Maize Genomics and Genetics 2024, Vol.15, No.5, 239-246 http://cropscipublisher.com/index.php/mgg 241 3.3 Insights into domestication and adaptation Comparative genomics has shed light on the domestication and adaptation of maize. Genomic analyses have identified domestication genes such as tb1 and zcn8, which control important traits like reduced tillering and flowering time. Additionally, adaptation to different environments has been facilitated by selection on genes related to stress responses (Huang, 2024). For instance, studies show that maize landraces adapted to high altitudes possess genetic changes that confer advantages such as earlier flowering times, driven by selection in both Mesoamerican and South American highlands (Takuno et al., 2015). Moreover, genomic segments displaying high heterozygosity in European maize are linked to adaptation traits such as cold tolerance and flowering time (Figure 1) (Brandenburg et al., 2017). Figure 1 Sample locations, genetic structuring and inferred routes of maize migration (Adopted from Brandenburg et al., 2017) Image caption: A: Geographic location of 66 landraces from which lines originated with colors of dots designating genetic groups defined a priori-a Spanish line for which the geographical coordinates are unknown is not represented. Arrows indicate inferred routes of maize migration with admixed groups displaying two arrows. Colors of the arrows correspond to the recipient group; B: Principal Component Analysis computed on 500k non-genic SNPs. Corresponding ellipses indicate the 95% CI of the Mahalanobis distance (Adopted from Brandenburg et al., 2017) 4 Functional Genomics in Maize 4.1 Identification of functional elements Comparative genomics has been instrumental in identifying conserved regulatory elements in maize. These elements, such as conserved non-coding sequences (CNSs), play critical roles in gene regulation, including chromatin interaction sites and cis-regulatory elements. In the Andropogoneae tribe, which includes maize, CNSs have been associated with DNA replication, methylation, and histone modification. Studies show that variations in CNSs can lead to significant differences in gene expression, with the absence of CNSs contributing to the loss of gene expression in certain contexts (Song et al., 2020). Another key discovery is that long-range cis-regulatory elements are widespread in the maize genome and contribute to the regulation of genes controlling agronomic traits. These elements, located far from their target genes, are involved in complex chromatin loops that influence gene expression (Ricci et al., 2019). 4.2 Gene expression and regulation Gene expression regulation in maize varies significantly between tissues and developmental stages. Comparative analyses using RNA-Seq data have revealed how regulatory networks, including transcription factor binding motifs and non-coding RNAs, contribute to organ-specific gene expression. Open chromatin assays have identified chromatin-accessible regions associated with regulatory elements that control gene expression during
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