Genome-Wide Identification and Expression Pattern Analysis of the Late Embryogenesis Abundant (LEA) Family in Foxtail Millet (Setaria italica L.)

<b>Background/Objectives</b>: Late embryogenesis abundant (LEA) proteins regulate stress responses and contribute significantly to plant stress tolerance. As a model species for stress resistance studies, foxtail millet (<i>Setaria italica</i>) lacks comprehensive characterization of its <i>LEA</i> gene family. This study aimed to comprehensively identify <i>SiLEA</i> genes in foxtail millet and elucidate their functional roles and tissue-specific expression patterns. <b>Methods</b>: Genome-wide identification of <i>SiLEA</i> genes was conducted, followed by phylogenetic reconstruction, <i>cis</i>-acting element analysis of promoters, synteny analysis, and expression profiling. <b>Results</b>: Ninety-four <i>SiLEA</i> genes were identified and classified into nine structurally distinct subfamilies, which are unevenly distributed across all nine chromosomes. Phylogenetic analysis showed closer clustering of <i>SiLEA</i> genes with sorghum and rice orthologs than with <i>Arabidopsis thaliana AtLEA</i> genes. Synteny analysis indicated the <i>LEA</i> gene family expansion through tandem and segmental duplication. Promoter <i>cis</i>-element analysis linked <i>SiLEA</i> genes to plant growth regulation, stress responses, and hormone signaling. Transcriptome analysis revealed tissue-specific expression patterns among <i>SiLEA</i> members, while RT-qPCR verified ABA-induced transcriptional regulation of <i>SiLEA</i> genes. <b>Conclusions</b>: This study identified 94 <i>SiLEA</i> genes grouped into nine subfamilies with distinct spatial expression profiles. ABA treatment notably upregulated <i>SiASR-2</i>, <i>SiASR-5</i>, and <i>SiASR-6</i> in both shoots and roots.