NGS-Based Multi-Allelic InDel Genotyping and Fingerprinting Facilitate Genetic Discrimination in Grapevine (Vitis vinifera L.)

文献类型： 外文期刊

第一作者： Jia, Guiying

作者： Jia, Guiying;Zhang, Na;Yang, Yingxia;Zhang, Hong;Guo, Yutong;Wang, Qian;Zhang, He;Chen, Rui;Huang, Jianquan;Lyu, Mingjie;Jia, Guiying;Zhang, Hong;Guo, Yutong;Yang, Yingxia;Jin, Qingdong;Jiang, Jianfu;Wu, Jianjin

作者机构：

关键词： grapevine; multi-allelic InDels; next-generation sequencing; fingerprinting; population structure

期刊名称：HORTICULTURAE （ 影响因子：3.1； 五年影响因子：3.1 ）

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年卷期： 2024 年 10 卷 7 期

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收录情况： SCI

摘要： Molecular markers play a crucial role in marker-assisted breeding and varietal identification. However, the application of insertion/deletion markers (InDels) in grapevines has been limited by the low throughput and separability of gel electrophoresis. To developed effective InDel markers for grapevines, this study reports a novel, effective and high-throughput pipeline for InDel marker development and identification. After rigorous filtering, 11 polymorphic multi-allelic InDel markers were selected. These markers were then used to perform genetic identification of 123 elite grape cultivars using agarose gel electrophoresis and next-generation sequencing (NGS). The polymorphism rate of the InDel markers identified by gels was 37.92%, while the NGS-based results demonstrated a higher polymorphism rate of 61.12%. Finally, the NGS-based fingerprints successfully distinguished 122 grape varieties (99.19%), surpassing the gels, which could distinguish 116 grape varieties (94.31%). Specifically, we constructed phylogenetic trees based on the genotyping results from both gels and NGS. The population structure revealed by the NGS-based markers displayed three primary clusters, consisting of the patterns of the evolutionary divergence and geographical origin of the grapevines. Our work provides an efficient workflow for multi-allelic InDel marker development and practical tools for the genetic discrimination of grape cultivars.

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