Environmental Association Analyses Identify Candidates for Abiotic Stress Tolerance in Glycine soja, the Wild Progenitor of Cultivated Soybeans

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Japan, Korea, China, Russia

Source information

Data was derived from Song Q. et al's 2015 study genotyping SNPs from domesticated and wild soybean accessions

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Title

Environmental Association Analyses Identify Candidates for Abiotic Stress Tolerance in Glycine soja, the Wild Progenitor of Cultivated Soybeans

Published Date

2016-09-26T16:53:19Z

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Author Contact

Kantar, Michael B
kant0063@umn.edu

Type

Dataset
Genomics Data

Abstract

Understanding the genetics basis of adaption is a fundamental goal of biological research. The present study explores an ex situ conservation collection, the USDA germplasm collection, genotyped at 32,416 SNPs, to identify population structure and test for associations with bioclimatic and biophysical variables in Glycine soja, the wild progenitor of Glycine max (soybean). Candidate loci were detected that putatively contribute to adaptation to abiotic stresses.

Description

The sampled accessions in this study are derived from the SNPs genotyped by Song et al. (2015) and catalogued in the USDA soybean germplasm collection (http://soybase.org/snps/index.php). Accessions without latitudinal and longitudinal data were excluded, as were those with greater than 10% of data missing. Additionally, eight accessions from Taiwan and Northern Russia were excluded due to those being geographical outliers. A list of accessions used in the study can be found in the data files below. Environmental association was performed using data from public repositories of global bioclimatic (WorldClim) and biophysical variables (ISRIC), and a list of the variables retrieved per accession can be found in the data files below.

Funding Information

United Soybean Board
Minnesota Varietal Development Fund
MnDRIVE 2014 Global Food Ventures Fellowship

Referenced by

Anderson, J. E., Kono, T. J., Stupar, R. M., Kantar, M. B., & Morrell, P. L. (2016). Environmental association analyses identify candidates for abiotic stress tolerance in Glycine soja, the wild progenitor of cultivated soybeans. G3: Genes, Genomes, Genetics, 6(4), 835-843.
http://dx.doi.org/10.1534/g3.116.026914
Code used to analyze data:
https://github.com/MorrellLAB/Soja_Env_Association

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Funding information

United Soybean Board
Minnesota Varietal Development Fund
MnDRIVE 2014 Global Food Ventures Fellowship

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View/Download file
File View/OpenDescriptionSize
soybean_accessions.txtData for 533 accessions used in study21.83 KB
bioclimatic_biophysical_variables.txtBioclimatic and biophysical data171.79 KB
readme.txtDescription of data3.54 KB

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