Development of Omni InDel and supporting database for maize
Zhihao Liu1,2, Yikun Zhao1, Yunlong Zhang1
1Key Laboratory of Crop DNA Fingerprinting Innovation and Utilization (Co-construction by Ministry and Province), Ministry of Agriculture and Rural Affairs, Beijing Academy of Agricultural and Forest Sciences (BAAFS), Beijing, China.
Frontiers in Plant Science
|July 17, 2023
Summary
This study introduces Omni InDels, a comprehensive set of insertion-deletion (InDel) variants for maize, soybean, and rice. These markers enhance genomic diversity analysis and marker development for various plant research applications.
Area of Science:
- Genomics
- Molecular Biology
- Plant Science
Background:
- Insertions-deletions (InDels) are abundant genomic markers, alongside SSRs and SNPs.
- Current InDel analysis often overlooks the full spectrum of genomic InDel diversity.
Purpose of the Study:
- To develop a comprehensive InDel resource (Omni InDels) for maize, soybean, and rice.
- To classify InDels and develop easily detectable and highly polymorphic marker sets.
- To create a user-friendly database for accessing and visualizing InDel variants.
Main Methods:
- Genome sequencing data and assembly were used to identify InDels ranging from 1 bp to Mb.
- InDels were classified, and a subset of easily typed 'Perfect InDels' was screened.
- Authenticity was verified across 3,587 germplasm resources from 11 groups.
- A 'Multi-InDel' set was developed to increase polymorphism for detection on multiple platforms.
Main Results:
- Developed Omni InDels encompassing a wide range of variant sizes for three key crops.
- Identified 'Perfect InDels' and validated their authenticity across diverse germplasm.
- Created 'Multi-InDels' that significantly enhance site polymorphism.
- Launched an online database with a 'Variant viewer' for InDel site visualization.
Conclusions:
- Omni InDels provide a valuable, comprehensive resource for InDel variant mining and marker development.
- The developed marker sets and database facilitate broader application in plant genomics and breeding.
- This resource enhances the understanding and utilization of InDel diversity across important crop genomes.
