Method for Genome-Wide Association Study: A Soybean Example

Robyn Anderson; Cassandria Tay Fernandez; Yuxuan Yuan; Agnieszka A Golicz; David Edwards; Philipp E Bayer

doi:10.1007/978-1-0716-0235-5_7

Method for Genome-Wide Association Study: A Soybean Example

Methods Mol Biol. 2020:2107:147-158. doi: 10.1007/978-1-0716-0235-5_7.

Authors

Robyn Anderson¹, Cassandria Tay Fernandez¹, Yuxuan Yuan¹, Agnieszka A Golicz², David Edwards¹, Philipp E Bayer³

Affiliations

¹ School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia.
² Faculty of Veterinary and Agricultural Sciences, Plant Molecular Biology and Biotechnology Laboratory, University of Melbourne, Melbourne, VIC, Australia.
³ School of Biological Sciences and Institute of Agriculture, University of Western Australia, Perth, WA, Australia. Philipp.Bayer@uwa.edu.au.

PMID: 31893446
DOI: 10.1007/978-1-0716-0235-5_7

Abstract

Genome-wide association studies (GWAS) are a valuable approach to identify single nucleotide polymorphisms (SNPs) associated with a phenotype of interest. There are now a variety of R-packages and command line tools available to perform GWAS. Here, we provide an example downloading and filtering SNP data, followed by GWAS analysis using the R-package rMVP.

Keywords: Genome Wide Association Study; R; Soybean; bcftools; rMVP; vcf.

MeSH terms

Genome-Wide Association Study / methods*
Glycine max / genetics*
Humans
Linkage Disequilibrium
Phenotype
Polymorphism, Single Nucleotide*
Quantitative Trait Loci
Software