I have performed the population structure analysis of around 400 accessions. The structure software identified two sub-populations. Now I am interested to perform GWAS. The general rule regarding the usage of the number of principal components is:
Number of principle components to use = Number of principle components identified by Structure software -1
If I follow this rule then shall I use just one principle component in GWAS as the structure software identified two sub-populations so 2-1 =1.
Is it a good idea to use just one principle component in GWAS or shall I look at some other factors such as variation possessed by each principle component?
I have attached the Figure reflecting the variation possess by each principal component.
I will highly appreciate it if anyone please suggest to me how many principle components shall I use in my GWAS analysis.
