Three pollen QTLs are sufficient to partially break stylar unilateral incompatibility of Solanum pennellii

[bullet] In tomato clade, both self-incompatibility(S-) locus-dependent and -independent mechanisms are present in unilateral incompatibility (UI). Several stylar UI factors mediating S-locus-independent mechanism have been gradually uncovered, however, related pollen UI (pui) factors still await more studies. [bullet]Quantitative trait loci (QTL) mapping, comparative transcriptomics and introgression lines (ILs) /inbred backcross lines (BILs)-based functional analysis were applied for identification and functional validation of pui QTLs between self-compatible (SC) Solanum lycopersicum and SC S. pennellii LA0716. [bullet]In addition to the reported pui10.1 (SpFPS2), two pui QTLs (pui6.2 and pui12.1) were identified. Pollen tubes of cultivated tomatoes introgressed with three pui loci could partially break the stylar UI response in LA0716 styles. Furthermore, a conserved function of pui12.1 was found in the styles of SC S. habrochaites LA0407 and SC S. chmielewskii LA1028. Three candidate genes linked to pui6.2 and pui12.1 were screened for further analysis. [bullet]This study reveals a potential synergistic relationship of the three pui QTLs in breaking stylar UI response of LA0716 and will advance our understanding of the genetic mechanisms underlying UI in the tomato clade. HighlightOur data revealed that breaking the stylar unilateral incompatibility of Solanum pennellii LA0716 requires not only the reported pollen UI (pui) factor but also another two pui QTLs identified in this study.