Altering tomato seed fatty acid composition via non-transgenic disruption of NF-Y transcription factors using zinc finger nucleases

Improving tomato (Solanum lycopersicum) fruit quality and nutritional content is a key focus in modern breeding. Targeting transcription factors (TFs), which control metabolic pathways, presents a powerful strategy to achieve this. This study investigated the role of the heterotrimeric TF NF-Y in tomato seed characteristics, specifically seed phenotypes, germination and fatty acid composition. Tomato seeds, often a discarded byproduct of processing, are a valuable source of oil rich in essential fatty acids. To investigate NF-Y’s function, we used zinc finger nucleases (ZFNs), a non-transgenic gene editing technology, to create disruption lines of L1L4/NF-YB (lines M7_5, M29_2) and NF-YA8 (line MT_1) in tomato. Analysis of nf-ya8 mutant fruits revealed a subset with increased seed counts. Furthermore, mutant seeds exhibited altered morphology, characterized by reduced size and a distinctive coating. Analysis of seed oil from wild-type and nf-y mutant lines revealed significant alterations in major fatty acids such as linoleic, oleic, palmitic and stearic acid. These findings highlight the crucial role of NF-Y, specifically NF-YA8, in regulating seed development, germination timing, and fatty acid biosynthesis in tomato, offering insights into potential strategies for manipulating seed traits through genetic modification.