GWAS Protocol for native maize from Morelos, MX

This was the coding section for my thesis, which consisted on the identification of single nucleotide polymorphisms (SNPs) related to draught resistance of native Zea mays L. from Morelos, MX.

Thanks to the Dr. Cassab's research group at IBt - UNAM for letting me share this part of my project.

Use Project

The R Project is located in the r-project/ directory; without datasets.

You can download the zip file directly. Or clone this repository with:

git clone https://github.com/robolvhez/gwas_native-maize.git

Obtain Data

UNIX Systems (Linux or macOS)

If you use a Linux machine or macOS, you can extract data from DMz23_119.tar.gz zipped files using this command on terminal:

# UNIX Systems
tar -xzvf DMz23_119.tar.gz -C r-project/data/

This should extract all files into the data/ directory from which R will read data.

Windows

On Windows systems, unzip manually the DMz23_119.zip file and move the contents to r-project/data/.

GWAS Procedure

This GWAS was performed in TASSEL 5.0, according to user's manual for the MLM (Mixed Linear Model) workflow.

Phenotype and genotype datasets are provided in the DMz23_119 compressed files.