We are working on root-stock development of cultivated tomato by using Solanum lycopersicum and S. habrochaites. We would like to develop F1 of those species for using as root-stock. But S. habrochaites has two kinds of mating system self-compatible (SC) and self-incompatible (SI). We would like to select SI genotypes using DNA based markers. Although we have tried to use the DNA markers for genotyping published by Broz et al. : New Phytologist (2017) 213: 440–454, doi: 10.1111/nph.14130. But those markers did not match with the USDA collection (102 accessions). Could anybody suggest me the any other alternatives for genotyping our materials.