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BMC Bioinformatics. 2019 Jul 24;20(Suppl 13):384. doi: 10.1186/s12859-019-2859-5.

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

Author information

1
Department of Plant Science and Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, Republic of Korea.
2
Plant Genomics and Breeding Institute, Seoul National University, Seoul, Republic of Korea.
3
Division of Applied Life Science Department at Gyeongsang National University, PMBBRC, Jinju, Republic of Korea.
4
Division of Life Science Department at Gyeongsang National University, Jinju, Republic of Korea.
5
College of Pharmacy and Research Institute of Pharmaceutical Sciences, Gyeongsang National University, Jinju, South Korea.
6
Division of Applied Life Science Department at Gyeongsang National University, PMBBRC, Jinju, Republic of Korea. kangyangjae@gnu.ac.kr.
7
Division of Life Science Department at Gyeongsang National University, Jinju, Republic of Korea. kangyangjae@gnu.ac.kr.

Abstract

BACKGROUND:

The 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 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. 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.

CONCLUSION:

The 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.

KEYWORDS:

Genome-based breeding; Germplasm identification; Machine learning; Next generation sequencing; Soybean

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