Exploring the role of FAT genes in Solanaceae species through genome‐wide analysis and genome editing

Plants produce numerous fatty acid derivatives, and some of these compounds have significant regulatory functions, such as governing effector‐induced resistance, systemic resistance, and other defense pathways. This study systematically identified and characterized eight FAT genes (Acyl‐acyl carrier protein thioesterases), four in the Solanum lycopersicum and four in the Solanum tuberosum genome. Phylogenetic analysis classified these genes into four distinct groups, exhibiting conserved domain structures across different plant species. Promoter analysis revealed various cis‐acting elements, most of which are associated with stress responsiveness and growth and development. Micro‐RNA (miRNA) analysis identified specific miRNAs, notably miRNA166, targeting different FAT genes in both species. Utilizing clustered regularly interspaced short palindromic repeats/CRISPR‐associated protein 9 (CRISPR/Cas9)‐mediated knockout, mutant lines for SlFATB1 and SlFATB3 were successfully generated and exhibited diverse mutation types. Biochemical evaluation of selected mutant lines revealed significant changes in fatty acid composition, with linoleic and linolenic acid content variations. The study also explored the impact of FAT gene knockout on tomato leaf architecture through scanning electron microscopy, providing insights into potential morphological alterations. Knocking out of FAT genes resulted in a significant reduction in both trichome and stoma density. These findings contribute to a comprehensive understanding of FAT genes in Solanaceous species, encompassing genetic, functional, and phenotypic aspects. Core Ideas Knocking out of SlFATB1 and SlFATB3 genes can affect the plant architecture. SlFATB1/SlFATB3 mutated lines have significant changes in fatty acid composition. The same number of FAT genes are available in tomato and potato. Plain Language Summary This study identified and characterized eight FAT genes in tomatoes and potatoes, categorizing them into distinct groups with conserved structures. Promoter analysis showed stress‐related elements, while miRNA analysis revealed miRNA166's role in targeting these genes. CRISPR/Cas9 knockout generated mutant lines for two genes, showing varied mutations. Biochemical analysis indicated altered fatty acid composition. Knockout affected leaf architecture, reducing trichome and stoma density, offering insights into FAT genes' genetic, functional, and phenotypic roles in Solanaceous species.