Maize Genomics and Genetics 2024, Vol.15, No.5, 239-246 http://cropscipublisher.com/index.php/mgg 242 maize inflorescence development. These elements shape the development of male and female reproductive organs by guiding tissue-specific transcription factors (Parvathaneni et al., 2020). The integration of transcriptome data has enabled the construction of gene regulatory networks (GRNs), which further explain how gene expression is controlled in various maize tissues such as leaves, roots, and seeds (Huang et al., 2018). 4.3 Functional diversification of genes Gene duplication events have been a major driver of functional diversification in maize. Following whole-genome duplication (WGD) events, duplicated genes in maize have evolved different functions, especially through subfunctionalization in different tissues. Studies on maize subgenomes indicate that some duplicated genes experience stronger purifying selection, leading to divergence in gene expression and functional roles. This subgenomic evolution contributes to maize’s ability to adapt to diverse environments (Pophaly and Tellier, 2015). A notable case of functional diversification involves the α-zein gene family, where tandem duplications have resulted in variation in gene expression across different maize haplotypes, highlighting both conservation and diversification in the regulatory patterns of duplicated genes (Hurst et al., 2021). 5 Applications of Comparative Genomics in Maize Improvement 5.1 Breeding for disease resistance Comparative genomics has been extensively used to identify genes associated with disease resistance in maize, including resistance to Fusarium ear rot, maize lethal necrosis (MLN), and fall armyworm (FAW). Genome-wide association studies (GWAS) and quantitative trait locus (QTL) mapping have identified several genomic loci linked to disease resistance. For example, multiple SNP markers have been associated with resistance to MLN, gray leaf spot, and turcicum leaf blight in different environments, providing valuable insights for marker-assisted breeding programs (Sadessa et al., 2022). Similarly, resistance to Fusarium ear rot has been linked to specific SNPs located on maize chromosomes 2, 3, 4, 5, 9, and 10, offering insights into the development of resistant maize lines (Chen et al., 2016). 5.2 Enhancing stress tolerance Abiotic stress tolerance in maize, particularly drought and heat tolerance, has been a significant focus of comparative genomics studies. Quantitative trait loci (QTL) mapping and genome-wide association studies (GWAS) have identified regions of the genome linked to drought stress tolerance. Recent advancements in molecular breeding techniques, including marker-assisted selection (MAS) and genomic selection, have been used to develop drought-tolerant maize varieties, particularly in regions like Sub-Saharan Africa where drought is a significant challenge (Wang et al., 2019). Moreover, genetic tools such as CRISPR-Cas9 and transgenic approaches have contributed to the development of maize lines with enhanced tolerance to multiple stresses (Figure 2) (Malenica et al., 2021). Figure 2 Most important stress factors in maize (Adopted from Malenica et al., 2021)
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