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

• Published in: BMC bioinformatics Vol. 20; no. Suppl 13; p. 384
• Main Authors: Ha, Jungmin, Jeon, Ho Hwi, Woo, Dong U, Lee, Yejin, Park, Halim, Lee, Joohyeong, Kang, Yang Jae
• Format: Journal Article
• Language: English
• Published: England BioMed Central Ltd 24-07-2019; BioMed Central; BMC
• Subjects: Cluster Analysis; Databases, Factual; DNA sequencing; Genetic aspects; Genome, Plant; Genome-based breeding; Genomes; Genomics; Genotype; Germplasm identification; Glycine max - classification; Glycine max - genetics; Glycine max - growth & development; High-Throughput Nucleotide Sequencing; Linux (Operating system); Machine Learning; Next generation sequencing; Phenotype; Phylogeny; Principal Component Analysis; Quarantine; Seeds; Seeds - genetics; Soybean; Soybeans; Technology application; User-Computer Interface; Web services; South Korea; Germplasm identification; Genome-based breeding; Soybean; Next generation sequencing; Machine learning
• ISSN: 1471-2105; 1471-2105
• DOI: 10.1186/s12859-019-2859-5

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.
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.
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.