Determination of hybrid-seed genetic purity in wax gourd using newly developed InDel markers based on whole-genome resequencing

Wax gourd (Benincasa hispida) is highly appreciated for its nutritional and therapeutic value, especially throughout Asia. As the market for wax gourd expands, new varieties of unknown purity are being promoted. In this study, the unpublished ‘GX-19’ wax gourd genome elucidated by our research group was used as reference genome. Two high-generation inbred lines (‘HX-1’ and ‘HX-6’) were resequenced and 330 pairs of InDel primers were designed and synthesised. Following screening, 11 pairs of InDel markers were identified and used to determine the degree of genetic purity of wax-gourd hybrid seeds. InDel molecular markers were used to identify the purity of 17 hybrids, including ‘Lvxianzi 2’, ‘Fenxianzi 1’, ‘Jinyuan 1’, ‘Yinyuan 4’, ‘Chunfeng 868’, ‘Xinjinyu’ and ‘Meihua 8’. Additionally, we showed that the amplification fragment from DNA extracted using the alkali rapid-extraction method developed in this study was identical to that of the fragment amplified from DNA extracted using a modified CTAB method. When the InDel molecular marker-based purity determination of five wax gourd hybrids was compared with that using the growing out test, the results were highly consistent. A stable, accurate, efficient and straightforward approach is provided to determine the genetic purity of hybrid wax gourd seeds.