A novel F-box gene, SlSE2.2, is responsible for the stigma exsertion degree in tomato (Solanum lycopersicum)

Tomato stigma exsertion is an important trait in positional sterility genotypes, which can eliminate the need for manual emasculation and promote hybrid production. In this study, we discovered a new tomato accession, J59, with a stably inherited stigma exsertion trait. To explore the regulatory genes of the stigma exsertion trait, J59 and inserted stigma genotypes M82 were crossed to obtain mapping populations. Through three years mapping, a quantitative trait locus (QTL) associated with the stigma exsertion trait was narrowed down to a 52.635 kb interval on chromosome 2, Solyc02g087270 was identified as the candidate gene responsible for this trait, named SlSE2.2. This gene encoded an F-box protein of the FBA subfamily. Sequences analysis revealed that an 11 bp deletion occurred in the first exon of SlSE2.2 in J59, resulting in premature termination of translation. Subcellular localization revealed that SlSE2.2 is located to the nucleus. Knockout of SlSE2.2 increased anther and style lengths, which reduced the values of anther length minus pistil length, changing the relative length of anthers and pistils, called stigma exsertion degree, whereas, overexpression of SlSE2.2 showed the opposite phenotype. Hormone levels analysis revealed that SlSE2.2 negatively modulated IAA, ETH, and JA levels and positively modulated ABA content. Transcriptomic analysis showed that SlSE2.2 affected the expression of SlIAA19, SlIAA36, SlETR6, SlJAZ, and SlSnRK2 related to the hormone signal transduction. This study identified the important role of a new gene, SlSE2.2, which provided a helpful insight to explore the regulatory mechanisms of stigma exsertion degree in tomato.