Maize Genomics and Genetics 2024, Vol.15, No.4, 204-217 http://cropscipublisher.com/index.php/mgg 211 variations underlying important agronomic traits, such as plant architecture, flowering time, and yield-related traits. For instance, a study on 137 maize elite inbred lines identified several candidate genes, including ZmARF16, ZmARF34, and ZmTCP40, that regulate various plant architecture- and yield-related traits. These findings demonstrate the effectiveness of combining phenotypic, gene expression, and population genetics analyses to uncover key regulatory genes and functional variations (Li et al., 2023). Additionally, the integration of chromatin accessibility profiles and transcription factor occupancy data has provided insights into the regulatory landscape of maize. For example, profiling accessible chromatin and nucleosome occupancy during early reproductive development revealed regulatory elements that contribute to organogenesis and tissue-specific regulation. This approach has identified new SNP-trait associations in known regulators of inflorescence development, as well as new candidate genes, thereby enhancing our understanding of the cis-regulatory landscape in maize (Parvathaneni et al., 2019). 5.3 Identification of key regulatory networks in maize The identification of key regulatory networks is crucial for understanding the complex gene regulatory mechanisms in maize. Gene regulatory networks (GRNs) link transcription factors (TFs) to their target genes, representing maps of potential transcriptional regulation. By analyzing a large number of maize transcriptome datasets, researchers have generated multiple coexpression-based GRNs that capture distinct TF-target associations and biological processes. These networks have identified putative regulators of important metabolic pathways and provided potential targets for breeding or biotechnological applications (Zhou et al., 2020). Furthermore, the integration of chromatin characteristics, such as DNA methylation, chromatin accessibility, and histone modifications, has enabled the prediction of distal enhancer candidates in maize. These enhancer candidates, which display tissue-specificity and regulatory functions, have been validated through chromatin profiling and gene expression analyses. This approach has expanded the toolbox for functional characterization of gene regulation in maize, highlighting the importance of long-range cis-regulatory elements in controlling gene expression and agronomic traits (Oka et al., 2017; Parvathaneni et al., 2020). In conclusion, advancements in transcriptome sequencing technologies, functional genomics studies, and the identification of key regulatory networks have significantly enhanced researchers understanding of gene expression and regulation in maize. These insights are crucial for improving maize breeding strategies and developing high-yielding, stress-tolerant maize cultivars. 6 Epigenetics and Its Role in Maize Breeding 6.1 Introduction to epigenetic mechanisms in plants Epigenetics refers to heritable changes in gene expression that do not involve alterations in the DNA sequence itself. These changes are primarily mediated through mechanisms such as DNA methylation, histone modifications, and RNA-directed DNA methylation (RdDM) (Samantara et al., 2021; Gupta and Salgotra, 2022; Tonosaki et al., 2022). In plants, these epigenetic modifications play a crucial role in regulating gene expression, thereby influencing plant development, stress responses, and phenotypic plasticity (Iwasaki and Paszkowski, 2014; Kakoulidou et al., 2021). The concept of epigenetic memory, where chromatin states are propagated through cell divisions, allows plants to retain information about past environmental conditions and adapt accordingly (Iwasaki, and Paszkowski, 2014; Huang et al., 2017). 6.2 Epigenetic modifications and their impact on trait expression Epigenetic modifications can significantly impact the expression of agronomic traits in maize. DNA methylation, one of the primary epigenetic mechanisms, involves the addition of methyl groups to cytosine residues in DNA, leading to changes in chromatin structure and gene expression (Agarwal et al., 2020; Gupta and Salgotra, 2022). Histone modifications, such as acetylation, methylation, and phosphorylation, also play a critical role in regulating chromatin dynamics and gene activity (Duan et al., 2018; Samantara et al., 2021). These modifications can either activate or repress gene expression, depending on the specific chemical groups added to the histones.
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