I cleaned up your question a bit to make it clearer to understand. Asking a clear question will get you a faster and more specific answer so it's a good idea to put some time into crafting your words and doing a little bit of background research first.

I'm not clear on exactly what you want to do a SNP analysis for -- I'm not sure you know either. Are you trying to tie a SNP to functional gene diversity? -- you'll probably need some laboratory experiments to back those conclusions up. Are you trying to use SNPs for phylogenetic hypothesis generation/testing?

Most of the tools for SNP analysis in humans also work in plants -- I've had to use many of them because I am unaware of any specific SNP tools for plants (except for this R package). My current SNP pipeline uses SnpEff/SnpSift for SNP detection. I'm also using CORTEX for assembly based variant calling.

There are many many questions here about SNP calling -- here's a few.