Version 1
: Received: 1 January 2021 / Approved: 4 January 2021 / Online: 4 January 2021 (16:25:22 CET)
How to cite:
Jung, Y.; You, N.; Nam, S. A Computational Study for Identifying Agronomically Essential Biomarkers Using nsSNP Data of Korean Soybeans. Preprints2021, 2021010060. https://doi.org/10.20944/preprints202101.0060.v1
Jung, Y.; You, N.; Nam, S. A Computational Study for Identifying Agronomically Essential Biomarkers Using nsSNP Data of Korean Soybeans. Preprints 2021, 2021010060. https://doi.org/10.20944/preprints202101.0060.v1
Jung, Y.; You, N.; Nam, S. A Computational Study for Identifying Agronomically Essential Biomarkers Using nsSNP Data of Korean Soybeans. Preprints2021, 2021010060. https://doi.org/10.20944/preprints202101.0060.v1
APA Style
Jung, Y., You, N., & Nam, S. (2021). A Computational Study for Identifying Agronomically Essential Biomarkers Using nsSNP Data of Korean Soybeans. Preprints. https://doi.org/10.20944/preprints202101.0060.v1
Chicago/Turabian Style
Jung, Y., Nahyun You and Sangyong Nam. 2021 "A Computational Study for Identifying Agronomically Essential Biomarkers Using nsSNP Data of Korean Soybeans" Preprints. https://doi.org/10.20944/preprints202101.0060.v1
Abstract
Soybean is a highly nutritious legume grown globally as a food and feed crop. An examination of a collection of 10 cultivated and 6 wild Korean soybean varieties showed that there is phenotypic variability notable in different soybeans. Therefore, to develop a list of biomarker candidates useful for growing soybeans of better quality and quantity, the genes of 16 Korean soybean varieties were compared with those of the reference Glycine max var. Williams 82. The comparison was made through gene sequencing to facilitate selection of nsSNPs. The objective of the study was to find out the structural and functional variations caused by nsSNPs and discuss whether the collection of Korean soybean varieties qualifies as biomarkers based on their phenotypic traits.
Analysis of the data collected was done using four software: SIFT, Polyphen, PANTHER, and I-mutant 2.0, which are designed to detect the rate of functional and structural variations caused by the nsSNPs in cultivated and wild soybean varieties. Genotypic information obtained in the analysis was used to develop a core collection of biomarkers based on whether nsSNP content was found in more than half of the 16 samples. Therefore, the list of biomarker candidates developed from this study showed that Korean soybean could provide valuable information needed in both future crop genetic research and identification of biomarkers.
Keywords
Korean soybean varieties; nsSNP; Biomarker; SIFT; Polyphen; PANTHER; I-mutant 2.0
Subject
Biology and Life Sciences, Plant Sciences
Copyright:
This is an open access article distributed under the Creative Commons Attribution License which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
