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

文献类型： 外文期刊

作者： Jia, Guiying 1 ; Zhang, Na 1 ; Yang, Yingxia 1 ; Jin, Qingdong 3 ; Jiang, Jianfu 4 ; Zhang, Hong 1 ; Guo, Yutong 1 ; Wang, Qian 1 ; Zhang, He 1 ; Wu, Jianjin 5 ; Chen, Rui 1 ; Huang, Jianquan 1 ; Lyu, Mingjie 1 ;

作者机构： 1.Tianjin Acad Agr Sci, State Key Lab Vegetable Biobreeding, Tianjin 300192, Peoples R China

2.Nankai Univ, Coll Life Sci, Tianjin 300071, Peoples R China

3.Huazhong Agr Univ, Coll Plant Sci & Technol, Natl Key Lab Crop Genet Improvement, Natl Ctr Oil Crop Improvement Wuhan, Wuhan 430070, Peoples R China

4.Chinese Acad Agr Sci, Zhengzhou Fruit Res Inst, Zhengzhou 450009, Peoples R China

5.Tianjin Agr Dev Serv Ctr, Tianjin 300061, Peoples R China

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 ）

ISSN：

年卷期： 2024 年 10 卷 7 期

页码：

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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