Genome-Wide Analysis of the LEA Gene Family in Pineapple (Ananas comosus L.) Reveals Its Potential Roles in Cold Stress Response and Reproductive Development

Late Embryogenesis Abundant (LEA) proteins play vital roles in plant responses to abiotic stress and developmental regulation. Pineapple (<i>Ananas comosus</i> L.) is a major tropical fruit crop with high economic value, but its production is often threatened by cold stress, particularly in regions at the northern margin of its cultivation. Despite the recognized importance of LEA proteins in stress adaptation, their genomic landscape and functional characteristics in pineapple remain largely unexplored. In this study, 37 <i>AcLEA</i> genes were identified in the pineapple (<i>Ananas comosus</i> L.) genome and classified into six subfamilies, with <i>LEA_2</i> being the largest. Most AcLEA proteins were predicted to be hydrophilic, thermally stable, and intrinsically disordered, consistent with typical LEA protein characteristics. Phylogenetic and collinearity analyses revealed species-specific expansion patterns, primarily driven by segmental duplication events. Most duplicated gene pairs shared similar exon-intron structures, motif compositions, and expression profiles, although several displayed signs of functional divergence based on distinct expression patterns, Ka/Ks ratios > 1, and motif differences. Promoter <i>cis</i>-element, transcription factor, and miRNA network predictions indicated that <i>AcLEA</i> genes are widely involved in stress responses as well as growth and development. Expression profiling showed that many <i>AcLEA</i> genes including <i>AcLEA32</i>, <i>AcLEA7</i>, <i>AcLEA9</i>, <i>AcLEA30</i>, <i>AcLEA29</i>, <i>AcLEA33</i>, and <i>AcLEA18</i> were significantly upregulated under cold stress and declined upon stress removal, indicating a potential role in cold tolerance. Some <i>AcLEA</i> genes, such as <i>AcLEA32</i> and <i>AcLEA33</i>, showed faster and stronger induction under cold stress in the cold-tolerant cultivar "Comte de Paris" (BL) compared to the sensitive cultivar "Tainong No. 20" (NN), suggesting that differential gene responsiveness may contribute to cultivar-specific cold tolerance. Additionally, most <i>AcLEA</i> genes exhibited distinct spatiotemporal expression patterns across floral organs and fruit at various developmental stages, suggesting their involvement in reproductive development. These findings provide a foundation for future functional studies and highlight candidate genes for improving cold resilience and developmental traits in pineapple through molecular breeding.