| Summary: | <i>Gypsophila paniculata</i> is the only species in the genus <i>Gypsophila</i> that has been used as cut flowers, and the sequencing of its genome has just been completed, opening a new chapter in its molecular genetic breeding. The molecular marker system is the basis for genetic molecular research in the era of genomics, whereas it is still a gap for <i>G. paniculata</i>. In this study, we constructed a genome-wide InDel marker system of <i>G. paniculata</i> after genome resequencing of another wild-type accession with white flowers. Consequently, 407 InDel markers at a distance of ~2 Mb were designed for all 17 chromosomes. Later, the validation of these markers by PCR revealed that 289 markers could distinguish alleles of the two wild-type alleles clearly. The predicted polymorphisms of two wild-type alleles were then transferred to the commercial cultivars, which displayed a rich polymorphism among four commercial cultivars. Our research established the first genome-level genetic map in <i>G. paniculata</i>, providing a comprehensive set of marker systems for its molecular research.
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