Genome-wide identification and characterization of FORMIN gene family in potato (Solanum tuberosum L.) and their expression profiles in response to drought stress condition

• Published in: PloS one 2024-08, Vol.19 (8), p.e0309353
• Main Authors: Khatun, Mst Sumaiya, Islam, Md Shohel Ul, Shing, Pollob, Zohra, Fatema Tuz, Rashid, Shuraya Beente, Rahman, Shaikh Mizanur, Sarkar, Md Abdur Rauf
• Format: Article
• Language: English
• Subjects: Abscisic acid; Actin; Adaptation; Analysis; Bangladesh; Biological activity; Biology and Life Sciences; Chloroplasts; Chromosomes; Cultivars; Cytoskeleton; Drought; Drought resistance; Droughts; Evaluation; Flowers & plants; Formins - genetics; Gene expression; Gene Expression Profiling; Gene Expression Regulation, Plant; Gene regulation; Genes; Genetic aspects; Genome, Plant; Genome-wide association studies; Genomes; Genomic analysis; Influence; Localization; MicroRNAs; MicroRNAs - genetics; miRNA; Multigene Family; Phylogenetics; Phylogeny; Plant breeding; Plant Proteins - genetics; Plant Proteins - metabolism; Potatoes; Proteins; Regulatory sequences; Research and Analysis Methods; Signal transduction; Similarity; Software; Solanum tuberosum; Solanum tuberosum - genetics; Solanum tuberosum - metabolism; Stress, Physiological - genetics; Structure-function relationships; Subgroups; Vegetables
• ISSN: 1932-6203; 1932-6203
• DOI: 10.1371/journal.pone.0309353

Formin proteins, characterized by the FH2 domain, are critical in regulating actin-driven cellular processes and cytoskeletal dynamics during abiotic stress. However, no genome-wide analysis of the formin gene family has yet to be conducted in the economically significant plant potato (Solanum tuberosum L.). In this study, 26 formin genes were identified and characterized in the potato genome (named as StFH), each containing the typical FH2 domain and distributed across the ten chromosomes. The StFH was categorized into seven subgroups (A-G) and the gene structure and motif analysis demonstrated higher structural similarities within the subgroups. Besides, the StFH exhibited ancestry and functional similarities with Arabidopsis. The Ka/Ks ratio indicated that StFH gene pairs were evolving through purifying selection, with five gene pairs exhibiting segmental duplications and two pairs exhibiting tandem duplications. Subcellular localization analysis suggested that most of the StFH genes were located in the chloroplast and plasma membrane. Moreover, 54 cis-acting regulatory elements (CAREs) were identified in the promoter regions, some of which were associated with stress responses. According to gene ontology analysis, the majority of the StFH genes were involved in biological processes, with 63 out of 74 GO terms affecting actin polymerization. Six major transcription factor families, including bZIP, C2H2, ERF, GATA, LBD, NAC, and HSF, were identified that were involved in the regulation of StFH genes in various abiotic stresses, including drought. Further, the 60 unique microRNAs targeted 24 StFH by regulating gene expression in response to drought stress were identified. The expression of StFH genes in 14 different tissues, particularly in drought-responsive tissues such as root, stem, shoot apex, and leaf, underscores their significance in managing drought stress. RNA-seq analysis of the drought-resistant Qingshu No. 9 variety revealed the potential role of up-regulated genes, including StFH2, StFH10, StFH19, and StFH25, in alleviating drought stress. Overall, these findings provide crucial insights into the response to drought stress in potatoes and can be utilized in breeding programs to develop potato cultivars with enhanced drought-tolerant traits.