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Published on: April 4, 2018
SoyDBean: a database for SNPs reconciliation by multiple versions of soybean reference genomes
Yejin Lee1,2, Dong U Woo1,2, Yang Jae Kang3,4
1Division of Bio and Medical Bigdata Department (BK4 Program), Gyeongsang National University, 501, Jinju-daero, Jinju-si, Gyeongsangnam-do, 52828, Republic of Korea.
Researchers created a reliable soybean (Glycine max [L.] Merr.) single nucleotide polymorphism (SNP) dataset by verifying genetic variations across multiple genomes. This curated data ensures accuracy for future genetic diversity studies.
Area of Science:
- Plant Genomics
- Bioinformatics
- Crop Science
Background:
- Advancements in sequencing technology have led to numerous soybean whole genome sequences, revealing extensive genetic variations.
- Assessing the quality of these published variants is crucial due to varying bioinformatic methods and parameters used.
- There is a need to verify the caliber of genetic variations within the current soybean reference genome.
Purpose of the Study:
- To identify a dependable set of single nucleotide polymorphisms (SNPs) consistent across multiple soybean reference genomes.
- To reconfirm genetic variations using diverse whole genome sequencing data from public databases.
- To establish a high-quality SNP dataset for soybean genetic diversity research.
Main Methods:
- Collected and analyzed whole genome sequencing data from publicly available soybean databases.
- Developed and applied bioinformatic pipelines to reconcile and verify SNP coordinates across different reference assemblies.
- Cross-referenced variants using multiple datasets to ensure reliability and consistency.
Main Results:
- Generated datasets containing thoroughly verified SNP coordinates between soybean reference assemblies.
- Established the 'SoyDBean' database, a curated collection of high-quality soybean genetic variations.
- The database provides a dependable resource for understanding soybean genetic diversity.
Conclusions:
- The 'SoyDBean' database offers a validated set of SNPs, addressing the need for quality assessment in soybean genetic variation data.
- This resource facilitates more accurate and reliable research into soybean (Glycine max [L.] Merr.) genetic diversity and breeding.
- Public accessibility of the 'SoyDBean' database (http://soydbean.plantprofile.net/) promotes collaborative advancements in soybean genomics.
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