Development of InDel markers and construction of DNA fingerprints of wax gourd (Benincasa hispida) based on whole genome re-sequencing

文献类型： 外文期刊

第一作者： Su, Liwen

作者： Su, Liwen;Cheng, Zhikui;Wu, Yongguan;Deng, Yan;Bai, Wenhui;Chen, Zhihao;Chen, Xianglei;Wang, Peng;Liu, Zhengguo;Li, Jingying;Li, Yan

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关键词： Wax gourd; Whole genome re-sequencing; InDel marker; DNA fingerprints

期刊名称：SCIENTIA HORTICULTURAE （ 影响因子：4.2； 五年影响因子：4.6 ）

ISSN： 0304-4238

年卷期： 2025 年 349 卷

页码：

收录情况： SCI

摘要： The development of new wax gourd varieties is accelerating. However, the limited genetic data on wax gourd populations and the lack of advanced molecular marker identification techniques have posed significant challenges to the commercial breeding of wax gourd. In this study, we performed whole-genome re-sequencing of 55 wax gourd germplasm resources to identify insertion-deletion (InDel) markers. A total of 964,087 InDels were identified across the 55 germplasm resources, yielding an average density of approximately 1098 InDels per Mb. From these, 33 InDel markers were selected through polymerase chain reaction (PCR) amplification technique. The average values for the major allele frequency, gene diversity index (Hs), expected heterozygosity (He), and polymorphism information content (PIC) of 33 InDel markers were 0.641, 0.444, 0.351, and 0.344, respectively. Based on the in-depth study and analysis of 33 InDel markers, 12 core InDel markers were screened in accordance with the principle of minimizing the number of primers, and the DNA fingerprint of 84 commercial varieties of wax gourd was successfully constructed. Subsequently, the heterozygous genotypes of the markers in the fingerprint were verified, and the results showed that among the 37 commercial varieties of wax gourd, each variety had 1 to 7 pairs of InDel markers that could be used for seed purity identification. This study developed InDel markers for wax gourd variety identification and seed purity verification, and constructed DNA fingerprints, which provides a basis for wax gourd genetic diversity, variety identification, property rights disputes and molecular breeding.

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