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

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Authors
Ha, Jungmin; Jeon, Ho Hwi; Woo, Dong U; Lee, Yejin; Park, Halim; Lee, Joohyeong; Kang, Yang Jae
Issue Date
2019-07-24
Publisher
BioMed Central
Citation
BMC Bioinformatics. 2019 Jul 24;20(Suppl 13):384
Keywords
SoybeanGermplasm identificationGenome-based breedingNext generation sequencingMachine
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.
ISSN
1471-2105
Language
English
URI
http://hdl.handle.net/10371/160876
DOI
https://doi.org/10.1186/s12859-019-2859-5
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College of Agriculture and Life Sciences (농업생명과학대학)Research Institute of Agriculture and Life Sciences (농업생명과학연구원)Journal Papers (저널논문_농업생명과학연구원)
College of Agriculture and Life Sciences (농업생명과학대학)Dept. of Plant Science (식물생산과학부)Journal Papers (저널논문_식물생산과학부)
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