Pan-Genome-Wide Investigation and Expression Analysis of <i>GATA</i> Gene Family in Maize
2025
Fangfang Zhao | Xia Li | Ziqi Chen | Changhong Guo
GATA is a crucial transcription factor involved in plant growth, development, and responses to abiotic stress. Therefore, identifying and exploring GATA transcription factors in maize is of significant importance. In this study, we identified 75 <i>ZmGATA</i> genes based on the pan-genome of maize, which includes 26 high-quality maize genomes. These consist of 58 core genes (present in all 26 lines), 12 non-essential genes (present in 2 to 23 lines), 2 near-core genes (present in 24 to 25 lines), and 3 private genes (present in only 1 line). By evaluating the Ka/Ks ratio of the <i>ZmGATA</i> genes in 26 maize varieties, we found that the Ka/Ks ratios of <i>ZmGATA31</i>, <i>ZmGATA32</i>, <i>ZmGATA36</i>, and <i>ZmGATA9</i> were greater than 1, which may indicate that these four genes are under positive selection. In contrast, the Ka/Ks ratios of other <i>ZmGATA</i> genes were less than 1, suggesting that these genes may be under purifying selection. In the 26 maize genomes, we observed a significant difference in the expression of <i>ZmGATA8</i> between varieties affected by structural variations (SVs) and those not affected. In certain varieties, SVs altered conserved structures. Additionally, we analyzed the expression levels of <i>ZmGATA</i> genes in different maize tissues and under abiotic stress. <i>ZmGATA38</i> and <i>ZmGATA39</i> were highly expressed in the endosperm, thereby influencing starch synthesis, while <i>ZmGATA7</i>, <i>ZmGATA10</i>, <i>ZmGATA19</i>, <i>ZmGATA28</i>, and <i>ZmGATA40</i> were found to be associated with abiotic stress responses. These findings provide valuable new resources for functional research on <i>ZmGATA</i>.
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