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.
- 相关文献
作者其他论文 更多>>
-
Insights into the genomic divergence of maize heterotic groups in China
作者：Xue, Yingjie;Zhao, Yikun;Zhang, Yunlong;Wang, Rui;Liu, Zhihao;Wang, Weiwei;Zhu, Shaoxi;Fan, Yaming;Xu, Liwen;Zhao, Wei;Zhao, Jiuran;Wang, Fengge;Li, Xiaohui
关键词：genetic difference; germplasm resource; heterotic group; maize; population differentiation
-
Beware of Sealing Film of Petri Dishes!-Alters the Expression of a Large Number of Genes
作者：Ma, Yun;Li, Fang;Wang, Xuyang;Wang, Ronghuan;Zhao, Jiuran;Li, Fang;Wang, Xuyang;Sun, Qingpeng
关键词：sealingfilms; Arabidopsis seedlings; transcriptome; CO2 concentrations
-
Large-scale metabolomic landscape of edible maize reveals convergent changes in metabolite differentiation and facilitates its breeding improvement
作者：Li, Chunhui;Li, Zhiyong;Lu, Baishan;Shi, Yaxing;Xiao, Senlin;Dong, Hui;Zhang, Ruyang;Liu, Hui;Jiao, Yanyan;Xu, Li;Su, Aiguo;Wang, Xiaqing;Zhao, Yanxin;Wang, Shuai;Fan, Yanli;Luo, Meijie;Xi, Shengli;Yu, Ainian;Wang, Fengge;Ge, Jianrong;Tian, Hongli;Yi, Hongmei;Wang, Ronghuan;Song, Wei;Zhao, Jiuran;Lv, Yuanda;Li, Huihui
关键词：waxy maize; sweet maize; metabolite differentiation; diversifying selection; metabolome database
-
DPE1, a novel allelic of BT1, is critical for maize endosperm development and carbohydrate metabolism
作者：Wang, Shuai;Wang, Yuandong;Zhang, Ruyang;Liu, Qian;Wang, Tianyi;Li, Zhiyong;Wang, Xiaqing;Li, Chunhui;Xiao, Senlin;Jiao, Yanyan;Xing, Jinfeng;Sun, Xuan;Zhao, Yanxin;Wang, Jidong;Su, Aiguo;Xu, Ruibing;Wang, Ronghuan;Song, Wei;Zhao, Jiuran
关键词：Endosperm; ADP-glucose transporter; Carbohydrate metabolism; Zea mays; DPE1
-
Integrated transcriptomic and proteomic analysis identified key folate biosynthesis gene in waxy maize
作者：Jiao, Yanyan;Shi, Yaxing;Dong, Hui;Pan, Yujing;Liu, Hui;Li, Zhiyong;Wang, Xiaqing;Li, Chunhui;Wang, Tianyi;Wang, Shuai;Wang, Ronghuan;Lu, Baishan;Song, Wei;Zhao, Jiuran
关键词：Biofortification; Folate accumulation; Proteome; Transcriptome; Waxy maize
-
A Scalable and Robust Chloroplast Genotyping Solution: Development and Application of SNP and InDel Markers in the Maize Chloroplast Genome
作者：Wang, Rui;Yang, Yang;Tian, Hongli;Yi, Hongmei;Xu, Liwen;Ge, Jianrong;Zhao, Yikun;Wang, Lu;Wang, Fengge;Lv, Yuanda;Zhou, Shiliang
关键词：chloroplast; SNP; InDel; high throughput; genotyping; maize
-
LociScan, a tool for screening genetic marker combinations for plant variety discrimination
作者：Yang, Yang;Tian, Hongli;Yi, Hongmei;Shi, Zi;Wang, Lu;Fan, Yaming;Wang, Fengge;Zhao, Jiuran
关键词：Plant variety discrimination; Genetic marker combination; Variety discrimination power; Genetic algorithm
