GWAS for Alfalfa BSA samples using FarmCPU
For this project we used 215 Alfalfa plants from three location (Washington 100, Utah 100 and Wisconsin 15) to self for 2 generation. With each generation of selfing we selected pairs of strong vigor and weak vigor plants within a line. These selected plants based on their health is used for final association analysis. For the final Analysis, 121 plants selected based on their vigor were chosen with stong plant coded as 1 and weak plant coded as 0 for association analysis. Along with this, we used location, generation, pools and group as covariates. Three location (Washington, Utah as 0 and Wisconsin as 1), two generation (Generation 1 as 0 and Genetion 2 as 1), pools (individual as 0 and pool as 1) and group which was the separate cluster when plotting Principal Component 1 and Principal Component 2.