Genetic purity identification of wax gourd (Benincasa hispida) hybrids through InDel markers linked to seed size and shape genes

Wax gourd holds significant economic value, and accurate and rapid identification of seed purity is becoming increasingly essential. Although genes regulating wax gourd seed shape and size have been reported, the development of InDel markers tightly linked to these genes for hybrid seed purity identification remains unexplored. To address this need, we resequenced four high-generation inbred lines (bilateral-seeded inbred line KF43, unilateral-seeded inbred line A-1, large-seeded inbred line MY-1 and small-seeded inbred line GX71) and identified InDel marker pairs, Mc10-8 (tightly linked to seed size genes) and Mc04-13 (tightly linked to seed shape genes), situated 0.1 Mb and 0.3 Mb downstream of genes Bch10G006400 and Bch04G005460, respectively. The purity of hybrids 'Yinyuan 4', 'A45' and 'Fenxianzi 3' was determined using the InDel marker Mc10-8 and for 'Xiaozi 1', 'Xiaozi 2' and 'HF-1' using the InDel marker Mc04-13. The six hybrids with InDel markers were grow-out tested for purity identification, showed highly consistent results, establishing these markers as stable, accurate and efficient tools for determining the genetic purity of wax gourd hybrids. Collectively, our findings could help optimise agricultural practices, thereby ensuring the sustained production of high-quality and genetically pure wax gourd hybrids.