Soybean-VCF2Genomes: a database to identify the closest accession in soybean germplasm collection

Jungmin Ha,Dong U Woo,Halim Park,Ho Hwi Jeon,Yang Jae Kang,Yejin Lee,Joohyeong Lee

doi:10.1186/s12859-019-2859-5

Jungmin Ha, Dong U Woo + Show 5 more

Open Access

https://doi.org/10.1186/s12859-019-2859-5

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Abstract

BackgroundThe development of next generation sequencer (NGS) and the analytical methods allowed the researchers to profile their samples more precisely and easier than before. Especially for agriculture, the certification of the genomic background of their plant materials would be important for the reliability of seed market and stable yield as well as for quarantine procedure. However, the analysis of NGS data is still difficult for non-computational researchers or breeders to verify their samples because majority of current softwares for NGS analysis require users to access unfamiliar Linux environment.Main bodyHere, we developed a web-application, “Soybean-VCF2Genomes”, http://pgl.gnu.ac.kr/soy_vcf2genome/ to map single sample variant call format (VCF) file against known soybean germplasm collection for identification of the closest soybean accession. Based on principal component analysis (PCA), we simplified genotype matrix for lowering computational burden while maintaining accurate clustering. With our web-application, users can simply upload single sample VCF file created by more than 10x resequencing strategy to find the closest samples along with linkage dendrogram of the reference genotype matrix.ConclusionThe information of the closest soybean cultivar will allow breeders to estimate relative germplasmic position of their query sample to determine soybean breeding strategies. Moreover, our VCF2Genomes scheme can be extended to other plant species where the whole genome sequences of core collection are publicly available.

Highlights

The development of generation sequencer (NGS) and the analytical methods allowed the researchers to profile their samples more precisely and easier than before
Main body: Here, we developed a web-application, “Soybean-VCF2Genomes”, http://pgl.gnu.ac.kr/soy_vcf2genome/ to map single sample variant call format (VCF) file against known soybean germplasm collection for identification of the closest soybean accession
Our VCF2Genomes scheme can be extended to other plant species where the whole genome sequences of core collection are publicly available

Summary

Conclusion

As whole genome sequences of global soybean germplasms have been accumulated in public databases, the identification of genomic background of unknown/query samples would be possible using reference genotype matrix. We built light weight reference genotype matrix using PCA and web-application, Soybean-VCF2Genomes, where user can upload their single sample VCF file for analysis. Using the web-application, the closest accessions to unknown/query sample can be identified and it would help researchers or breeders to understand their plant materials precisely. Additional file 1: MAF filtered genotype matrix of soybean germplasm. (XLSX 50509 kb) Additional file 2: NCBI SRA accessions for testing germplasm clustering.

Background