maize domestication and improvement (Huang et al., 2016). 4.2 Gene expression patterns and their agricultural relevance Gene expression patterns play a crucial role in determining the phenotypic traits of maize and teosinte. The regulation of gene expression is influenced by both genetic and environmental factors, which together shape the plant's ability to adapt to different conditions. For example, the gene expression analysis of the maize-teosinte population has identified 25, 60 expression quantitative trait loci (eQTL) for 17 311 genes, revealing a significant range of expression variation (Figure 1) (Wang et al., 2017). 4.3 Regulatory networks and pathways The regulatory networks and pathways governing gene expression in maize and teosinte are complex and involve numerous genes and regulatory elements. One of the key regulatory genes is teosinte branched1 (tb1), which controls plant architecture by suppressing the growth of axillary branches. The expression patterns of tb1 inmaize and teosinte are highly correlated with the plant's growth suppression, highlighting its role in the domestication process (Hubbard et al., 2002). Another significant regulatory pathway involves the teosinte glume architecture1 (tga1) gene, which influences kernel casing and exposure. The tga1 gene has been crucial in the transition from encased kernels in teosinte to exposed kernels in maize, facilitating easier harvest and consumption (Dorweiler et al., 1993). Furthermore, recent studies have uncovered the role of long non-coding RNAs (lncRNAs) in regulating gene expression. In maize, around 18 165 high-confidence lncRNAs have been identified, with 6 873 conserved between maize and teosinte. These lncRNAs exhibit distinct genomic characteristics and play a role in gene regulation, indicating their potential impact on the plant's phenotype and adaptation (Han et al., 2018). The regulatory networks and pathways in maize and teosinte are further influenced by transposable elements, which contribute to genomic and transcriptomic variation. Transposable elements can affect gene expression by altering the chromatin structure and creating new regulatory elements, thereby impacting the plant's adaptability and evolution (Li et al., 2021). The functional genomics and gene expression studies of teosinte and maize have provided valuable insights into the genetic and regulatory mechanisms underlying their domestication and adaptation. Identifying functional
RkJQdWJsaXNoZXIy MjQ4ODYzNQ==