Origin of a self-compatibility associated MITE in Petota and its application in hybrid potato breeding

Hybrid potato breeding offers a promising solution to tackle the challenges in potato breeding. However, most diploids are self-incompatible (SI), which hinders the development of inbred lines. S-locus inhibitor (Sli) is a 'master key' gene capable of conferring self-compatibility (SC) to most of the SI diploids, yet the regulatory mechanism underlying its male gamete-specific expression remains unclear, limiting its breeding potential. This study has uncovered that a miniature inverted-repeat transposable element (Mi-549) within the Sli promoter can affect the methylation pattern of the promoter, thereby regulating the pollen-specific expression of Sli as well as the SC phenotype in diploids. We delved into the origin of Mi-549 within Petota and found that Mi-549 was likely acquired fortuitously in wild Solanum lesteri but was not favored during domestication, probably due to the asexual propagation nature of potato. Although Mi-549 and its impacts on Sli as well as SC are not selected, screening of Mi-549 identified three novel SC accessions that belong to S. lesteri, Solanum neocardenasii and Solanum stenotomum, which enrich the germplasm pool associated with stress and pest resistance and hold significant value for breeding applications.