Identification of the FLA Gene Family in Soybean and Preliminary Functional Analysis of Its Drought-Responsive Candidate Genes

Background/Objectives: Fasciclin-like arabinogalactan proteins (FLAs) are critical components of the plant cell wall, playing vital roles in development and abiotic stress responses. However, a systematic genome-wide analysis of the FLA family in soybean (Glycine max L.), a major legume crop susceptible to drought, is lacking. This study aimed to comprehensively identify GmFLA members and investigate their potential functions in drought tolerance. Methods: We identified GmFLA genes via BLASTP (v2.16.0) and Hidden Markov Model (HMM) searches against the soybean genome. Subsequent analyses encompassed their physicochemical properties, chromosomal distribution, gene structure, phylogenetic relationships, conserved domains, cis-acting elements, and subcellular localization. Drought-responsive candidates were screened using a Gene Expression Omnibus (GEO) dataset, and their expression profiles were validated under drought stress using quantitative real-time PCR (qRT-PCR). Results: A total of 55 GmFLA genes were identified and unevenly distributed across 14 chromosomes. Most genes featured a single-exon structure and contained a conserved Fasciclin domain, with predicted localization primarily to the chloroplast. Phylogenetic analysis grouped them into three distinct subclasses with Arabidopsis homologs, suggesting lineage-specific expansion. Promoter analysis revealed an abundance of stress- and hormone-related cis-elements. Expression analysis identified five candidate genes (GmFLA5, GmFLA15, GmFLA40, GmFLA47, and GmFLA54) that showed tissue-specific expression changes under drought treatment. Conclusions: This study provides the first comprehensive genomic characterization of the GmFLA gene family and identifies candidate GmFLAs with drought-responsive expression patterns. Our findings establish a foundation for future functional research to investigate their potential roles in soybean drought response. Furthermore, these candidates serve as potential targets for further investigation in strategies aimed at improving soybean drought tolerance.