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Development of Omni InDel and supporting database for maize

文献类型： 外文期刊

作者： Liu, Zhihao 1 ; Zhao, Yikun 1 ; Zhang, Yunlong 1 ; Xu, Liwen 1 ; Zhou, Ling 3 ; Yang, Weiguang 2 ; Zhao, Han 3 ; Zhao, Jiuran 1 ; Wang, Fengge 1 ;

作者机构： 1.Beijing Acad Agr & Forest Sci BAAFS, Minist Agr & Rural Affairs, Key Lab Crop DNA Fingerprinting Innovat & Utilizat, Beijing, Peoples R China

2.Jilin Agr Univ, Coll Agr, Changchun, Peoples R China

3.Jiangsu Acad Agr Sci, Inst Crop Germplasm & Biotechnol, Prov Key Lab Agrobiol, Nanjing, Jiangsu, Peoples R China

关键词： Omni InDel; maize; InDel; crops; database

期刊名称：FRONTIERS IN PLANT SCIENCE （ 影响因子：5.6； 五年影响因子：6.8 ）

ISSN： 1664-462X

年卷期： 2023 年 14 卷

页码：

收录情况： SCI

摘要： Insertions-deletions (InDels) are the second most abundant molecular marker in the genome and have been widely used in molecular biology research along with simple sequence repeats (SSR) and single-nucleotide polymorphisms (SNP). However, InDel variant mining and marker development usually focuses on a single type of dimorphic InDel, which does not reflect the overall InDel diversity across the genome. Here, we developed Omni InDels for maize, soybean, and rice based on sequencing data and genome assembly that included InDel variants with base lengths from 1 bp to several Mb, and we conducted a detailed classification of Omni InDels. Moreover, we screened a set of InDels that are easily detected and typed (Perfect InDels) from the Omni InDels, verified the site authenticity using 3,587 germplasm resources from 11 groups, and analyzed the germplasm resources. Furthermore, we developed a Multi-InDel set based on the Omni InDels; each Multi-InDel contains multiple InDels, which greatly increases site polymorphism, they can be detected in multiple platforms such as fluorescent capillary electrophoresis and sequencing. Finally, we developed an online database website to make Omni InDels easy to use and share and developed a visual browsing function called "Variant viewer" for all Omni InDel sites to better display the variant distribution.

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